diff --git a/.gitignore b/.gitignore
index 07c8c927c8ab2e786fa331d238e6a99262262838..77cc40ece6a4a7473e164e8e54458d43e9b3c4be 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,4 +1,5 @@
addons/interpro.xml
+addons/java_libraries/*
build/built-jar.properties
!dist
dist/*
@@ -6,3 +7,143 @@ dist/*
*.class
*.jar
+# Created by https://www.toptal.com/developers/gitignore/api/intellij,maven,netbeans
+# Edit at https://www.toptal.com/developers/gitignore?templates=intellij,maven,netbeans
+
+### Intellij ###
+# Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio, WebStorm and Rider
+# Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839
+
+# User-specific stuff
+.idea/**/workspace.xml
+.idea/**/tasks.xml
+.idea/**/usage.statistics.xml
+.idea/**/dictionaries
+.idea/**/shelf
+
+# AWS User-specific
+.idea/**/aws.xml
+
+# Generated files
+.idea/**/contentModel.xml
+
+# Sensitive or high-churn files
+.idea/**/dataSources/
+.idea/**/dataSources.ids
+.idea/**/dataSources.local.xml
+.idea/**/sqlDataSources.xml
+.idea/**/dynamic.xml
+.idea/**/uiDesigner.xml
+.idea/**/dbnavigator.xml
+
+# Gradle
+.idea/**/gradle.xml
+.idea/**/libraries
+
+# Gradle and Maven with auto-import
+# When using Gradle or Maven with auto-import, you should exclude module files,
+# since they will be recreated, and may cause churn. Uncomment if using
+# auto-import.
+# .idea/artifacts
+# .idea/compiler.xml
+# .idea/jarRepositories.xml
+# .idea/modules.xml
+# .idea/*.iml
+# .idea/modules
+# *.iml
+# *.ipr
+
+# CMake
+cmake-build-*/
+
+# Mongo Explorer plugin
+.idea/**/mongoSettings.xml
+
+# File-based project format
+*.iws
+
+# IntelliJ
+out/
+
+# mpeltonen/sbt-idea plugin
+.idea_modules/
+
+# JIRA plugin
+atlassian-ide-plugin.xml
+
+# Cursive Clojure plugin
+.idea/replstate.xml
+
+# Crashlytics plugin (for Android Studio and IntelliJ)
+com_crashlytics_export_strings.xml
+crashlytics.properties
+crashlytics-build.properties
+fabric.properties
+
+# Editor-based Rest Client
+.idea/httpRequests
+
+# Android studio 3.1+ serialized cache file
+.idea/caches/build_file_checksums.ser
+
+### Intellij Patch ###
+# Comment Reason: https://github.com/joeblau/gitignore.io/issues/186#issuecomment-215987721
+
+# *.iml
+# modules.xml
+# .idea/misc.xml
+# *.ipr
+
+# Sonarlint plugin
+# https://plugins.jetbrains.com/plugin/7973-sonarlint
+.idea/**/sonarlint/
+
+# SonarQube Plugin
+# https://plugins.jetbrains.com/plugin/7238-sonarqube-community-plugin
+.idea/**/sonarIssues.xml
+
+# Markdown Navigator plugin
+# https://plugins.jetbrains.com/plugin/7896-markdown-navigator-enhanced
+.idea/**/markdown-navigator.xml
+.idea/**/markdown-navigator-enh.xml
+.idea/**/markdown-navigator/
+
+# Cache file creation bug
+# See https://youtrack.jetbrains.com/issue/JBR-2257
+.idea/$CACHE_FILE$
+
+# CodeStream plugin
+# https://plugins.jetbrains.com/plugin/12206-codestream
+.idea/codestream.xml
+
+### Maven ###
+target/
+pom.xml.tag
+pom.xml.releaseBackup
+pom.xml.versionsBackup
+pom.xml.next
+release.properties
+dependency-reduced-pom.xml
+buildNumber.properties
+.mvn/timing.properties
+# https://github.com/takari/maven-wrapper#usage-without-binary-jar
+.mvn/wrapper/maven-wrapper.jar
+
+### Maven Patch ###
+# Eclipse m2e generated files
+# Eclipse Core
+.project
+# JDT-specific (Eclipse Java Development Tools)
+.classpath
+
+### NetBeans ###
+**/nbproject/private/
+**/nbproject/Makefile-*.mk
+**/nbproject/Package-*.bash
+build/
+nbbuild/
+dist/
+nbdist/
+.nb-gradle/
+
+# End of https://www.toptal.com/developers/gitignore/api/intellij,maven,netbeans
diff --git a/.gitmodules b/.gitmodules
new file mode 100644
index 0000000000000000000000000000000000000000..017ebca1d890075d50c42bf82947492d73186c44
--- /dev/null
+++ b/.gitmodules
@@ -0,0 +1,3 @@
+[submodule "ASTER"]
+ path = ASTER
+ url = https://github.com/chaoszhang/ASTER.git
diff --git a/.idea/compiler.xml b/.idea/compiler.xml
new file mode 100644
index 0000000000000000000000000000000000000000..ce7685e5830fc4896c49aa6f0062a96d48defcc5
--- /dev/null
+++ b/.idea/compiler.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+ <component name="CompilerConfiguration">
+ <annotationProcessing>
+ <profile name="Maven default annotation processors profile" enabled="true">
+ <sourceOutputDir name="target/generated-sources/annotations" />
+ <sourceTestOutputDir name="target/generated-test-sources/test-annotations" />
+ <outputRelativeToContentRoot value="true" />
+ <module name="pantools" />
+ </profile>
+ </annotationProcessing>
+ </component>
+</project>
\ No newline at end of file
diff --git a/.idea/encodings.xml b/.idea/encodings.xml
new file mode 100644
index 0000000000000000000000000000000000000000..aa00ffab7828f4818589659c804ec2cfd99baed3
--- /dev/null
+++ b/.idea/encodings.xml
@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+ <component name="Encoding">
+ <file url="file://$PROJECT_DIR$/src/main/java" charset="UTF-8" />
+ <file url="file://$PROJECT_DIR$/src/main/resources" charset="UTF-8" />
+ </component>
+</project>
\ No newline at end of file
diff --git a/.idea/inspectionProfiles/Project_Default.xml b/.idea/inspectionProfiles/Project_Default.xml
new file mode 100644
index 0000000000000000000000000000000000000000..13fe0dbacb9e8509fe394efbd49c76f9342cdc66
--- /dev/null
+++ b/.idea/inspectionProfiles/Project_Default.xml
@@ -0,0 +1,6 @@
+<component name="InspectionProjectProfileManager">
+ <profile version="1.0">
+ <option name="myName" value="Project Default" />
+ <inspection_tool class="GrazieInspection" enabled="false" level="TYPO" enabled_by_default="false" />
+ </profile>
+</component>
\ No newline at end of file
diff --git a/.idea/jarRepositories.xml b/.idea/jarRepositories.xml
new file mode 100644
index 0000000000000000000000000000000000000000..712ab9d985c20018a0c97b93d2148ac1ffe588a5
--- /dev/null
+++ b/.idea/jarRepositories.xml
@@ -0,0 +1,20 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+ <component name="RemoteRepositoriesConfiguration">
+ <remote-repository>
+ <option name="id" value="central" />
+ <option name="name" value="Central Repository" />
+ <option name="url" value="https://repo.maven.apache.org/maven2" />
+ </remote-repository>
+ <remote-repository>
+ <option name="id" value="central" />
+ <option name="name" value="Maven Central repository" />
+ <option name="url" value="https://repo1.maven.org/maven2" />
+ </remote-repository>
+ <remote-repository>
+ <option name="id" value="jboss.community" />
+ <option name="name" value="JBoss Community repository" />
+ <option name="url" value="https://repository.jboss.org/nexus/content/repositories/public/" />
+ </remote-repository>
+ </component>
+</project>
\ No newline at end of file
diff --git a/.idea/misc.xml b/.idea/misc.xml
new file mode 100644
index 0000000000000000000000000000000000000000..14941d78d27654f05bd8fdba7973c4f17862a11a
--- /dev/null
+++ b/.idea/misc.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+ <component name="ExternalStorageConfigurationManager" enabled="true" />
+ <component name="MavenProjectsManager">
+ <option name="originalFiles">
+ <list>
+ <option value="$PROJECT_DIR$/pom.xml" />
+ </list>
+ </option>
+ </component>
+ <component name="ProjectRootManager" version="2" languageLevel="JDK_11" project-jdk-name="11" project-jdk-type="JavaSDK" />
+</project>
\ No newline at end of file
diff --git a/.idea/vcs.xml b/.idea/vcs.xml
new file mode 100644
index 0000000000000000000000000000000000000000..022c9399f5da765e08ff51724b5d85a7ad64f801
--- /dev/null
+++ b/.idea/vcs.xml
@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+ <component name="VcsDirectoryMappings">
+ <mapping directory="" vcs="Git" />
+ <mapping directory="$PROJECT_DIR$/ASTER" vcs="Git" />
+ </component>
+</project>
\ No newline at end of file
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..6a943a7c921f27f030e2f78a253f8ada0460bf12
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,13 @@
+repos:
+ - repo: local
+ hooks:
+ - id: maven-compile
+ name: Compile with Maven
+ description: Compile all code with mvn compile
+ entry: mvn
+ args:
+ - compile
+ language: system
+ pass_filenames: false
+ types: [java]
+
diff --git a/ASTER b/ASTER
new file mode 160000
index 0000000000000000000000000000000000000000..ce55e0c5871c47843009116710c00f6b0535645c
--- /dev/null
+++ b/ASTER
@@ -0,0 +1 @@
+Subproject commit ce55e0c5871c47843009116710c00f6b0535645c
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 740f8b461fa6020273afd02047e6c4c17f725c01..584d65ce0db6f50097caf8379417e1ea0fb44fda 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,30 @@
All notable changes to Pantools will be documented in this file.
+## [3.4.0] - 2022-05-04
+
+### Added
+- Version and commit ID are reported when PanTools is initialized.
+- `--allow-polytomies` argument for `consensus_tree`.
+- Included option to bin numerical values in `add_phenotypes`.
+
+### Changed
+- `msa_group`,`msa_of_multiple_groups`, `msa_of_regions` are reorganised in new function `msa`.
+- `pangenome_structure` uses a colorblindfriendly palette.
+- `create_tree_templates` uses a colorblindfriendly palette when using 8 phenotypes or less.
+- `add_antismash` now only works with Antismash versions >= 6.0.
+
+### Fixed
+- Changed the orientation of the 'has_busco' relationship
+
+## [3.3.0] - 2021-12-23
+
+### Changed
+- Migrate to Maven
+- Executable .jar file moved from `pantools/dist` to `pantools/target`
+
+### Fixed
+- Reading gzip-compressed input files
+
## [3.2.0] - 2021-11-25
### Added
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
new file mode 100644
index 0000000000000000000000000000000000000000..61d7caf95af1d0797d37a70a8ab8574615df1f73
--- /dev/null
+++ b/CONTRIBUTING.md
@@ -0,0 +1,172 @@
+# Contributing to _PanTools_
+
+## Get in touch
+
+There are many ways to get in touch with the _PanTools_ team!
+
+- GitLab [issues][pantools-issues] and [merge requests][pantools-mergerequests]
+ - Join a discussion, collaborate on an ongoing task and exchange your thoughts with others. You will have to request a guest role to start contributing.
+ - Can't find your idea being discussed anywhere?
+ [Open a new issue](https://git.wur.nl/bioinformatics/pantools/-/issues/new)! (See our [Where to start: issues](#where-to-start-issues) section below.)
+- Contact the Project Lead of the _PanTools_ project - Sandra Smit - by email at [sandra.smit@wur.nl](mailto:sandra.smit@wur.nl).
+
+## Contributing through GitLab
+
+[Git][git] is a really useful tool for version control.
+[GitLab][gitlab] sits on top of Git and supports collaborative and distributed working.
+
+We know that it can be daunting to start using Git and GitLab if you haven't worked with them in the past, but the _PanTools_ maintainers are here to help you figure out any of the jargon or confusing instructions you encounter.
+
+GitLab has a helpful page on [getting started with GitLab][gitlab-gettingstarted].
+
+In order to contribute via GitLab, you'll need to [set up an account][gitlab-signup] and [sign in][gitlab-signin].
+Remember that you can ask us any questions you need to along the way.
+
+## Writing in Markdown
+
+Most of the writing that you'll do will be in [Markdown][markdown].
+You can think of Markdown as a few little symbols around your text that will allow GitLab to render the text with a little bit of formatting.
+For example, you could write words as **bold** (`**bold**`), or in _italics_ (`_italics_`), or as a [link][rick-roll] (`[link](https://youtu.be/dQw4w9WgXcQ)`) to another webpage.
+
+Also when writing in Markdown, please start each new sentence on a new line.
+Having each sentence on a new line will make no difference to how the text is displayed, there will still be paragraphs, but it makes the diffs produced during the merge request review easier to read!
+
+
+## Where to start: issues
+
+Before you open a new issue, please check if any of our [open issues](https://git.wur.nl/bioinformatics/pantools/-/issues?scope=all&state=opened) cover your idea already.
+
+## Making a change with a merge request
+
+We appreciate all contributions to _PanTools_.
+**THANK YOU** for helping us build this useful resource.
+
+All project management, conversations and questions related to the _PanTools_ project happens here in the _PanTools_ repository.
+
+The following steps are a guide to help you contribute in a way that will be easy for everyone to review and accept with ease.
+
+### 1. Comment on an [existing issue][pantools-issues] or open a new issue referencing your addition
+
+This allows other members of the _PanTools_ team to confirm that you aren't overlapping with work that's currently underway and that everyone is on the same page with the goal of the work you're going to carry out.
+
+[This blog](https://www.igvita.com/2011/12/19/dont-push-your-pull-requests/) is a nice explanation of why putting this work in upfront is so useful to everyone involved.
+
+You will need a guest role to create new issues using the _PanTools_ repository website. You can request a guest role by [getting in touch](#get-in-touch).
+
+Alternatively, you can send an [email][pantools-email] to create a new issue. The title of the email will be used as the issue title and the email body will be put in the issue description.
+Note that we are in the process of setting up this email functionality; when this is done, we will update the email link here.
+
+### 2. [Fork][gitlab-fork] the [_PanTools_ repository][pantools-repo]
+
+This is now your own unique copy of _PanTools_.
+Changes here won't affect anyone else's work, so it's a safe space to explore edits to the code!
+
+Make sure to [keep your fork up to date][gitlab-syncfork] with the main repository, otherwise, you can end up with lots of dreaded [merge conflicts][gitlab-mergeconflicts].
+
+The repository website only provides functionality for forking inside the same server (git.wur.nl). You can fork the _PanTools_ project onto another GitLab server. Forking onto a GitHub server is currently not possible, but this is being worked on.
+First create a blank repository on GitLab, let's assume it's called https://gitlab.com/johndoe/my-pantools
+Use the following commands in a directory where you wish to fork _PanTools_.
+
+~~~bash
+mkdir my-pantools
+cd my-pantools
+git init
+git remote add origin https://gitlab.com/johndoe/my-pantools
+git remote add upstream https://git.wur.nl/bioinformatics/pantools
+#There are now two remotes: origin (your remote fork) and upstream (the pantools repository).
+
+git pull upstream master #Get the pantools content.
+git push --set-upstream origin master #Push this content to the origin (fork).
+~~~
+
+### 3. Make the changes you've discussed
+
+Try to keep the changes focused.
+If you submit a large amount of work all in one go it will be much more work for whoever is reviewing your merge request.
+
+While making your changes, commit often and write good, detailed commit messages.
+[This blog](https://chris.beams.io/posts/git-commit/) explains how to write a good Git commit message and why it matters.
+It is also perfectly fine to have a lot of commits - including ones that break code.
+A good rule of thumb is to push up to GitLab when you _do_ have passing tests then the continuous integration (CI) has a good chance of passing everything.
+
+If you feel tempted to "branch out" then please make a [new branch][gitlab-branches] and a [new issue](https://git.wur.nl/bioinformatics/pantools/-/issues/new) to go with it. [This blog](https://nvie.com/posts/a-successful-git-branching-model/) details the different Git branching models.
+
+Please do not re-write history!
+That is, please do not use the [rebase](https://docs.gitlab.com/ee/topics/git/git_rebase.html) command to edit previous commit messages, combine multiple commits into one, or delete or revert commits that are no longer necessary.
+
+Are you new to Git and GitLab or just want a detailed guide on getting started with version control? Check out the [Version Control chapter](https://the-turing-way.netlify.com/version_control/version_control.html) in _The Turing Way_ Book!
+
+### 4. Submit a [merge request][gitlab-mergerequest]
+
+We encourage you to open a merge request as early in your contributing process as possible.
+This allows everyone to see what is currently being worked on.
+It also provides you, the contributor, feedback in real-time from both the community and the continuous integration as you make commits (which will help prevent stuff from breaking).
+
+When you are ready to submit a merge request, please describe in the merge request body:
+
+- The problem you're trying to fix in the merge request, reference any related issue and use fixes/close to automatically close them, if pertinent.
+- A list of changes proposed in the merge request.
+- What the reviewer should concentrate their feedback on.
+
+By providing as much detail as possible, you will make it really easy for someone to review your contribution!
+
+If you have opened the merge request early and know that its contents are not ready for review or to be merged, add "[WIP]" at the start of the merge request title, which stands for "Work in Progress".
+When you are happy with it and are happy for it to be merged into the main repository, change the "[WIP]" in the title of the merge request to "[Ready for review]".
+
+A member of the _PanTools_ team will then review your changes to confirm that they can be merged into the main repository.
+A [review][gitlab-review] will probably consist of a few questions to help clarify the work you've done.
+Keep an eye on your GitLab notifications and be prepared to join in that conversation.
+
+You can update your [fork][gitlab-fork] of the _PanTools_ [repository][pantools-repo] and the merge request will automatically update with those changes.
+You don't need to submit a new merge request when you make a change in response to a review.
+
+You can also submit merge requests to other contributors' branches!
+Do you see an [open merge request](https://git.wur.nl/bioinformatics/pantools/-/merge_requests?scope=all&state=opened ) that you find interesting and want to contribute to?
+Simply make your edits on their files and open a merge request to their branch!
+
+GitLab has a [nice introduction][gitlab-flow] to the merge request workflow, but please [get in touch](#get-in-touch) if you have any questions.
+
+## Local development
+
+You can build and run _PanTools_ locally. Please refer to the [manual][pantools-manual] for instructions on how to build, and run _PanTools_.
+
+## Recognizing Contributions
+
+We welcome and recognise all kinds of contributions, from fixing small errors, to developing documentation, maintaining the project infrastructure, writing code or reviewing existing resources.
+
+### Current Contributors
+
+The _PanTools_ team wants to graciously thank the following people for their contributions to the _PanTools_ project.
+
+- Astrid van der Brandt
+- Dirk-Jan van Workum
+- Eef Jonkheer
+- Matthijs Moed
+- Sandra Smit
+- Siavash Sheikhizadeh
+- Thijs van Lankveld
+
+---
+
+_These Contributing Guidelines have been adapted from the [Contributing Guidelines](https://github.com/bids-standard/bids-starter-kit/blob/master/CONTRIBUTING.md) of the [BIDS Starter Kit](https://github.com/bids-standard/bids-starter-kit)! (License: CC-BY)_
+
+[pantools-repo]: https://git.wur.nl/bioinformatics/pantools
+[pantools-issues]: https://git.wur.nl/bioinformatics/pantools/-/issues
+[pantools-mergerequests]: https://git.wur.nl/bioinformatics/pantools/-/merge_request
+[pantools-manual]: https://www.bioinformatics.nl/pangenomics/manual/
+[pantools-email]: mailto:broken_link
+[git]: https://git-scm.com
+[gitlab]: https://gitlab.com
+[gitlab-signup]: https://gitlab.com/users/sign_up
+[gitlab-signin]:https://gitlab.com/users/sign_in
+[gitlab-gettingstarted]:https://about.gitlab.com/get-started/
+[gitlab-fork]: https://docs.gitlab.com/ee/user/project/repository/forking_workflow.html
+[gitlab-syncfork]: https://about.gitlab.com/blog/2016/12/01/how-to-keep-your-fork-up-to-date-with-its-origin/
+[gitlab-mergeconflicts ]:https://docs.gitlab.com/ee/topics/git/merge_conflicts.html
+[gitlab-branches]: https://docs.gitlab.com/ee/user/project/repository/web_editor.html#create-a-new-branch
+[gitlab-rebase]:https://docs.gitlab.com/ee/topics/git/git_rebase.html
+[gitlab-mergerequest]: https://docs.gitlab.com/ee/user/project/merge_requests/creating_merge_requests.html
+[gitlab-review]: https://docs.gitlab.com/ee/development/code_review.html
+[gitlab-flow]: https://docs.gitlab.com/ee/topics/gitlab_flow.html
+[markdown]: https://daringfireball.net/projects/markdown
+[rick-roll]: https://www.youtube.com/watch?v=dQw4w9WgXcQ
\ No newline at end of file
diff --git a/README.md b/README.md
index fcbe99ba9b13b2b4940d7424617232e054c1f36e..7e28cd524e54729727ccf8b824f2179cb05d9699 100755
--- a/README.md
+++ b/README.md
@@ -25,44 +25,48 @@ PanTools currently provides these functionalities:
- Phylogenetic methods
- Optimal homology grouping using BUSCO
-## Compiling PanTools
-**NB: still under construction, end goal is to easily create a fat jar using the commandline**
+## Cloning this git
+For cloning this git, please run:
+```bash
+git clone --recursive https://git.wur.nl/bioinformatics/pantools.git
+```
-To compile PanTools, there are two options:
-- Create a slim jar using the following commands:
- ```
- git clone https://git.wur.nl/bioinformatics/pantools.git
- cd pantools/
- rm nbproject/private/private.*
- ant -Dplatforms.JDK_1.8.home=/path/to/<openjdk 8 home> clean jar
- ```
-
- Next, check whether PanTools is compiled correctly by running:
- ```
- java -cp $(echo addons/java_libraries/*.jar dist/pantools.jar | sed 's/ /:/g') pantools.Pantools --help
- ```
- This should display the help of PanTools
-
- For easily running PanTools, add the following line to ~/.bashrc:
- ```
- alias pantools="java -cp $(echo /path/to/pantools/addons/java_libraries/*.jar /path/to/pantools/dist/pantools.jar | sed 's/ /:/g') pantools.Pantools"
- ```
+And check out a desired version (e.g. `v3.4.0`):
+```bash
+git checkout v3.4.0
+```
-## Creating a bundled jar
-To create a runnable, standalone jar with all dependencies included, run the `package-for-store` with Ant:
+## Building a runnable jar
+To build a standalone jar that can be run on any machine with a compatible JVM without any dependencies, install [Maven](https://maven.apache.org) and JDK version 8.
+Then run `mvn package` in the PanTools root directory:
```bash
-ant package-for-store
+mvn package
```
-This will create a file called `pantools.jar` in the `store/` directory, which can be copied to any location without the need for also copying the dependent libraries of PanTools.
+<!--
+Note: tests are broken at the moment, which is why we're skipping the Maven test phase with `-DskipTests=true`.
+-->
+
+`mvn package` will generate two jar files in the `target/` directory.
+The standalone jar file is named `pantools-<VERSION>.jar`, with `<VERSION>` being the PanTools version you have checked out.
+To run it, use (we'll take version `v3.4.0` as an example):
+
+```bash
+java -jar target/pantools-3.4.0.jar
+```
## Requirements, Installation, Usage
-An extensive manual is available at [http://www.bioinformatics.nl/pangenomics/manual/](http://www.bioinformatics.nl/pangenomics/manual/)
+An extensive manual is available at [pantools.readthedocs.io](https://pantools.readthedocs.io/).
-When running `pantools add_functional_annotations`, an InterPro database needs to be present in the `addons/` directory.
-Calling the following bash script will download an InterPro database:
-~~~(bash)
-addons/wget_interpro.sh
-~~~
+To use the `consensus_tree` functionality, PanTools depends on ASTER. For compiling this submodule, please run:
+```bash
+cd ASTER
+g++ -std=gnu++11 -march=native -Ofast -pthread astral.cpp -o astral
+g++ -std=gnu++11 -march=native -Ofast -pthread astral-pro.cpp -o astral-pro
+```
+In case the directory pantools/ASTER is empty, please run the following to retrieve its contents:
+```bash
+git submodule update --init --recursive
+```
diff --git a/addons/ASTER/LICENSE b/addons/ASTER/LICENSE
deleted file mode 100644
index 0ad25db4bd1d86c452db3f9602ccdbe172438f52..0000000000000000000000000000000000000000
--- a/addons/ASTER/LICENSE
+++ /dev/null
@@ -1,661 +0,0 @@
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-ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
-
- 16. Limitation of Liability.
-
- IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
-WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
-THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
-GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
-USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
-DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
-PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
-EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
-SUCH DAMAGES.
-
- 17. Interpretation of Sections 15 and 16.
-
- If the disclaimer of warranty and limitation of liability provided
-above cannot be given local legal effect according to their terms,
-reviewing courts shall apply local law that most closely approximates
-an absolute waiver of all civil liability in connection with the
-Program, unless a warranty or assumption of liability accompanies a
-copy of the Program in return for a fee.
-
- END OF TERMS AND CONDITIONS
-
- How to Apply These Terms to Your New Programs
-
- If you develop a new program, and you want it to be of the greatest
-possible use to the public, the best way to achieve this is to make it
-free software which everyone can redistribute and change under these terms.
-
- To do so, attach the following notices to the program. It is safest
-to attach them to the start of each source file to most effectively
-state the exclusion of warranty; and each file should have at least
-the "copyright" line and a pointer to where the full notice is found.
-
- <one line to give the program's name and a brief idea of what it does.>
- Copyright (C) <year> <name of author>
-
- This program is free software: you can redistribute it and/or modify
- it under the terms of the GNU Affero General Public License as published
- by the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
-
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU Affero General Public License for more details.
-
- You should have received a copy of the GNU Affero General Public License
- along with this program. If not, see <https://www.gnu.org/licenses/>.
-
-Also add information on how to contact you by electronic and paper mail.
-
- If your software can interact with users remotely through a computer
-network, you should also make sure that it provides a way for users to
-get its source. For example, if your program is a web application, its
-interface could display a "Source" link that leads users to an archive
-of the code. There are many ways you could offer source, and different
-solutions will be better for different programs; see section 13 for the
-specific requirements.
-
- You should also get your employer (if you work as a programmer) or school,
-if any, to sign a "copyright disclaimer" for the program, if necessary.
-For more information on this, and how to apply and follow the GNU AGPL, see
-<https://www.gnu.org/licenses/>.
diff --git a/addons/ASTER/README.md b/addons/ASTER/README.md
deleted file mode 100644
index fc63f4101fcf0e2eb171a7ab5d7d890ac70242dd..0000000000000000000000000000000000000000
--- a/addons/ASTER/README.md
+++ /dev/null
@@ -1,73 +0,0 @@
-# Accurate Species Tree EstimatoR
-A family of ASTRAL-like algorithms
-
-# ASTERISK
-Accurate Species Tree Estimation by diRectly Inferring from Site Kernels
-
-# Compile for Linux/Unix
-`g++ -std=gnu++11 -march=native -Ofast -pthread asterisk.cpp -o asterisk`
-
-# Run
-asterisk [-o oFilePath -r nRound -s nSample -p probability -t nThread -y] inputList
-
--o path to output file (default: stdout)
-
--r number of total rounds of placements (default: 4)
-
--s number of total rounds of subsampling (default: 4)
-
--p subsampling probability of keeping each taxon (default: 0.5)
-
--t number of threads (default: 1)
-
--y take one input in PHYLIP format instead of a list of inputs in FASTA format
-
-inputList: the path to a file containing a list of paths to input aligned gene files, one file per line
-
-Gene files must be in FASTA format. The header line should be ">Species_Name".
-
-Example run:
-
-`./asterisk example/list.txt`
-
-`./asterisk -y example/example.phylip`
-
-# Assumptions for Statistical Consistency
-## The multi-species coalescent model
-1. The gene trees are generated independently, and as the number of genes goes to infinity, ASTERISK is statistically consistent.
-2. The coalescent units do not need to be the same across branches.
-
-## Gene tree and sequence model
-1. The mutation rates (per time) do not need to be the same across branches, and within each branch across different time, the mutation rate does not need to scale the same way as coalescent does, as long as being reasonable (e.g. infimum/minimum above zero and capped).
-2. The length of each gene can be arbitrary and may be dependent on parameters above, as long as being reasonable (e.g. infimum/minimum above zero and capped).
-
-## Felsenstein 1981 model-like
-1. Base frequencies are provided and allowed to vary from 0.25, but the rate matrix must be F81-like.
-2. The sum of top 2 base frequencies must be less than 1. In other words, the number of categories must be at least 3, which unfortunately excludes binary inputs (e.g. major or minor alleles) but allowing nucleotides (4) and amino acids (20). (Base positions with the number of effective categories no more than 2 will neither contribute to nor bias the inferred species tree.)
-3. Different base positions (or genes) are allowed to have different base frequencies and be dependent on parameters above, as long as being reasonable (e.g. non-zero for at least 3 categories) and provided.
-
-
-# astral(-pro)
-Optimizing ASTRAL(-pro) objective function using ASTER method
-
-# Compile for Linux/Unix
-`g++ -std=gnu++11 -march=native -Ofast -pthread astral.cpp -o astral`
-
-`g++ -std=gnu++11 -march=native -Ofast -pthread astral-pro.cpp -o astral-pro`
-
-# Run
-astral(-pro) [-o oFilePath -r nRound -s nSample -p probability -t nThread -a taxonNameMaps] inputGeneTrees
-
--o path to output file (default: stdout)
-
--r number of total rounds of placements (default: 4)
-
--s number of total rounds of subsampling (default: 4)
-
--p subsampling probability of keeping each taxon (default: 0.5)
-
--t number of threads (default: 1)
-
--a a list of gene name to taxon name maps, each line contains one gene name followed by one taxon name separated by a space or tab
-
-inputGeneTrees: the path to a file containing all gene trees in Newick format
diff --git a/addons/ASTER/algorithms.hpp b/addons/ASTER/algorithms.hpp
deleted file mode 100644
index f4bb3e6da17031578129894fb48f56e7aa312e45..0000000000000000000000000000000000000000
--- a/addons/ASTER/algorithms.hpp
+++ /dev/null
@@ -1,1255 +0,0 @@
-typedef unsigned __int128 hash_t;
-
-#include<vector>
-#include<array>
-#include<utility>
-#include<random>
-#include<unordered_set>
-#include<unordered_map>
-#include<algorithm>
-#include<tuple>
-#include<string>
-#include<thread>
-#include<mutex>
-
-#ifdef SUPPORT
-#include "incbeta.c"
-#include <cmath>
-#endif
-
-using namespace std;
-
-struct Hasher{
- size_t operator()(const hash_t h) const{
- return (size_t) h;
- }
-};
-
-const int ROUND_NN = 50;
-
-struct PlacementAlgorithm{
-
- struct Node{
- Node(int leafId = -1): leafId(leafId){}
-
- int parent = -1, heavy = -1, light = -1; //parent 0, heavy 1, light 2
- int leafId = -1, leafCnt = 1;
- score_t sYes = 0, sNo = 0;
- bool placeHeavy = false, placeLight = false;
- };
-
- vector<hash_t> taxonHash; // sum of hash = 0
- vector<tuple<hash_t, hash_t, score_t> > tripHash;
- vector<int> order;
- vector<Node> nodes;
- int rootNodeId = -1, rootLeafId = -1, orderId = 0;
- int rNN;
-
- Tripartition trip;
-
- PlacementAlgorithm(const vector<hash_t> &taxonHash, const TripartitionInitializer &tripInit, int rNN = ROUND_NN): taxonHash(taxonHash), trip(tripInit), rNN(rNN){}
-
- int& heavy(int v){
- return nodes[v].heavy;
- }
-
- int& light(int v){
- return nodes[v].light;
- }
-
- int& parent(int v){
- return nodes[v].parent;
- }
-
- int& leafId(int v){
- return nodes[v].leafId;
- }
-
- int& leafCnt(int v){
- return nodes[v].leafCnt;
- }
-
- score_t& sYes(int v){
- return nodes[v].sYes;
- }
-
- score_t& sNo(int v){
- return nodes[v].sNo;
- }
-
- bool& placeHeavy(int v){
- return nodes[v].placeHeavy;
- }
-
- bool& placeLight(int v){
- return nodes[v].placeLight;
- }
-
- int makeNode(int v, int u, bool modifyRoot = false){
- int w = nodes.size();
- nodes.emplace_back(-1);
- parent(w) = parent(v);
- if (parent(v) == -1) {
- if (modifyRoot) rootNodeId = w;
- }
- else if (heavy(parent(w)) == v) heavy(parent(w)) = w;
- else light(parent(w)) = w;
- parent(v) = w; parent(u) = w;
- heavy(w) = v; light(w) = u;
- for (; w != -1; w = parent(w)){
- if (leafCnt(heavy(w)) < leafCnt(light(w))){
- int t = heavy(w);
- heavy(w) = light(w);
- light(w) = t;
- }
- leafCnt(w) = leafCnt(heavy(w)) + leafCnt(light(w));
- }
- return nodes.size() - 1;
- }
-
- void addSibling(int v, int i){
- int u = nodes.size();
- nodes.emplace_back(i);
- makeNode(v, u, true);
- }
-
- void forceLeftHeavy(int v){
- if (leafId(v) != -1) leafCnt(v) = 1;
- else {
- if (leafCnt(heavy(v)) < leafCnt(light(v))){
- int t = heavy(v);
- heavy(v) = light(v);
- light(v) = t;
- }
- leafCnt(v) = leafCnt(heavy(v)) + leafCnt(light(v));
- }
- }
-
- void defaultInitializer(){
- if (rootLeafId == -1){
- rootLeafId = order[orderId];
- //trip.addTotal(order[orderId]);
- orderId++;
- }
- if (rootNodeId == -1){
- rootNodeId = nodes.size();
- nodes.emplace_back(order[orderId]);
- //trip.addTotal(order[orderId]);
- orderId++;
- }
- forceLeftHeavy(rootNodeId);
- }
-
- void switchSubtree(int v, int src, int tgt){
- if (leafId(v) != -1){
- //trip.rmv(src, leafId(v));
- //trip.add(tgt, leafId(v));
- trip.update(tgt, leafId(v));
- }
- else{
- switchSubtree(light(v), src, tgt);
- switchSubtree(heavy(v), src, tgt);
- }
- }
-
- void scoringPlacementDP(int v, int i){
- if (leafId(v) != -1){
- //Wv|-|i
- sNo(v) = 0;
- //W|v|i
- trip.update(1, leafId(v));
- sYes(v) = trip.score();
- placeHeavy(v) = false;
- placeLight(v) = false;
- }
- else{
- //AC|B|i
- scoringPlacementDP(light(v), i);
- //ABC|-|i
- switchSubtree(light(v), 1, 0);
- //BC|A|i
- scoringPlacementDP(heavy(v), i);
- //C|A|Bi
- switchSubtree(light(v), 0, 2);
- score_t up, left, right, sibling;
- right = trip.score();
- //C|Ai|B
- trip.update(1, i);
- left = trip.score();
- //Ci|A|B
- trip.update(0, i);
- up = trip.score();
- //C|A|Bi
- trip.update(2, i);
- //C|AB|i
- switchSubtree(light(v), 2, 1);
- sibling = trip.score();
- sNo(v) = sNo(light(v)) + sNo(heavy(v)) + up;
- sYes(v) = sNo(v) + sibling;
- placeHeavy(v) = false;
- placeLight(v) = false;
- if (sYes(v) < sYes(light(v)) + sNo(heavy(v)) + right){
- sYes(v) = sYes(light(v)) + sNo(heavy(v)) + right;
- placeHeavy(v) = false;
- placeLight(v) = true;
- }
- if (sYes(v) < sNo(light(v)) + sYes(heavy(v)) + left){
- sYes(v) = sNo(light(v)) + sYes(heavy(v)) + left;
- placeHeavy(v) = true;
- placeLight(v) = false;
- }
- }
- }
-
- int locateBranchAdding(int i){
- //trip.addTotal(i);
- trip.update(2, i);
- trip.update(0, rootLeafId);
- switchSubtree(rootNodeId, -1, 0);
- scoringPlacementDP(rootNodeId, i);
- int v = rootNodeId;
- while (placeHeavy(v) || placeLight(v)){
- if (placeHeavy(v)) v = heavy(v);
- else v = light(v);
- }
- return v;
- }
-
- void place(int i){
- addSibling(locateBranchAdding(i), i);
- }
-
- int locateBranch(int i){
- int v = locateBranchAdding(i);
- trip.update(-1, i); //trip.rmvTotal(i);
- return v;
- }
-
- inline score_t nnPerform(int v, int best_case, score_t top_score){
- if (best_case == 1){
- int u = light(v), c = heavy(u), d = light(u), ab = heavy(v);
- parent(ab) = u; heavy(u) = ab;
- parent(c) = u; light(u) = c;
- parent(u) = v; heavy(v) = u;
- parent(d) = v; light(v) = d;
- leafCnt(u) = leafCnt(heavy(u)) + leafCnt(light(u));
- return nnLocal(v, true, top_score);
- }
- if (best_case == 2){
- int u = light(v), c = heavy(u), d = light(u), ab = heavy(v);
- parent(ab) = u; heavy(u) = ab;
- parent(d) = u; light(u) = d;
- parent(u) = v; heavy(v) = u;
- parent(c) = v; light(v) = c;
- leafCnt(u) = leafCnt(heavy(u)) + leafCnt(light(u));
- return nnLocal(v, true, top_score);
- }
- if (best_case == 3){
- int u = heavy(v), a = heavy(u), b = light(u), cd = light(v);
- parent(b) = u; heavy(u) = b;
- parent(cd) = u; light(u) = cd;
- parent(a) = v; heavy(v) = a;
- parent(u) = v; light(v) = u;
- leafCnt(u) = leafCnt(heavy(u)) + leafCnt(light(u));
- return nnLocal(v, true, top_score);
- }
- if (best_case == 4){
- int u = heavy(v), a = heavy(u), b = light(u), cd = light(v);
- parent(a) = u; heavy(u) = a;
- parent(cd) = u; light(u) = cd;
- parent(u) = v; heavy(v) = u;
- parent(b) = v; light(v) = b;
- leafCnt(u) = leafCnt(heavy(u)) + leafCnt(light(u));
- return nnLocal(v, true, top_score);
- }
- return top_score;
- }
-
- score_t nnLocal(int v, bool recurse, score_t e_ab_cd){
- //E|ABCD|-
- if (recurse) {
- if (rNN <= 0) return e_ab_cd;
- rNN--;
- }
-
- //E|AB|CD
- switchSubtree(light(v), 1, 2);
- score_t abe_c_d = 0, cde_a_b = 0;
- if (leafId(light(v)) == -1){
- int c = heavy(light(v)), d = light(light(v));
- //ABE|C|D
- switchSubtree(heavy(v), 1, 0);
- switchSubtree(c, 2, 1);
- abe_c_d = trip.score();
- //ABE|CD|-
- switchSubtree(d, 2, 1);
- if (recurse) abe_c_d = nnLocal(light(v), false, abe_c_d);
- //E|AB|CD
- switchSubtree(heavy(v), 0, 1);
- switchSubtree(light(v), 1, 2);
- }
- if (leafId(heavy(v)) == -1){
- int b = light(heavy(v));
- //CDE|A|B
- switchSubtree(light(v), 2, 0);
- switchSubtree(b, 1, 2);
- cde_a_b = trip.score();
- //CDE|AB|-
- switchSubtree(b, 2, 1);
- if (recurse) cde_a_b = nnLocal(heavy(v), false, cde_a_b);
- //E|AB|CD
- switchSubtree(light(v), 0, 2);
- }
- int best_case = 0;
- score_t best_score = abe_c_d + cde_a_b + e_ab_cd, top_score = e_ab_cd;
- if (leafId(light(v)) == -1){
- int c = heavy(light(v)), d = light(light(v));
- //DE|AB|C
- switchSubtree(d, 2, 0);
- score_t de_ab_c = trip.score();
- //E|ABD|C
- switchSubtree(d, 0, 1);
- score_t e_abd_c = trip.score();
- //E|ABC|D
- switchSubtree(d, 1, 2);
- switchSubtree(c, 2, 1);
- score_t e_abc_d = trip.score();
- //CE|AB|D
- switchSubtree(c, 1, 0);
- score_t ce_ab_d = trip.score();
-
- if (best_score < cde_a_b + de_ab_c + e_abc_d) {
- best_score = cde_a_b + de_ab_c + e_abc_d;
- best_case = 1;
- top_score = e_abc_d;
- }
- if (best_score < cde_a_b + ce_ab_d + e_abd_c) {
- best_score = cde_a_b + ce_ab_d + e_abd_c;
- best_case = 2;
- top_score = e_abd_c;
- }
- //E|AB|CD
- switchSubtree(c, 0, 2);
- }
- if (leafId(heavy(v)) == -1){
- int a = heavy(heavy(v)), b = light(heavy(v));
- //BE|A|CD
- switchSubtree(b, 1, 0);
- score_t be_a_cd = trip.score();
- //E|A|BCD
- switchSubtree(b, 0, 2);
- score_t e_a_bcd = trip.score();
- //E|ACD|B
- switchSubtree(light(v), 2, 1);
- score_t e_acd_b = trip.score();
- //AE|B|CD
- switchSubtree(light(v), 1, 2);
- switchSubtree(a, 1, 0);
- switchSubtree(b, 2, 1);
- score_t ae_b_cd = trip.score();
-
- if (best_score < abe_c_d + ae_b_cd + e_a_bcd) {
- best_score = abe_c_d + ae_b_cd + e_a_bcd;
- best_case = 3;
- top_score = e_a_bcd;
- }
- if (best_score < abe_c_d + be_a_cd + e_acd_b) {
- best_score = abe_c_d + be_a_cd + e_acd_b;
- best_case = 4;
- top_score = e_acd_b;
- }
- //E|AB|CD
- switchSubtree(a, 0, 1);
- }
- //E|ABCD|-
- switchSubtree(light(v), 2, 1);
- return nnPerform(v, best_case, top_score);
- }
-
- score_t nnMove(int v){
- if (leafId(v) != -1){
- trip.update(1, leafId(v));
- return 0;
- }
- else{
- //ABE|CD|-
- score_t abe_c_d = nnMove(light(v));
- score_t ae_b_cd = 0;
- if (leafId(heavy(v)) == -1){
- int b = light(heavy(v));
- //AE|B|CD
- switchSubtree(b, 0, 1);
- switchSubtree(light(v), 1, 2);
- ae_b_cd = trip.score();
- //ABCDE|-|-
- switchSubtree(b, 1, 0);
- switchSubtree(light(v), 2, 0);
- }
- //ABCDE|-|-
- else switchSubtree(light(v), 1, 0);
- //CDE|AB|-
- score_t cde_a_b = nnMove(heavy(v));
- //E|AB|CD
- switchSubtree(light(v), 0, 2);
- score_t e_ab_cd = trip.score();
- int best_case = 0;
- score_t best_score = abe_c_d + cde_a_b + e_ab_cd, top_score = e_ab_cd;
-
- if (leafId(light(v)) == -1){
- int c = heavy(light(v)), d = light(light(v));
- //DE|AB|C
- switchSubtree(d, 2, 0);
- score_t de_ab_c = trip.score();
- //E|ABD|C
- switchSubtree(d, 0, 1);
- score_t e_abd_c = trip.score();
- //E|ABC|D
- switchSubtree(d, 1, 2);
- switchSubtree(c, 2, 1);
- score_t e_abc_d = trip.score();
- //CE|AB|D
- switchSubtree(c, 1, 0);
- score_t ce_ab_d = trip.score();
-
- if (best_score < cde_a_b + de_ab_c + e_abc_d) {
- best_score = cde_a_b + de_ab_c + e_abc_d;
- best_case = 1;
- top_score = e_abc_d;
- }
- if (best_score < cde_a_b + ce_ab_d + e_abd_c) {
- best_score = cde_a_b + ce_ab_d + e_abd_c;
- best_case = 2;
- top_score = e_abd_c;
- }
- //E|AB|CD
- switchSubtree(c, 0, 2);
- }
- if (leafId(heavy(v)) == -1){
- int b = light(heavy(v));
- //E|A|BCD
- switchSubtree(b, 1, 2);
- score_t e_a_bcd = trip.score();
- //BE|A|CD
- switchSubtree(b, 2, 0);
- score_t be_a_cd = trip.score();
- //E|ACD|B
- switchSubtree(b, 0, 2);
- switchSubtree(light(v), 2, 1);
- score_t e_acd_b = trip.score();
-
- if (best_score < abe_c_d + ae_b_cd + e_a_bcd) {
- best_score = abe_c_d + ae_b_cd + e_a_bcd;
- best_case = 3;
- top_score = e_a_bcd;
- }
- if (best_score < abe_c_d + be_a_cd + e_acd_b) {
- best_score = abe_c_d + be_a_cd + e_acd_b;
- best_case = 4;
- top_score = e_acd_b;
- }
- //E|AB|CD
- switchSubtree(b, 2, 1);
- switchSubtree(light(v), 1, 2);
- }
- //E|ABCD|-
- switchSubtree(light(v), 2, 1);
- return nnPerform(v, best_case, top_score);
- }
- }
-
- pair<bool, hash_t> tripHashGenerator(int v){
- if (leafId(v) != -1){
- //trip.reset();
- //trip.rmv(0, leafId(v));
- //trip.add(1, leafId(v));
- trip.update(1, leafId(v));
- return {leafId(v) == 0, taxonHash[leafId(v)]};
- }
- else{
- //AC|B|-
- pair<bool, hash_t> hLight = tripHashGenerator(light(v));
- //ABC|-|-
- switchSubtree(light(v), 1, 0);
- //BC|A|-
- pair<bool, hash_t> hHeavy = tripHashGenerator(heavy(v));
- //C|A|B
- switchSubtree(light(v), 0, 2);
- score_t s = trip.score();
- //C|AB|-
- switchSubtree(light(v), 2, 1);
- if (hHeavy.first) tripHash.push_back(make_tuple(hLight.second, -hHeavy.second-hLight.second, s));
- else if (hLight.first) tripHash.push_back(make_tuple(hHeavy.second, -hHeavy.second-hLight.second, s));
- else tripHash.push_back(make_tuple(hHeavy.second, hLight.second, s));
- return {hHeavy.first || hLight.first, hHeavy.second + hLight.second};
- }
-
- }
-
- void run(){
- defaultInitializer();
- for (; orderId < order.size(); orderId++){
- if (orderId & 15 == 0) cerr << "Placing " << orderId << "/" << order.size() << endl;
- place(order[orderId]);
- }
- if (rNN >= 0) {
- trip.update(0, rootLeafId);
- switchSubtree(rootNodeId, -1, 0);
- nnMove(rootNodeId);
- cerr << "#localmove:" << ROUND_NN - rNN << "/" << ROUND_NN << endl;
- }
- trip.update(0, rootLeafId);
- switchSubtree(rootNodeId, -1, 0);
- tripHashGenerator(rootNodeId);
- }
-
-
- string printSubtree(int v){
- if (leafId(v) != -1) return to_string(leafId(v));
- return string("(") + printSubtree(heavy(v)) + "," + printSubtree(light(v)) + ")";
- }
-
- string printTree(){
- return string("(") + printSubtree(rootNodeId) + "," + to_string(rootLeafId) + ");";
- }
-
- string printSubtree(int v, const vector<string> &names){
- if (leafId(v) != -1) return names[leafId(v)];
- return string("(") + printSubtree(heavy(v), names) + "," + printSubtree(light(v), names) + ")";
- }
-
- string printTree(const vector<string> &names){
- return string("(") + printSubtree(rootNodeId, names) + "," + names[rootLeafId] + ");";
- }
-};
-
-struct ConstrainedOptimizationAlgorithm{
- struct Node{
- Node(int leafId, hash_t hash): leafId(leafId), hash(hash){}
-
- hash_t hash, bestChild = 0;
- score_t bestScore = 0;
- int roundId = 0, leafId;
- unordered_map<hash_t, tuple<int, int, score_t>, Hasher> children;
- };
-
- vector<Node> nodes;
- unordered_map<hash_t, int, Hasher> hash;
- vector<hash_t> taxonHash;
- const vector<string> names;
- mt19937_64 generator;
- uniform_int_distribution<hash_t> randomHash;
- uniform_real_distribution<double> randP;
- const TripartitionInitializer &tripInit;
- const int ntaxa;
- int roundId = 0;
- mutex mtx;
-
- ConstrainedOptimizationAlgorithm(const int ntaxa, const TripartitionInitializer &tripInit, const vector<string> &names, const int seed = 2333): ntaxa(ntaxa), tripInit(tripInit), names(names), generator(seed){
- taxonHash.push_back(0);
- for (int i = 1; i < ntaxa; i++){
- hash_t r = randomHash(generator);
- taxonHash.push_back(r);
- hash[r] = nodes.size();
- nodes.emplace_back(i, r);
- taxonHash[0] -= r;
- }
- }
-
- ConstrainedOptimizationAlgorithm(const ConstrainedOptimizationAlgorithm &alg): ntaxa(alg.ntaxa), tripInit(alg.tripInit), names(alg.names), nodes(alg.nodes), hash(alg.hash), taxonHash(alg.taxonHash){}
-
- int subsampleSubtree(int v, PlacementAlgorithm &pAlg, const unordered_set<int> &selected){
- if (nodes[v].leafId != -1){
- if (selected.count(nodes[v].leafId)){
- //pAlg.trip.addTotal(nodes[v].leafId);
- if (pAlg.rootLeafId == -1){
- pAlg.rootLeafId = nodes[v].leafId;
- return -1;
- }
- else {
- pAlg.nodes.emplace_back(nodes[v].leafId);
- return pAlg.nodes.size() - 1;
- }
- }
- else {
- pAlg.order.push_back(nodes[v].leafId);
- return -1;
- }
- }
- else {
- tuple<int, int, score_t> t = nodes[v].children[nodes[v].bestChild];
- if (pAlg.rootLeafId != -1){
- int nodeL = subsampleSubtree(get<0>(t), pAlg, selected);
- int nodeR = subsampleSubtree(get<1>(t), pAlg, selected);
- if (nodeL != -1){
- if (nodeR != -1) return pAlg.makeNode(nodeL, nodeR, false);
- else return nodeL;
- }
- else return nodeR;
- }
- else {
- int nodeL = subsampleSubtree(get<0>(t), pAlg, selected);
- if (pAlg.rootLeafId == -1) return subsampleSubtree(get<1>(t), pAlg, selected);
- else if (nodeL == -1) return pAlg.rootNodeId = subsampleSubtree(get<1>(t), pAlg, selected);
- else {
- int nodeR = subsampleSubtree(get<1>(t), pAlg, selected);
- if (nodeR == -1) return nodeL;
- else {
- pAlg.makeNode(nodeL, nodeR, true);
- return nodeR;
- }
- }
- }
- }
- }
-
- void createPlacementAlgorithm(PlacementAlgorithm &pAlg, const unordered_set<int> &selected){
- if (roundId != 0){
- if (selected.count(0)){
- pAlg.rootLeafId = 0;
- //pAlg.trip.addTotal(0);
- pAlg.rootNodeId = subsampleSubtree(hash[-taxonHash[0]], pAlg, selected);
- }
- else {
- pAlg.order.push_back(0);
- subsampleSubtree(hash[-taxonHash[0]], pAlg, selected);
- }
- }
- else{
- for (int i = 0; i < ntaxa; i++){
- pAlg.order.push_back(i);
- }
- }
- shuffle(pAlg.order.begin(), pAlg.order.end(), generator);
- }
-
- int subsampleSubtree(int v, PlacementAlgorithm &pAlg, double subsampleRate){
- if (nodes[v].leafId != -1){
- if (randP(generator) < subsampleRate){
- //pAlg.trip.addTotal(nodes[v].leafId);
- if (pAlg.rootLeafId == -1){
- pAlg.rootLeafId = nodes[v].leafId;
- return -1;
- }
- else {
- pAlg.nodes.emplace_back(nodes[v].leafId);
- return pAlg.nodes.size() - 1;
- }
- }
- else {
- pAlg.order.push_back(nodes[v].leafId);
- return -1;
- }
- }
- else {
- tuple<int, int, score_t> t = nodes[v].children[nodes[v].bestChild];
- if (pAlg.rootLeafId != -1){
- int nodeL = subsampleSubtree(get<0>(t), pAlg, subsampleRate);
- int nodeR = subsampleSubtree(get<1>(t), pAlg, subsampleRate);
- if (nodeL != -1){
- if (nodeR != -1) return pAlg.makeNode(nodeL, nodeR, false);
- else return nodeL;
- }
- else return nodeR;
- }
- else {
- int nodeL = subsampleSubtree(get<0>(t), pAlg, subsampleRate);
- if (pAlg.rootLeafId == -1) return subsampleSubtree(get<1>(t), pAlg, subsampleRate);
- else if (nodeL == -1) return pAlg.rootNodeId = subsampleSubtree(get<1>(t), pAlg, subsampleRate);
- else {
- int nodeR = subsampleSubtree(get<1>(t), pAlg, subsampleRate);
- if (nodeR == -1) return nodeL;
- else {
- pAlg.makeNode(nodeL, nodeR, true);
- return nodeR;
- }
- }
- }
- }
- }
-
- void createPlacementAlgorithm(PlacementAlgorithm &pAlg, double subsampleRate){
- if (roundId != 0){
- if (randP(generator) < subsampleRate){
- pAlg.rootLeafId = 0;
- //pAlg.trip.addTotal(0);
- pAlg.rootNodeId = subsampleSubtree(hash[-taxonHash[0]], pAlg, subsampleRate);
- }
- else {
- pAlg.order.push_back(0);
- subsampleSubtree(hash[-taxonHash[0]], pAlg, subsampleRate);
- }
- }
- else{
- for (int i = 0; i < ntaxa; i++){
- pAlg.order.push_back(i);
- }
- }
- shuffle(pAlg.order.begin(), pAlg.order.end(), generator);
- }
-
- PlacementAlgorithm createPlacementAlgorithm(double subsampleRate){
- PlacementAlgorithm pAlg(taxonHash, tripInit);
- createPlacementAlgorithm(pAlg, subsampleRate);
- return pAlg;
- }
-
- int guildSubtree(PlacementAlgorithm &pAlg, const string &tree, const unordered_map<string, int> &name2id, int &i, unordered_set<int> &added){
- int ret;
- if (tree[i] != '('){
- string s;
- for (; tree[i] != ':' && tree[i] != ')' && tree[i] != ',' && tree[i] != ';'; i++){
- if (tree[i] != '\"' && tree[i] != '\'') s += tree[i];
- }
- int id = name2id.at(s);
- //pAlg.trip.addTotal(id);
- added.insert(id);
- if (pAlg.rootLeafId == -1){
- pAlg.rootLeafId = id;
- ret = -1;
- }
- else {
- pAlg.nodes.emplace_back(id);
- ret = pAlg.nodes.size() - 1;
- }
- }
- else {
- i++;
- if (pAlg.rootLeafId != -1){
- int nodeL = guildSubtree(pAlg, tree, name2id, i, added);
- int nodeR = guildSubtree(pAlg, tree, name2id, i, added);
- if (nodeL != -1){
- if (nodeR != -1) ret = pAlg.makeNode(nodeL, nodeR, false);
- else ret = nodeL;
- }
- else ret = nodeR;
- }
- else {
- int nodeL = guildSubtree(pAlg, tree, name2id, i, added);
- if (pAlg.rootLeafId == -1) ret = guildSubtree(pAlg, tree, name2id, i, added);
- else if (nodeL == -1) ret = pAlg.rootNodeId = guildSubtree(pAlg, tree, name2id, i, added);
- else {
- int nodeR = guildSubtree(pAlg, tree, name2id, i, added);
- if (nodeR == -1) ret = nodeL;
- else {
- pAlg.makeNode(nodeL, nodeR, true);
- ret = nodeR;
- }
- }
- }
- }
- while (tree[i] != ')' && tree[i] != ',' && tree[i] != ';') i++;
- i++;
- return ret;
- }
-
- void addGuideTree(const string tree, const unordered_map<string, int> &name2id, int rnn = ROUND_NN){
- unordered_set<int> added;
- PlacementAlgorithm pAlg(taxonHash, tripInit, rnn);
- int i = 0;
- guildSubtree(pAlg, tree, name2id, i, added);
- for (int i = 0; i < ntaxa; i++){
- if (added.count(i) == 0) pAlg.order.push_back(i);
- }
- { const lock_guard<mutex> lock(mtx); shuffle(pAlg.order.begin(), pAlg.order.end(), generator); }
- pAlg.run();
- cerr << pAlg.printTree(names) << endl;
- { const lock_guard<mutex> lock(mtx); addTripartitions(pAlg.tripHash); }
- }
-
- int hash2node(hash_t h){
- if (hash.count(h) == 0){
- hash[h] = nodes.size();
- nodes.emplace_back(-1, h);
- }
- return hash[h];
- }
-
- void addTripartitions(const vector<tuple<hash_t, hash_t, score_t> > tripHash){
- for (const tuple<hash_t, hash_t, score_t> t: tripHash){
- int left = hash2node(get<0>(t)), right = hash2node(get<1>(t)), parent = hash2node(get<0>(t) + get<1>(t));
- nodes[parent].children[get<0>(t)] = make_tuple(left, right, get<2>(t));
- nodes[parent].children[get<1>(t)] = make_tuple(left, right, get<2>(t));
- }
- }
-
- void optimalTreeDP(int v){
- if (nodes[v].roundId == roundId) return;
- for (pair<hash_t, tuple<int, int, score_t> > child: nodes[v].children){
- optimalTreeDP(get<0>(child.second));
- optimalTreeDP(get<1>(child.second));
- if (nodes[v].roundId < roundId || nodes[v].bestScore < nodes[get<0>(child.second)].bestScore + nodes[get<1>(child.second)].bestScore + get<2>(child.second)){
- nodes[v].roundId = roundId;
- nodes[v].bestScore = nodes[get<0>(child.second)].bestScore + nodes[get<1>(child.second)].bestScore + get<2>(child.second);
- nodes[v].bestChild = child.first;
- }
- }
- nodes[v].roundId = roundId;
- }
-
- score_t computeOptimalTree(){
- roundId++;
- optimalTreeDP(hash2node(-taxonHash[0]));
- return nodes[hash[-taxonHash[0]]].bestScore;
- }
-
- string printOptimalSubtree(int v){
- if (nodes[v].leafId != -1) return names[nodes[v].leafId];
- tuple<int, int, score_t> t = nodes[v].children[nodes[v].bestChild];
- return string("(") + printOptimalSubtree(get<0>(t)) + "," + printOptimalSubtree(get<1>(t)) + ")";
- }
-
- string printOptimalTree(){
- return string("(") + printOptimalSubtree(hash[-taxonHash[0]]) + "," + names[0] + ");";
- }
-
- string printOptimalSubtreeWithScore(int v){
- if (nodes[v].leafId != -1) return names[nodes[v].leafId];
- tuple<int, int, score_t> t = nodes[v].children[nodes[v].bestChild];
- return string("(") + printOptimalSubtreeWithScore(get<0>(t)) + "," + printOptimalSubtreeWithScore(get<1>(t)) + "):" + to_string(get<2>(t));
- }
-
- string printOptimalTreeWithScore(){
- return string("(") + printOptimalSubtreeWithScore(hash[-taxonHash[0]]) + "," + names[0] + ");";
- }
-
- void batchWork(vector<PlacementAlgorithm> &jobs, int start, int end){
- for (int i = start; i < end; i++){
- jobs[i].run();
- cerr << jobs[i].printTree(names) << endl;
- }
- }
-
- pair<score_t, string> run(int nJobs = 1, int nThrds = 1, double subsampleRate = 0, bool allowTwoStepRun = true){
- if (nJobs == 0) return {computeOptimalTree(), printOptimalTree()};
- if (allowTwoStepRun && ntaxa >= 100) return twoStepRun(nJobs, nThrds);
- vector<PlacementAlgorithm> jobs;
- vector<thread> thrds;
- for (int i = 0; i < nJobs; i++){
- jobs.push_back(createPlacementAlgorithm(subsampleRate));
- }
- for (int i = 1; i < nThrds; i++){
- thrds.emplace_back(&ConstrainedOptimizationAlgorithm::batchWork, this, ref(jobs), i * nJobs / nThrds, (i + 1) * nJobs / nThrds);
- }
- batchWork(jobs, 0, nJobs / nThrds);
- for (int i = 1; i < nThrds; i++){
- thrds[i - 1].join();
- }
- for (int i = 0; i < nJobs; i++){
- addTripartitions(jobs[i].tripHash);
- }
-
- return {computeOptimalTree(), printOptimalTree()};
- }
-
- void batchConstrainedWork(int start, int end, const string tree, const unordered_map<string, int> &name2id){
- for (int i = start; i < end; i++){
- addGuideTree(tree, name2id, -1);
- }
- }
-
- pair<score_t, string> constrainedRun(int nJobs, int nThrds, const string tree, const unordered_map<string, int> &name2id){
- vector<thread> thrds;
- for (int i = 1; i < nThrds; i++){
- thrds.emplace_back(&ConstrainedOptimizationAlgorithm::batchConstrainedWork, this, i * nJobs / nThrds, (i + 1) * nJobs / nThrds, tree, ref(name2id));
- }
- batchConstrainedWork(0, nJobs / nThrds, tree, name2id);
- for (int i = 1; i < nThrds; i++){
- thrds[i - 1].join();
- }
-
- return {computeOptimalTree(), printOptimalTree()};
- }
-
- static bool placeNode(PlacementAlgorithm &pAlg, vector<PlacementAlgorithm::Node> &pNodes, int &rootNodeId, int i, unordered_map<int, int> &nodeRemap){
- int v = pAlg.locateBranchAdding(i);
- if (nodeRemap.count(v)){
- pAlg.addSibling(v, i);
- int w = pAlg.parent(v), u = (pAlg.light(w) == v) ? pAlg.heavy(w) : pAlg.light(w);
- int mV = nodeRemap[v], mW = pNodes.size(), mU = pNodes.size() + 1;
- pNodes.emplace_back(-1);
- pNodes.emplace_back(i);
- nodeRemap[w] = mW;
- nodeRemap[u] = mU;
- if (pAlg.rootNodeId == w) rootNodeId = mW;
- else {
- if (pNodes[pNodes[mV].parent].heavy == mV) pNodes[pNodes[mV].parent].heavy = mW;
- else pNodes[pNodes[mV].parent].light = mW;
- }
- pNodes[mW].parent = pNodes[mV].parent;
- pNodes[mV].parent = mW;
- pNodes[mU].parent = mW;
- pNodes[mW].heavy = mV;
- pNodes[mW].light = mU;
- return true;
- }
- else {
- //pAlg.trip.rmvTotal(i);
- pAlg.trip.update(-1, i);
- return false;
- }
- }
-
- void twoStepWorkflow(PlacementAlgorithm &pAlg){
- int N, rId;
- { const lock_guard<mutex> lock(mtx); N = ntaxa; rId = roundId; }
- int n = sqrt(N);
- vector<int> order;
- if (rId == 0){
- mtx.lock();
- ConstrainedOptimizationAlgorithm alg(*this);
- for (int i = 1; i < N; i++) order.push_back(i);
- shuffle(order.begin(), order.end(), generator);
- order.push_back(order[0]);
- order[0] = 0;
- hash_t hashsum = 0;
- for (int i = 1; i < n; i++) hashsum += taxonHash[order[i]];
- mtx.unlock();
-
- pAlg.taxonHash[0] = -hashsum;
- alg.taxonHash[0] = -hashsum;
- for (int r = 0; r < n; r++){
- cerr << "Guide Tree " << r << "/" << n << endl;
- for (int i = 0; i < n; i++) pAlg.order.push_back(order[i]);
- { const lock_guard<mutex> lock(mtx); shuffle(pAlg.order.begin(), pAlg.order.end(), generator); }
- pAlg.run();
- alg.addTripartitions(pAlg.tripHash);
- for (int i = 0; i < n; i++) pAlg.trip.update(-1, order[i]); //pAlg.trip.rmvTotal(order[i]);
- pAlg.tripHash.clear();
- pAlg.order.clear();
- pAlg.nodes.clear();
- pAlg.rootNodeId = -1;
- pAlg.rootLeafId = -1;
- pAlg.orderId = 0;
- pAlg.rNN = ROUND_NN;
- }
- alg.computeOptimalTree();
- //cerr << alg.printOptimalTree() << endl;
- alg.createPlacementAlgorithm(pAlg, 1);
- { const lock_guard<mutex> lock(mtx); pAlg.taxonHash[0] = taxonHash[0]; }
- }
- else{
- for (int i = 0; i < N; i++) order.push_back(i);
- { const lock_guard<mutex> lock(mtx); shuffle(order.begin(), order.end(), generator); }
- unordered_set<int> selected;
- for (int i = 0; i < n; i++) selected.insert(order[i]);
- { const lock_guard<mutex> lock(mtx); createPlacementAlgorithm(pAlg, selected); }
- cerr << "Subsampled nodes: " << pAlg.nodes.size() << endl;
- }
- {
- vector<int> abnormalOrder;
- vector<PlacementAlgorithm::Node> pNodes(pAlg.nodes);
- int rootNodeId = pAlg.rootNodeId;//, rootLeafId = pAlg.rootLeafId;
- {
- vector<PlacementAlgorithm::Node> originalNodes(pAlg.nodes);
- int originalRootNodeId = pAlg.rootNodeId;//, originalRootLeafId = pAlg.rootLeafId;
-
- vector<vector<int> > nodeBranch(pNodes.size());
- cerr << "pNodes: " << pNodes.size() << endl;
- for (int i = n; i < N; i++) {
- if ((i - n) & 127 == 0) cerr << "Binning " << i - n << "/" << N - n << endl;
- nodeBranch[pAlg.locateBranch(order[i])].push_back(order[i]);
- }
- int cnt = 0;
- for (int b = 0; b < nodeBranch.size(); b++){
- pAlg.nodes = originalNodes;
- pAlg.rootNodeId = originalRootNodeId;
- //pAlg.rootLeafId = originalRootLeafId;
- vector<int> added;
- unordered_map<int, int> nodeRemap;
- nodeRemap[b] = b;
- for (int i: nodeBranch[b]) {
- if (cnt & 127 == 0) cerr << "Placement " << cnt++ << "/" << N - n << endl;
- if (placeNode(pAlg, pNodes, rootNodeId, i, nodeRemap)) added.push_back(i);
- else abnormalOrder.push_back(i);
- }
- for (int i: added) pAlg.trip.update(-1, i); //pAlg.trip.rmvTotal(i);
- }
- }
- //for (int i = n; i < N; i++) pAlg.trip.addTotal(order[i]);
- //for (int i: abnormalOrder) pAlg.trip.rmvTotal(i);
- pAlg.order = abnormalOrder;
- pAlg.nodes = pNodes;
- pAlg.rootNodeId = rootNodeId;
- //pAlg.rootLeafId = rootLeafId;
- pAlg.orderId = 0;
- }
- cerr << "Remaining: " << pAlg.order.size() << endl;
- pAlg.run();
- }
-
- void twoStepBatchWork(int nJobs){
- for (int i = 0; i < nJobs; i++){
- PlacementAlgorithm job(taxonHash, tripInit);
- twoStepWorkflow(job);
- cerr << job.printTree(names) << endl;
- { const lock_guard<mutex> lock(mtx); addTripartitions(job.tripHash); }
- }
- }
-
- pair<score_t, string> twoStepRun(int nJobs, int nThrds){
- cerr << "Use two-step algorithm!\n";
- vector<thread> thrds;
-
- for (int i = 1; i < nThrds; i++){
- thrds.emplace_back(&ConstrainedOptimizationAlgorithm::twoStepBatchWork, this, (i + 1) * nJobs / nThrds - i * nJobs / nThrds);
- }
- twoStepBatchWork(nJobs / nThrds);
- for (int i = 1; i < nThrds; i++){
- thrds[i - 1].join();
- }
-
- return {computeOptimalTree(), printOptimalTree()};
- }
-
-#ifdef SUPPORT
- void switchSubtree(Quadrupartition &quad, int v, int s, int t){
- if (nodes[v].leafId != -1) {
- quad.update(t, nodes[v].leafId);
- }
- else {
- tuple<int, int, score_t> c = nodes[v].children[nodes[v].bestChild];
- switchSubtree(quad, get<0>(c), s, t);
- switchSubtree(quad, get<1>(c), s, t);
- }
- }
-
- string printOptimalSubtreeWithSupport(Quadrupartition &quad, int v, int u, int support, double lambda,
- unordered_map<int, tuple<array<double, 3>, array<double, 3>, string> > &qInfo){
- if (nodes[v].leafId != -1) {
- array<double, 3> t;
- if (support == 3) qInfo[v] = make_tuple(t, t, names[nodes[v].leafId]);
- return names[nodes[v].leafId];
- }
- //r|u|c0c1|-
- string res = "(";
- tuple<int, int, score_t> c = nodes[v].children[nodes[v].bestChild];
- //ru|c1|c0|-
- switchSubtree(quad, u, 1, 0);
- switchSubtree(quad, get<1>(c), 2, 1);
- res += printOptimalSubtreeWithSupport(quad, get<0>(c), get<1>(c), support, lambda, qInfo) + ",";
- //ru|c0|c1|-
- switchSubtree(quad, get<0>(c), 2, 1);
- switchSubtree(quad, get<1>(c), 1, 2);
- res += printOptimalSubtreeWithSupport(quad, get<1>(c), get<0>(c), support, lambda, qInfo) + ")";
- //r|u|c1|c0
- switchSubtree(quad, u, 0, 1);
- switchSubtree(quad, get<0>(c), 1, 3);
- array<double, 3> score = quad.score();
- //r|u|c0c1|-
- switchSubtree(quad, get<0>(c), 3, 2);
- if (score[0] + score[1] + score[2] < 1e-8) {
- if (support == 1) return res + to_string(1.0 / 3.0);
- else return res + "'support=(0,0,0);p=(0.333,0.333,0.333)'";
- }
- double tscore = score[0] + score[1] + score[2];
- double i0 = 1.0 - incbeta(score[0] + 1.0, tscore + lambda * 2 - score[0], 1.0 / 3.0);
- double i1 = 1.0 - incbeta(score[1] + 1.0, tscore + lambda * 2 - score[1], 1.0 / 3.0);
- double i2 = 1.0 - incbeta(score[2] + 1.0, tscore + lambda * 2 - score[2], 1.0 / 3.0);
- double lb0 = lgamma(score[0] + 1.0) + lgamma(tscore - score[0] + lambda * 2) - lgamma(tscore + 1.0 + lambda * 2);
- double lb1 = lgamma(score[1] + 1.0) + lgamma(tscore - score[1] + lambda * 2) - lgamma(tscore + 1.0 + lambda * 2);
- double lb2 = lgamma(score[2] + 1.0) + lgamma(tscore - score[2] + lambda * 2) - lgamma(tscore + 1.0 + lambda * 2);
- if (support == 1) res += to_string(i0 / (i0 + i1 * exp(log(2.0) * (score[1] - score[0]) + lb1 - lb0) + i2 * exp(log(2.0) * (score[2] - score[0]) + lb2 - lb0)));
- else {
- array<double, 3> p;
- p[0] = i0 / (i0 + i1 * exp(log(2.0) * (score[1] - score[0]) + lb1 - lb0) + i2 * exp(log(2.0) * (score[2] - score[0]) + lb2 - lb0));
- p[1] = i1 / (i1 + i0 * exp(log(2.0) * (score[0] - score[1]) + lb0 - lb1) + i2 * exp(log(2.0) * (score[2] - score[1]) + lb2 - lb1));
- p[2] = i2 / (i2 + i1 * exp(log(2.0) * (score[1] - score[2]) + lb1 - lb2) + i0 * exp(log(2.0) * (score[0] - score[2]) + lb0 - lb2));
- res += "'support=(" + to_string(score[0]) + "," + to_string(score[1]) + "," + to_string(score[2]) + ");p=(";
- res += to_string(p[0]) + "," + to_string(p[1]) + "," + to_string(p[2]) + ")'";
- if (support == 3) qInfo[v] = make_tuple(score, p, get<2>(qInfo[get<0>(c)]) + "," + get<2>(qInfo[get<1>(c)]));
- }
- if (3 * score[0] > tscore) res += ":" + to_string(max(0.0, -log(1.5 - 1.5 * score[0] / (tscore + lambda * 2))));
- else res += ":0";
- return res;
- }
-
- void printFreqQuadCSV(int v, int u, string top, ostream &fcsv, unordered_map<int, tuple<array<double, 3>, array<double, 3>, string> > &qInfo){
- if (nodes[v].leafId != -1) return;
- tuple<int, int, score_t> c = nodes[v].children[nodes[v].bestChild];
- printFreqQuadCSV(get<0>(c), get<1>(c), top + "," + get<2>(qInfo[u]), fcsv, qInfo);
- printFreqQuadCSV(get<1>(c), get<0>(c), top + "," + get<2>(qInfo[u]), fcsv, qInfo);
- double tscore = get<0>(get<0>(qInfo[v])) + get<1>(get<0>(qInfo[v])) + get<2>(get<0>(qInfo[v]));
- fcsv << "N" << v << "\tt1\t{" << get<2>(qInfo[get<0>(c)]) << "}|{" << get<2>(qInfo[get<1>(c)]) << "}#{" << get<2>(qInfo[u]) << "}|{" << top << "}\t"
- << get<0>(get<1>(qInfo[v])) << "\t" << get<0>(get<0>(qInfo[v])) << "\t" << tscore << endl;
- fcsv << "N" << v << "\tt2\t{" << top << "}|{" << get<2>(qInfo[get<1>(c)]) << "}#{" << get<2>(qInfo[u]) << "}|{" << get<2>(qInfo[get<0>(c)]) << "}\t"
- << get<1>(get<1>(qInfo[v])) << "\t" << get<1>(get<0>(qInfo[v])) << "\t" << tscore << endl;
- fcsv << "N" << v << "\tt3\t{" << get<2>(qInfo[get<0>(c)]) << "}|{" << top << "}#{" << get<2>(qInfo[u]) << "}|{" << get<2>(qInfo[get<1>(c)]) << "}\t"
- << get<2>(get<1>(qInfo[v])) << "\t" << get<2>(get<0>(qInfo[v])) << "\t" << tscore << endl;
-
- }
-
- string printOptimalTreeWithSupport(int support, double lambda){
- unordered_map<int, tuple<array<double, 3>, array<double, 3>, string> > qInfo;
- string res;
- Quadrupartition quad(tripInit);
- quad.update(0, 0);
- for (int i = 1; i < names.size(); i++) quad.update(2, i);
- int v = hash[-taxonHash[0]];
- tuple<int, int, score_t> c = nodes[v].children[nodes[v].bestChild];
- //0|c1|c0|-
- switchSubtree(quad, get<1>(c), 2, 1);
- res = "((" + printOptimalSubtreeWithSupport(quad, get<0>(c), get<1>(c), support, lambda, qInfo);
- //0|c0|c1|-
- switchSubtree(quad, get<1>(c), 1, 2);
- switchSubtree(quad, get<0>(c), 2, 1);
- res += "," + printOptimalSubtreeWithSupport(quad, get<1>(c), get<0>(c), support, lambda, qInfo);
- if (support == 3) {
- ofstream fcsv("freqQuad.csv");
- printFreqQuadCSV(get<0>(c), get<1>(c), names[0], fcsv, qInfo);
- printFreqQuadCSV(get<1>(c), get<0>(c), names[0], fcsv, qInfo);
- }
- return res + ")," + names[0] + ");";
- }
-#endif
-};
-
-#ifdef SUPPORT
-const string HELP_TEXT_1 = "feast [-c constraintSubtreeFilePath -g guideTreeFilePath -o oFilePath -r nRound -s nSample -p probability -t nThread -u supportLevel";
-const string HELP_TEXT_2 = R"V0G0N(] inputList
--c path to constraint subtree file
--g path to guide tree file
--o path to output file (default: stdout)
--r number of total rounds of placements (default: 5)
--s number of total rounds of subsampling (default: 0)
--p subsampling probability of keeping each taxon (default: 0.5)
--t number of threads (default: 1)
--l rate lambda of Yule process under which the species tree is modeled (default: 0.5)
--u output support level (0, default: no output support value, 1: branch local posterior probability, 2: detailed, 3: freqQuad.csv)
-)V0G0N";
-#else
-const string HELP_TEXT_1 = "binary_path [-c constraintSubtreeFilePath -g guideTreeFilePath -o oFilePath -r nRound -s nSample -p probability -t nThread";
-const string HELP_TEXT_2 = R"V0G0N(] inputList
--c path to constraint subtree file
--g path to guide tree file
--o path to output file (default: stdout)
--r number of total rounds of placements (default: 5)
--s number of total rounds of subsampling (default: 0)
--p subsampling probability of keeping each taxon (default: 0.5)
--t number of threads (default: 1)
-)V0G0N";
-#endif
-
-struct MetaAlgorithm{
- vector<string> files, names;
- int nThreads = 1, nRounds = 4, nSample = 4, nBatch = 8, fold = 0, nThread1, nThread2 = 1, support = 1;
- double p = 0.5, lambda = 0.5;
- string outputFile, guideFile, constraintFile, constraintTree;
- ofstream fileOut;
- unordered_map<string, int> name2id;
-
- TripartitionInitializer tripInit;
- vector<TripartitionInitializer> batchInit;
-
- MetaAlgorithm(){}
-
- MetaAlgorithm(int argc, char** argv, string helpTextS1, string helpTextS2){
- initialize(argc, argv, helpTextS1, helpTextS2);
- }
-
- void initialize(int argc, char** argv, string helpTextS1, string helpTextS2){
- if (argc == 1) {cerr << HELP_TEXT_1 << helpTextS1 << HELP_TEXT_2 << helpTextS2; exit(0);}
- for (int i = 1; i < argc; i += 2){
- if (strcmp(argv[i], "-y") == 0) {i--; continue;}
-
- if (strcmp(argv[i], "-c") == 0) constraintFile = argv[i + 1];
- if (strcmp(argv[i], "-g") == 0) guideFile = argv[i + 1];
- if (strcmp(argv[i], "-o") == 0) outputFile = argv[i + 1];
- if (strcmp(argv[i], "-r") == 0) sscanf(argv[i + 1], "%d", &nRounds);
- if (strcmp(argv[i], "-s") == 0) sscanf(argv[i + 1], "%d", &nSample);
- if (strcmp(argv[i], "-p") == 0) sscanf(argv[i + 1], "%lf", &p);
- if (strcmp(argv[i], "-t") == 0) sscanf(argv[i + 1], "%d", &nThreads);
- if (strcmp(argv[i], "-l") == 0) sscanf(argv[i + 1], "%lf", &lambda);
- if (strcmp(argv[i], "-u") == 0) sscanf(argv[i + 1], "%d", &support);
- if (strcmp(argv[i], "-h") == 0) {cerr << HELP_TEXT_1 << helpTextS1 << HELP_TEXT_2 << helpTextS2; exit(0);}
- }
-
- if (nRounds < nThreads && nRounds > 0){
- nThread2 = nThreads / nRounds;
- nThread1 = nRounds;
- }
- else {
- nThread2 = 1;
- nThread1 = nThreads;
- }
-
- batchInit.resize(nBatch);
- }
-
- void searchSpace(ConstrainedOptimizationAlgorithm &alg, const vector<int> &batchId, const vector<int> &seeds){
- for (int i = 0; i < batchId.size(); i++){
- ConstrainedOptimizationAlgorithm batchAlg(names.size(), batchInit[batchId[i]], names, seeds[i]);
- string tree = batchAlg.run(1, 1).second;
- alg.addGuideTree(tree, name2id);
- }
- }
-
- pair<score_t, string> generateSearchSpace(ConstrainedOptimizationAlgorithm &alg){
- if (nRounds > 0){
- vector<vector<int> > batchId(nThreads), seeds(nThreads);
- vector<thread> thrds;
-
- for (int i = 0; i < nRounds * fold; i++){
- batchId[i % nThreads].push_back(i % nBatch);
- seeds[i % nThreads].push_back(rand());
- }
-
- for (int i = 1; i < nThreads; i++){
- thrds.emplace_back(&MetaAlgorithm::searchSpace, this, ref(alg), ref(batchId[i]), ref(seeds[i]));
- }
-
- searchSpace(alg, batchId[0], seeds[0]);
-
- for (int i = 0; i < nThreads - 1; i++){
- thrds[i].join();
- }
- cerr << "*** End of Batching ***" << endl;
- }
- return alg.run(nRounds, nThread1);
- }
-
- pair<score_t, string> run(){
- ostream &fout = (outputFile == "") ? cout : fileOut;
- if (outputFile != "") fileOut.open(outputFile);
-
- cerr << "#Species: " << names.size() << endl;
- cerr << "#Rounds: " << nRounds << endl;
- cerr << "#Samples: " << nSample << endl;
- cerr << "#Threads: " << nThread1 << "x" << nThread2 << endl;
- cerr << "p = " << p << endl;
-
- ConstrainedOptimizationAlgorithm alg(names.size(), tripInit, names);
-
- if (guideFile != ""){
- ifstream fin(guideFile);
- string tree;
- while (getline(fin, tree)){
- alg.addGuideTree(tree, name2id);
- }
- }
-
- if (constraintFile != ""){
- ifstream fin(constraintFile);
- getline(fin, constraintTree);
- }
-
- auto res = (constraintTree == "") ? generateSearchSpace(alg) : alg.constrainedRun(nRounds, nThreads, constraintTree, name2id);
- if (constraintTree == "") {
- cerr << "*** Subsample Process ***" << endl;
- score_t prevS;
- do {
- prevS = res.first;
- res = alg.run(nSample, nThread1, p);
- }
- while (prevS < res.first);
- }
-
- string output = res.second;
- cerr << "Final Tree: " << output << endl;
- #ifdef SUPPORT
- if (support) output = alg.printOptimalTreeWithSupport(support, lambda);
- #endif
- fout << output << endl;
-
- return res;
- }
-};
diff --git a/addons/ASTER/asterisk-binary.cpp b/addons/ASTER/asterisk-binary.cpp
deleted file mode 100644
index 46621b2f6a41799a307350810791059a793fe54f..0000000000000000000000000000000000000000
--- a/addons/ASTER/asterisk-binary.cpp
+++ /dev/null
@@ -1,184 +0,0 @@
-#include<iostream>
-#include<fstream>
-#include<unordered_map>
-#include<cstdio>
-#include<cstdlib>
-#include<cstring>
-
-//#define LARGE_DATA
-#ifdef LARGE_DATA
-typedef long double score_t;
-typedef long long count_t;
-#else
-typedef double score_t;
-typedef int count_t;
-#endif
-
-#include "binary.hpp"
-#include "algorithms.hpp"
-
-using namespace std;
-
-TripartitionInitializer tripInit;
-
-vector<string> names;
-unordered_map<string, int> name2id;
-
-string formatName(const string name){
- string res;
- for (char c: name){
- if (c != '>' && c != ' ' && c != '\t') res += c;
- }
- return res;
-}
-
-void readFile(istream &fin){
- tripInit.seq.emplace_back(names.size());
- int cnt[2] = {}, id = -1, npos = 0;
- string line;
- while (getline(fin, line)){
- if (line[0] == '>') {
- id = name2id[formatName(line)];
- }
- else{
- for (char c: line){
- if (c == 'A' || c == 'a' || c == 'G' || c == 'g') { tripInit.seq.back()[id].push_back(0); cnt[0]++; }
- if (c == 'C' || c == 'c' || c == 'T' || c == 't') { tripInit.seq.back()[id].push_back(1); cnt[1]++; }
- if (c == 'X' || c == 'x' || c == 'N' || c == 'n' || c == '-') { tripInit.seq.back()[id].push_back(-1); }
- }
- if (npos < tripInit.seq.back()[id].size()) npos = tripInit.seq.back()[id].size();
- }
- }
- for (id = 0; id < names.size(); id++){
- while (tripInit.seq.back()[id].size() < npos) tripInit.seq.back()[id].push_back(-1);
- }
- tripInit.pi.push_back(cnt[0] / ((score_t) cnt[0] + cnt[1]));
-}
-
-void readPhilip(istream &fin){
- string line;
- int nTaxa, L;
- while (fin >> nTaxa){
- tripInit.seq.emplace_back(names.size());
- int cnt[4] = {}, npos = 0;
- fin >> L;
- for (int i = 0; i < nTaxa; i++){
- fin >> line;
- int id = name2id[line];
- getline(fin, line);
- for (char c: line){
- if (c == 'A' || c == 'a' || c == 'G' || c == 'g') { tripInit.seq.back()[id].push_back(0); cnt[0]++; }
- if (c == 'C' || c == 'c' || c == 'T' || c == 't') { tripInit.seq.back()[id].push_back(1); cnt[1]++; }
- if (c == 'X' || c == 'x' || c == 'N' || c == 'n' || c == '-') { tripInit.seq.back()[id].push_back(-1); }
- }
- if (npos < tripInit.seq.back()[id].size()) npos = tripInit.seq.back()[id].size();
- }
- for (int id = 0; id < names.size(); id++){
- while (tripInit.seq.back()[id].size() < npos) tripInit.seq.back()[id].push_back(-1);
- }
- tripInit.pi.push_back(cnt[0] / ((score_t) cnt[0] + cnt[1]));
- }
-}
-
-string helpText = R"V0G0N(feast [-o oFilePath -r nRound -s nSample -p probability -t nThread -y] inputList
--o path to output file (default: stdout)
--r number of total rounds of placements (default: 5)
--s number of total rounds of subsampling (default: 0)
--p subsampling probability of keeping each taxon (default: 0.5)
--t number of threads (default: 1)
--y take one input in PHYLIP format instead of a list of inputs in FASTA format
-inputList: the path to a file containing a list of paths to input aligned gene files, one file per line
-Gene files must be in FASTA format. The header line should be ">Species_Name".
-)V0G0N";
-
-int main(int argc, char** argv){
- vector<string> files;
-
- int nThreads = 1, nRounds = 4, nSample = 0;
- bool phylip = false;
- double p = 0.5;
- string outputFile;
- ofstream fileOut;
- if (argc == 1) {cerr << helpText; return 0;}
- for (int i = 1; i < argc; i += 2){
- if (strcmp(argv[i], "-y") == 0) {phylip = true; i--; continue;}
-
- if (strcmp(argv[i], "-o") == 0) outputFile = argv[i + 1];
- if (strcmp(argv[i], "-r") == 0) sscanf(argv[i + 1], "%d", &nRounds);
- if (strcmp(argv[i], "-s") == 0) sscanf(argv[i + 1], "%d", &nSample);
- if (strcmp(argv[i], "-p") == 0) sscanf(argv[i + 1], "%lf", &p);
- if (strcmp(argv[i], "-t") == 0) sscanf(argv[i + 1], "%d", &nThreads);
- if (strcmp(argv[i], "-h") == 0) {cerr << helpText; return 0;}
- }
- ostream &fout = (outputFile == "") ? cout : fileOut;
- if (outputFile != "") fileOut.open(outputFile);
-
- if (nRounds < nThreads){
- tripInit.nThreads = nThreads / nRounds;
- nThreads = nRounds;
- }
-
- if (phylip) {
- {
- ifstream fin(argv[argc - 1]);
- int n, L;
- string line;
- while (fin >> n){
- fin >> L;
- for (int i = 0; i < n; i++){
- string s;
- fin >> s;
- getline(fin, line);
- if(name2id.count(s) == 0) {
- name2id[s] = names.size();
- names.push_back(s);
- }
- }
- }
- }
- {
- ifstream fin(argv[argc - 1]);
- readPhilip(fin);
- }
- }
- else {
- ifstream listIn(argv[argc - 1]);
- for (string file; getline(listIn, file);){
- files.push_back(file);
- }
-
- for (string file: files){
- ifstream fin(file);
- string line;
- while (getline(fin, line)){
- if (line[0] != '>') continue;
- string s = formatName(line);
- if(name2id.count(s) == 0) {
- name2id[s] = names.size();
- names.push_back(s);
- }
- }
- }
- for (string file: files){
- ifstream fin(file);
- readFile(fin);
- }
- }
-
- cerr << "#Species: " << names.size() << endl;
- cerr << "#Genes: " << tripInit.pi.size() << endl;
- cerr << "#Rounds: " << nRounds << endl;
- cerr << "#Samples: " << nSample << endl;
- cerr << "#Threads: " << nThreads << "x" << tripInit.nThreads << endl;
- cerr << "p = " << p << endl;
-
- ConstrainedOptimizationAlgorithm alg(names.size(), tripInit, names);
- auto res = alg.run(nRounds, nThreads);
- cerr << "Score: " << (double) res.first << endl;
- cerr << res.second << endl;
-
- res = alg.run(nSample, nThreads, p);
- cerr << "Score: " << (double) res.first << endl;
- fout << res.second << endl;
- return 0;
-}
diff --git a/addons/ASTER/asterisk-pair.cpp b/addons/ASTER/asterisk-pair.cpp
deleted file mode 100644
index 979bd5938f6b7246f7fbaa271756214d58de57fe..0000000000000000000000000000000000000000
--- a/addons/ASTER/asterisk-pair.cpp
+++ /dev/null
@@ -1,235 +0,0 @@
-#include<iostream>
-#include<fstream>
-#include<unordered_map>
-#include<cstdio>
-#include<cstdlib>
-#include<cstring>
-
-#define LARGE_DATA
-#ifdef LARGE_DATA
-typedef long double score_t;
-typedef long long count_t;
-#else
-typedef double score_t;
-typedef int count_t;
-#endif
-
-#include "sequence-pair.hpp"
-#include "algorithms.hpp"
-
-using namespace std;
-
-TripartitionInitializer tripInit;
-
-int npos = 0;
-vector<string> names;
-unordered_map<string, int> name2id;
-
-string formatName(const string name){
- string res;
- for (char c: name){
- if (c != '>' && c != ' ' && c != '\t') res += c;
- }
- return res;
-}
-
-void readFile(istream &fin, const char CR1, const char CR2, const char CY1, const char CY2, const char CY3, const char cr1, const char cr2, const char cy1, const char cy2, const char cy3){
- int cnt[4] = {}, id = -1, oldNpos = npos;
- string line;
- while (getline(fin, line)){
- if (line[0] == '>') {
- if (id != -1 && npos < tripInit.seq[id].size()) npos = tripInit.seq[id].size();
- id = name2id[formatName(line)];
- }
- else{
- for (int i = 0; i + 1 < line.size(); i += 2){
- const char c1 = line[i], c2 = line[i + 1];
- const bool R1 = (c1 == CR1 || c1 == cr1 || c1 == CR2 || c1 == cr2);
- const bool R2 = (c2 == CR1 || c2 == cr1 || c2 == CR2 || c2 == cr2);
- const bool Y1 = (c1 == CY1 || c1 == cy1 || c1 == CY2 || c1 == cy2 || c1 == CY3 || c1 == cy3);
- const bool Y2 = (c2 == CY1 || c2 == cy1 || c2 == CY2 || c2 == cy2 || c2 == CY3 || c2 == cy3);
- const bool N1 = R1 || Y1 || (c1 == 'X' || c1 == 'x' || c1 == 'N' || c1 == 'n' || c1 == '-');
- const bool N2 = R2 || Y2 || (c2 == 'X' || c2 == 'x' || c2 == 'N' || c2 == 'n' || c2 == '-');
- if (R1 && R2){ tripInit.seq[id].push_back(0); cnt[0]++; }
- else if (R1 && Y2){ tripInit.seq[id].push_back(1); cnt[1]++; }
- else if (Y1 && R2){ tripInit.seq[id].push_back(2); cnt[2]++; }
- else if (Y1 && Y2){ tripInit.seq[id].push_back(3); cnt[3]++; }
- else if (N1 && N2){ tripInit.seq[id].push_back(-1); }
- }
- if (npos < tripInit.seq[id].size()) npos = tripInit.seq[id].size();
- }
- }
- for (id = 0; id < tripInit.seq.size(); id++){
- while (tripInit.seq[id].size() < npos) tripInit.seq[id].push_back(-1);
- }
- score_t cntsum = cnt[0] + cnt[1] + cnt[2] + cnt[3];
- while (tripInit.pi.size() < npos) tripInit.pi.push_back((cnt[0] * 2 + cnt[1] + cnt[2]) / (2 * cntsum));
- for (int p = oldNpos; p < npos; p++){
- int pcnt[4] = {};
- for (id = 0; id < tripInit.seq.size(); id++){
- if (tripInit.seq[id][p] != -1) pcnt[tripInit.seq[id][p]]++;
- }
- tripInit.weight.push_back(pcnt[0] + pcnt[1] + pcnt[2] + pcnt[3] - max({pcnt[0], pcnt[1], pcnt[2], pcnt[3]}) > 1);
- }
-}
-
-void readPhilip(istream &fin, const char CR1, const char CR2, const char CY1, const char CY2, const char CY3, const char cr1, const char cr2, const char cy1, const char cy2, const char cy3){
- string line;
- int nTaxa, L;
- while (fin >> nTaxa){
- int cnt[4] = {}, oldNpos = npos;
- fin >> L;
- for (int i = 0; i < nTaxa; i++){
- fin >> line;
- int id = name2id[line];
- getline(fin, line);
- for (int i = 0; i + 1 < line.size(); i += 2){
- const char c1 = line[i], c2 = line[i + 1];
- const bool R1 = (c1 == CR1 || c1 == cr1 || c1 == CR2 || c1 == cr2);
- const bool R2 = (c2 == CR1 || c2 == cr1 || c2 == CR2 || c2 == cr2);
- const bool Y1 = (c1 == CY1 || c1 == cy1 || c1 == CY2 || c1 == cy2 || c1 == CY3 || c1 == cy3);
- const bool Y2 = (c2 == CY1 || c2 == cy1 || c2 == CY2 || c2 == cy2 || c2 == CY3 || c2 == cy3);
- const bool N1 = R1 || Y1 || (c1 == 'X' || c1 == 'x' || c1 == 'N' || c1 == 'n' || c1 == '-');
- const bool N2 = R2 || Y2 || (c2 == 'X' || c2 == 'x' || c2 == 'N' || c2 == 'n' || c2 == '-');
- if (R1 && R2){ tripInit.seq[id].push_back(0); cnt[0]++; }
- else if (R1 && Y2){ tripInit.seq[id].push_back(1); cnt[1]++; }
- else if (Y1 && R2){ tripInit.seq[id].push_back(2); cnt[2]++; }
- else if (Y1 && Y2){ tripInit.seq[id].push_back(3); cnt[3]++; }
- else if (N1 && N2){ tripInit.seq[id].push_back(-1); }
- }
- if (npos < tripInit.seq[id].size()) npos = tripInit.seq[id].size();
- }
- for (int id = 0; id < tripInit.seq.size(); id++){
- while (tripInit.seq[id].size() < npos) tripInit.seq[id].push_back(-1);
- }
- score_t cntsum = cnt[0] + cnt[1] + cnt[2] + cnt[3];
- while (tripInit.pi.size() < npos) tripInit.pi.push_back((cnt[0] * 2 + cnt[1] + cnt[2]) / (2 * cntsum));
- //cerr << cntsum << "\t" << (cnt[0] * 2 + cnt[1] + cnt[2]) / (2 * cntsum) << "\t" << cnt[0] * cnt[3] / (1.0 * cnt[1] * cnt[2]) << endl;
- for (int p = oldNpos; p < npos; p++){
- int pcnt[4] = {};
- for (int id = 0; id < tripInit.seq.size(); id++){
- if (tripInit.seq[id][p] != -1) pcnt[tripInit.seq[id][p]]++;
- }
- tripInit.weight.push_back(pcnt[0] + pcnt[1] + pcnt[2] + pcnt[3] - max({pcnt[0], pcnt[1], pcnt[2], pcnt[3]}) > 1);
- }
- }
-}
-
-string helpText = R"V0G0N(feast [-o oFilePath -r nRound -s nSample -p probability -t nThread -y] inputList
--o path to output file (default: stdout)
--r number of total rounds of placements (default: 5)
--s number of total rounds of subsampling (default: 0)
--p subsampling probability of keeping each taxon (default: 0.5)
--t number of threads (default: 1)
--y take one input in PHYLIP format instead of a list of inputs in FASTA format
-inputList: the path to a file containing a list of paths to input aligned gene files, one file per line
-Gene files must be in FASTA format. The header line should be ">Species_Name".
-)V0G0N";
-
-int main(int argc, char** argv){
- vector<string> files;
-
- int nThreads = 1, nRounds = 4, nSample = 0;
- bool phylip = false;
- double p = 0.5;
- string outputFile;
- ofstream fileOut;
- if (argc == 1) {cerr << helpText; return 0;}
- for (int i = 1; i < argc; i += 2){
- if (strcmp(argv[i], "-y") == 0) {phylip = true; i--; continue;}
-
- if (strcmp(argv[i], "-o") == 0) outputFile = argv[i + 1];
- if (strcmp(argv[i], "-r") == 0) sscanf(argv[i + 1], "%d", &nRounds);
- if (strcmp(argv[i], "-s") == 0) sscanf(argv[i + 1], "%d", &nSample);
- if (strcmp(argv[i], "-p") == 0) sscanf(argv[i + 1], "%lf", &p);
- if (strcmp(argv[i], "-t") == 0) sscanf(argv[i + 1], "%d", &nThreads);
- if (strcmp(argv[i], "-h") == 0) {cerr << helpText; return 0;}
- }
- ostream &fout = (outputFile == "") ? cout : fileOut;
- if (outputFile != "") fileOut.open(outputFile);
-
- if (nRounds < nThreads){
- tripInit.nThreads = nThreads / nRounds;
- nThreads = nRounds;
- }
-
- if (phylip) {
- {
- ifstream fin(argv[argc - 1]);
- int n, L;
- string line;
- while (fin >> n){
- fin >> L;
- for (int i = 0; i < n; i++){
- string s;
- fin >> s;
- getline(fin, line);
- if(name2id.count(s) == 0) {
- name2id[s] = names.size();
- names.push_back(s);
- tripInit.seq.push_back({});
- }
- }
- }
- }
- //{ ifstream fin(argv[argc - 1]); readPhilip(fin, 'A', 'C', 'G', 'T', 0, 'a', 'c', 'g', 't', 0); }
- { ifstream fin(argv[argc - 1]); readPhilip(fin, 'A', 'G', 'C', 'T', 0, 'a', 'g', 'c', 't', 0); }
- //{ ifstream fin(argv[argc - 1]); readPhilip(fin, 'A', 'T', 'C', 'G', 0, 'a', 't', 'c', 'g', 0); }
- //{ ifstream fin(argv[argc - 1]); readPhilip(fin, 'A', 0, 'C', 'G', 'T', 'a', 0, 'c', 'g', 't'); }
- //{ ifstream fin(argv[argc - 1]); readPhilip(fin, 'C', 0, 'A', 'G', 'T', 'c', 0, 'a', 'g', 't'); }
- //{ ifstream fin(argv[argc - 1]); readPhilip(fin, 'G', 0, 'A', 'C', 'T', 'g', 0, 'a', 'c', 't'); }
- //{ ifstream fin(argv[argc - 1]); readPhilip(fin, 'T', 0, 'A', 'C', 'G', 't', 0, 'a', 'c', 'g'); }
- }
- else {
- ifstream listIn(argv[argc - 1]);
- for (string file; getline(listIn, file);){
- files.push_back(file);
- }
-
- for (string file: files){
- ifstream fin(file);
- string line;
- while (getline(fin, line)){
- if (line[0] != '>') continue;
- string s = formatName(line);
- if(name2id.count(s) == 0) {
- name2id[s] = names.size();
- names.push_back(s);
- tripInit.seq.push_back({});
- }
- }
- }
- for (string file: files){
- //{ ifstream fin(file); readFile(fin, 'A', 'C', 'G', 'T', 0, 'a', 'c', 'g', 't', 0); }
- { ifstream fin(file); readFile(fin, 'A', 'G', 'C', 'T', 0, 'a', 'g', 'c', 't', 0); }
- //{ ifstream fin(file); readFile(fin, 'A', 'T', 'C', 'G', 0, 'a', 't', 'c', 'g', 0); }
- //{ ifstream fin(file); readFile(fin, 'A', 0, 'C', 'G', 'T', 'a', 0, 'c', 'g', 't'); }
- //{ ifstream fin(file); readFile(fin, 'C', 0, 'A', 'G', 'T', 'c', 0, 'a', 'g', 't'); }
- //{ ifstream fin(file); readFile(fin, 'G', 0, 'A', 'C', 'T', 'g', 0, 'a', 'c', 't'); }
- //{ ifstream fin(file); readFile(fin, 'T', 0, 'A', 'C', 'G', 't', 0, 'a', 'c', 'g'); }
- }
- }
-
- for (int i = 0; i < names.size(); i++){
- tripInit.weightHelper.push_back(0);
- }
- tripInit.weightHelper.push_back(0);
-
- tripInit.npos = npos;
- cerr << "#Species: " << names.size() << endl;
- cerr << "#Bases: " << npos << endl;
- cerr << "#Rounds: " << nRounds << endl;
- cerr << "#Samples: " << nSample << endl;
- cerr << "#Threads: " << nThreads << "x" << tripInit.nThreads << endl;
- cerr << "p = " << p << endl;
-
- ConstrainedOptimizationAlgorithm alg(names.size(), tripInit, names);
- auto res = alg.run(nRounds, nThreads);
- cerr << "Score: " << (double) res.first << endl;
- cerr << res.second << endl;
-
- res = alg.run(nSample, nThreads, p);
- cerr << "Score: " << (double) res.first << endl;
- fout << res.second << endl;
- return 0;
-}
diff --git a/addons/ASTER/asterisk.cpp b/addons/ASTER/asterisk.cpp
deleted file mode 100644
index 1bf2938bbc6536bc936737eed01fcd2f04f29259..0000000000000000000000000000000000000000
--- a/addons/ASTER/asterisk.cpp
+++ /dev/null
@@ -1,261 +0,0 @@
-#include<iostream>
-#include<fstream>
-#include<unordered_map>
-#include<cstdio>
-#include<cstdlib>
-#include<cstring>
-#include<algorithm>
-
-//#define LARGE_DATA
-#ifdef LARGE_DATA
-typedef long double score_t;
-typedef long long count_t;
-#else
-typedef double score_t;
-typedef int count_t;
-#endif
-
-#include "sequence-pair.hpp"
-#include "algorithms.hpp"
-
-using namespace std;
-
-MetaAlgorithm meta;
-TripartitionInitializer &tripInit = meta.tripInit;
-
-int &npos = meta.tripInit.npos;
-vector<string> &names = meta.names;
-unordered_map<string, int> &name2id = meta.name2id;
-vector<vector<int> > sparse;
-int N, n;
-
-string formatName(const string name){
- string res;
- for (char c: name){
- if (c != '>' && c != ' ' && c != '\t') res += c;
- }
- return res;
-}
-
-void readFile(istream &fin, const char CR1, const char CR2, const char CY1, const char CY2, const char CY3, const char cr1, const char cr2, const char cy1, const char cy2, const char cy3){
- vector<vector<int> > dist(N, vector<int>(n)), total(N, vector<int>(n));
- vector<vector<bool> > R(N), Y(N);
- vector<pair<score_t, int> > D;
- int id = -1, np = 0, cntR = 0, cntY = 0;
- string line;
- while (getline(fin, line)){
- if (line[0] == '>') {
- id = name2id[formatName(line)];
- }
- else {
- for (char c: line){
- if (c == CR1 || c == cr1 || c == CR2 || c == cr2) { R[id].push_back(1); Y[id].push_back(0); cntR++; }
- if (c == CY1 || c == cy1 || c == CY2 || c == cy2 || c == CY3 || c == cy3) { R[id].push_back(0); Y[id].push_back(1); cntY++; }
- if (c == 'X' || c == 'x' || c == 'N' || c == 'n' || c == '-') { R[id].push_back(0); Y[id].push_back(0); }
- }
- if (R[id].size() > np) np = R[id].size();
- }
- }
- for (id = 0; id < N; id++){
- while (R[id].size() < np) { R[id].push_back(0); Y[id].push_back(0); }
- }
- for (int i = 0; i < N; i++){
- for (int k = 0; k < n; k++){
- int j = sparse[i][k];
- for (int p = 0; p < np; p++){
- dist[i][k] += (R[i][p] && Y[j][p]) || (Y[i][p] && R[j][p]);
- total[i][k] += (R[i][p] || Y[i][p]) && (Y[j][p] || R[j][p]);
- }
- }
- }
- for (int p = 0; p < np; p++){
- score_t P = 0;
- int Q = 0;
- for (int i = 0; i < N; i++){
- for (int k = 0; k < n; k++){
- int j = sparse[i][k];
- if (dist[i][k] > 0 && (R[i][p] || Y[i][p]) && (Y[j][p] || R[j][p])){
- Q++;
- P += ((R[i][p] && Y[j][p]) || (Y[i][p] && R[j][p])) / (score_t) dist[i][k] * total[i][k];
- }
- }
- }
- D.emplace_back(P / Q, p);
- }
- sort(D.begin(), D.end());
-
- for (int r = 0; r + 1 < np; r++){
- int p = D[r].second, q = D[r + 1].second;
- int pcnt[4] = {};
- for (int i = 0; i < N; i++){
- if (R[i][p] && R[i][q]) { tripInit.seq[i].push_back(0); pcnt[0]++; }
- else if (R[i][p] && Y[i][q]) { tripInit.seq[i].push_back(1); pcnt[1]++; }
- else if (Y[i][p] && R[i][q]) { tripInit.seq[i].push_back(2); pcnt[2]++; }
- else if (Y[i][p] && Y[i][q]) { tripInit.seq[i].push_back(3); pcnt[3]++; }
- else tripInit.seq[i].push_back(-1);
- }
- tripInit.pi.push_back(cntR / (score_t) (cntR + cntY));
- tripInit.weight.push_back(pcnt[0] + pcnt[1] + pcnt[2] + pcnt[3] - max({pcnt[0], pcnt[1], pcnt[2], pcnt[3]}) >= 2);
- npos++;
- }
-}
-
-void readPhilip(istream &fin, const char CR1, const char CR2, const char CY1, const char CY2, const char CY3, const char cr1, const char cr2, const char cy1, const char cy2, const char cy3){
- string line;
- int nTaxa, L;
- while (fin >> nTaxa){
- vector<vector<int> > dist(N, vector<int>(n)), total(N, vector<int>(n));
- vector<vector<bool> > R(N), Y(N);
- vector<pair<score_t, int> > D;
- int id = -1, np = 0, cntR = 0, cntY = 0;
- fin >> L;
- for (int i = 0; i < nTaxa; i++){
- fin >> line;
- int id = name2id[line];
- getline(fin, line);
- for (char c: line){
- if (c == CR1 || c == cr1 || c == CR2 || c == cr2) { R[id].push_back(1); Y[id].push_back(0); cntR++; }
- if (c == CY1 || c == cy1 || c == CY2 || c == cy2 || c == CY3 || c == cy3) { R[id].push_back(0); Y[id].push_back(1); cntY++; }
- if (c == 'X' || c == 'x' || c == 'N' || c == 'n' || c == '-') { R[id].push_back(0); Y[id].push_back(0); }
- }
- if (R[id].size() > np) np = R[id].size();
- }
- for (id = 0; id < N; id++){
- while (R[id].size() < np) { R[id].push_back(0); Y[id].push_back(0); }
- }
- for (int i = 0; i < N; i++){
- for (int k = 0; k < n; k++){
- int j = sparse[i][k];
- for (int p = 0; p < np; p++){
- dist[i][k] += (R[i][p] && Y[j][p]) || (Y[i][p] && R[j][p]);
- total[i][k] += (R[i][p] || Y[i][p]) && (Y[j][p] || R[j][p]);
- }
- }
- }
- for (int p = 0; p < np; p++){
- score_t P = 0;
- int Q = 0;
- for (int i = 0; i < N; i++){
- for (int k = 0; k < n; k++){
- int j = sparse[i][k];
- if (dist[i][k] > 0 && (R[i][p] || Y[i][p]) && (Y[j][p] || R[j][p])){
- Q++;
- P += ((R[i][p] && Y[j][p]) || (Y[i][p] && R[j][p])) / (score_t) dist[i][k] * total[i][k];
- }
- }
- }
- D.emplace_back(P / Q, p);
- }
- sort(D.begin(), D.end());
-
- for (int r = 0; r + 1 < np; r++){
- int p = D[r].second, q = D[r + 1].second;
- int pcnt[4] = {};
- for (int i = 0; i < N; i++){
- if (R[i][p] && R[i][q]) { tripInit.seq[i].push_back(0); pcnt[0]++; }
- else if (R[i][p] && Y[i][q]) { tripInit.seq[i].push_back(1); pcnt[1]++; }
- else if (Y[i][p] && R[i][q]) { tripInit.seq[i].push_back(2); pcnt[2]++; }
- else if (Y[i][p] && Y[i][q]) { tripInit.seq[i].push_back(3); pcnt[3]++; }
- else tripInit.seq[i].push_back(-1);
- }
- tripInit.pi.push_back(cntR / (score_t) (cntR + cntY));
- tripInit.weight.push_back(pcnt[0] + pcnt[1] + pcnt[2] + pcnt[3] - max({pcnt[0], pcnt[1], pcnt[2], pcnt[3]}) >= 2);
- npos++;
- }
- }
-}
-
-string HELP_TEXT = R"V0G0N(-y take one input in PHYLIP format instead of a list of inputs in FASTA format
-inputList: the path to a file containing a list of paths to input aligned gene files, one file per line
-Gene files must be in FASTA format. The header line should be ">Species_Name".
-)V0G0N";
-
-int main(int argc, char** argv){
- vector<string> files;
- bool phylip = false;
- string mappingFile;
- meta.initialize(argc, argv, " -y", HELP_TEXT);
-
- for (int i = 1; i < argc; i += 2){
- if (strcmp(argv[i], "-y") == 0) {phylip = true; i--; continue;}
- }
-
- if (phylip) {
- {
- ifstream fin(argv[argc - 1]);
- int M, L;
- string line;
- while (fin >> M){
- fin >> L;
- for (int i = 0; i < M; i++){
- string s;
- fin >> s;
- getline(fin, line);
- if(name2id.count(s) == 0) {
- name2id[s] = names.size();
- names.push_back(s);
- tripInit.seq.push_back({});
- }
- }
- }
- }
- N = names.size();
- n = 2 * log(N) * sqrt(N);
- for (int i = 0; i < N; i++){
- sparse.emplace_back();
- for (int j = 0; j < n; j++){
- sparse[i].push_back(rand() % N);
- }
- }
- { ifstream fin(argv[argc - 1]); readPhilip(fin, 'A', 'G', 'C', 'T', 0, 'a', 'g', 'c', 't', 0); }
- { ifstream fin(argv[argc - 1]); readPhilip(fin, 'A', 'C', 'G', 'T', 0, 'a', 'c', 'g', 't', 0); }
- { ifstream fin(argv[argc - 1]); readPhilip(fin, 'A', 'T', 'C', 'G', 0, 'a', 't', 'c', 'g', 0); }
- { ifstream fin(argv[argc - 1]); readPhilip(fin, 'A', 0, 'T', 'C', 'G', 'a', 0, 't', 'c', 'g'); }
- { ifstream fin(argv[argc - 1]); readPhilip(fin, 'T', 0, 'A', 'C', 'G', 't', 0, 'a', 'c', 'g'); }
- { ifstream fin(argv[argc - 1]); readPhilip(fin, 'C', 0, 'A', 'T', 'G', 'c', 0, 'a', 't', 'g'); }
- { ifstream fin(argv[argc - 1]); readPhilip(fin, 'G', 0, 'A', 'T', 'C', 'g', 0, 'a', 't', 'c'); }
- }
- else {
- ifstream listIn(argv[argc - 1]);
- for (string file; getline(listIn, file);){
- files.push_back(file);
- }
-
- for (string file: files){
- ifstream fin(file);
- string line;
- while (getline(fin, line)){
- if (line[0] != '>') continue;
- string s = formatName(line);
- if(name2id.count(s) == 0) {
- name2id[s] = names.size();
- names.push_back(s);
- tripInit.seq.push_back({});
- }
- }
- }
- N = names.size();
- n = 2 * log(N) * sqrt(N);
- for (int i = 0; i < N; i++){
- sparse.emplace_back();
- for (int j = 0; j < n; j++){
- sparse[i].push_back(rand() % N);
- }
- }
- for (string file: files){
- { ifstream fin(file); readFile(fin, 'A', 'G', 'C', 'T', 0, 'a', 'g', 'c', 't', 0); }
- { ifstream fin(file); readFile(fin, 'A', 'C', 'G', 'T', 0, 'a', 'c', 'g', 't', 0); }
- { ifstream fin(file); readFile(fin, 'A', 'T', 'C', 'G', 0, 'a', 't', 'c', 'g', 0); }
- { ifstream fin(file); readFile(fin, 'A', 0, 'T', 'C', 'G', 'a', 0, 't', 'c', 'g'); }
- { ifstream fin(file); readFile(fin, 'T', 0, 'A', 'C', 'G', 't', 0, 'a', 'c', 'g'); }
- { ifstream fin(file); readFile(fin, 'C', 0, 'A', 'T', 'G', 'c', 0, 'a', 't', 'g'); }
- { ifstream fin(file); readFile(fin, 'G', 0, 'A', 'T', 'C', 'g', 0, 'a', 't', 'c'); }
- }
- }
-
- cerr << "#Bases: " << npos << endl;
-
- score_t score = meta.run().first;
- cerr << "Score: " << (double) score << endl;
- return 0;
-}
diff --git a/addons/ASTER/astral-binaryweights.cpp b/addons/ASTER/astral-binaryweights.cpp
deleted file mode 100644
index 6c408bb29be746ca05a06530d3480103d534c2a5..0000000000000000000000000000000000000000
--- a/addons/ASTER/astral-binaryweights.cpp
+++ /dev/null
@@ -1,156 +0,0 @@
-#include<iostream>
-#include<fstream>
-#include<unordered_map>
-#include<cstdio>
-#include<cstdlib>
-#include<cstring>
-#include<string>
-
-using namespace std;
-
-//#define LARGE_DATA
-#ifdef LARGE_DATA
-typedef __int128 score_t;
-
-string to_string(const __int128 x){
- return to_string((double) x);
-}
-
-ostream& operator<<(ostream& cout, __int128 x){
- return cout << to_string(x);
-}
-#else
-typedef long long score_t;
-#endif
-
-#include "genetreewithbinaryweight.hpp"
-#include "algorithms.hpp"
-
-
-MetaAlgorithm meta;
-TripartitionInitializer &tripInit = meta.tripInit;
-vector<TripartitionInitializer> &batchInit = meta.batchInit;
-
-unordered_map<string, string> leafname_mapping;
-string TEXT;
-int pos = 0;
-int K = 0;
-int part = 0, iBatch = 0;
-vector<string> &names = meta.names;
-unordered_map<string, int> &name2id = meta.name2id;
-
-int MAPPING(int begin, int end){
- string s;
- for (int i = begin; i < end && TEXT[i] != ':'; i++){
- if (TEXT[i] != '\"' && TEXT[i] != '\'') s += TEXT[i];
- }
- if (leafname_mapping.count(s)) s = leafname_mapping[s];
- if (name2id.count(s) == 0){
- name2id[s] = names.size();
- names.push_back(s);
- for (int i = 0; i < meta.nThread2; i++){
- tripInit.leafParent[i].emplace_back();
- }
- }
- return name2id[s];
-}
-
-void parse(int parent = -1, bool isLeft = true){
- int cur = tripInit.nodes[part].size();
- tripInit.nodes[part].emplace_back();
- tripInit.nodes[part][cur].up = parent;
- if (parent != -1 && isLeft) tripInit.nodes[part][parent].small = cur;
- if (parent != -1 && !isLeft) tripInit.nodes[part][parent].large = cur;
-
- if (TEXT[pos] == '(') {
- pos++;
- parse(cur, true);
- pos++;
- parse(cur, false);
- vector<int> lst;
- lst.push_back(cur);
- tripInit.nodes[part][cur].weight = 0;
- while (TEXT[pos] != ')'){
- int left = lst[rand() % lst.size()];
- int up = tripInit.nodes[part].size();
- tripInit.nodes[part].emplace_back();
- lst.push_back(up);
- if (cur == left) cur = up;
- tripInit.nodes[part][up].weight = 0;
- int g = tripInit.nodes[part][left].up;
- if (g != -1){
- if (tripInit.nodes[part][g].small == left) tripInit.nodes[part][g].small = up;
- else tripInit.nodes[part][g].large = up;
- }
- tripInit.nodes[part][up].up = g;
- tripInit.nodes[part][left].up = up;
- tripInit.nodes[part][up].small = left;
- pos++;
- parse(up, false);
- }
- int i = ++pos;
- while (TEXT[pos] != ')' && TEXT[pos] != ',' && TEXT[pos] != ';') pos++;
- tripInit.nodes[part][cur].weight = 1;
- }
- else {
- int i = pos;
- while (TEXT[pos] != ')' && TEXT[pos] != ',') pos++;
- tripInit.leafParent[part][MAPPING(i, pos)].push_back(cur);
- tripInit.nodes[part][cur].weight = 1;
- }
-}
-
-void readInputTrees(string input, string mapping) {
- if (mapping != ""){
- ifstream fmap(mapping);
- string gname, sname;
- while (fmap >> gname){
- fmap >> sname;
- leafname_mapping[gname] = sname;
- }
- }
- ifstream fin(input);
- string line;
- while (getline(fin, line)) TEXT += line;
- while (pos < TEXT.size()){
- while (pos < TEXT.size() && TEXT[pos] != '(') pos++;
- if (pos < TEXT.size()) {
- part = K % tripInit.nodes.size();
- parse();
- K++;
- }
- }
-}
-
-string HELP = " -a taxonNameMaps -x maxWeight -n minWeight -d defaultWeight";
-string HELP_TEXT = R"V0G0N(-a a list of gene name to taxon name maps, each line contains one gene name followed by one taxon name separated by a space or tab
--x max possible weight in weight scale (default: 100)
--n min possible weight in weight scale (default: 0)
--d min default weight when weight not provided (default: 0)
-inputGeneTrees: the path to a file containing all gene trees in Newick format
-)V0G0N";
-
-int main(int argc, char** argv){
- string mappingFile;
- meta.initialize(argc, argv, HELP, HELP_TEXT);
-
- for (int i = 1; i < argc; i += 2){
- if (strcmp(argv[i], "-a") == 0) mappingFile = argv[i + 1];
- }
-
- for (int i = 0; i < meta.nThread2; i++){
- tripInit.nodes.emplace_back();
- tripInit.leafParent.emplace_back();
- }
- for (int i = 0; i < meta.nBatch; i++){
- batchInit[i].nodes.emplace_back();
- batchInit[i].leafParent.emplace_back();
- }
- readInputTrees(argv[argc - 1], mappingFile);
-
- cerr << "#Genetrees: " << K << endl;
-
- score_t score = meta.run().first;
- cerr << "Score: " << score << endl;
- return 0;
-}
diff --git a/addons/ASTER/astral-hybrid.cpp b/addons/ASTER/astral-hybrid.cpp
deleted file mode 100644
index cd5cb8c4338172c1f18e10fdcbd836120fa2b7fd..0000000000000000000000000000000000000000
--- a/addons/ASTER/astral-hybrid.cpp
+++ /dev/null
@@ -1,186 +0,0 @@
-#include<iostream>
-#include<fstream>
-#include<unordered_map>
-#include<cstdio>
-#include<cstdlib>
-#include<cstring>
-#include<string>
-
-using namespace std;
-
-//#define LARGE_DATA
-#ifdef LARGE_DATA
-typedef long double score_t;
-
-string to_string(long double x){
- return to_string((double) x);
-}
-
-score_t from_string(const string s){
- return stold(s);
-}
-
-ostream& operator<<(ostream& cout, long double x){
- return cout << to_string(x);
-}
-#else
-typedef double score_t;
-
-score_t from_string(const string s){
- return stod(s);
-}
-#endif
-
-#include "genetreewithhybridweight.hpp"
-#include "algorithms.hpp"
-
-
-MetaAlgorithm meta;
-TripartitionInitializer &tripInit = meta.tripInit;
-vector<TripartitionInitializer> &batchInit = meta.batchInit;
-
-unordered_map<string, string> leafname_mapping;
-string TEXT;
-int pos = 0;
-int K = 0;
-int part = 0, iBatch = 0;
-vector<string> &names = meta.names;
-unordered_map<string, int> &name2id = meta.name2id;
-score_t maxv = 100, minv = 0, defaultv = 0;
-
-int MAPPING(int begin, int end){
- string s;
- for (int i = begin; i < end && TEXT[i] != ':'; i++){
- if (TEXT[i] != '\"' && TEXT[i] != '\'') s += TEXT[i];
- }
- if (leafname_mapping.count(s)) s = leafname_mapping[s];
- if (name2id.count(s) == 0){
- name2id[s] = names.size();
- names.push_back(s);
- for (int i = 0; i < meta.nThread2; i++){
- tripInit.leafParent[i].emplace_back();
- }
- }
- return name2id[s];
-}
-
-score_t WEIGHT_S(int begin, int end){
- int i = begin;
- while (i < end && TEXT[i] != ':') i++;
- if (i == begin || i == end) return max(0.0, (defaultv - minv) / (maxv - minv));
- else return max(0.0, (from_string(TEXT.substr(begin, i - begin)) - minv) / (maxv - minv));
-}
-
-score_t WEIGHT_L(int begin, int end){
- int i = begin;
- while (i < end && TEXT[i] != ':') i++;
- if (i == end) return 1;
- else return exp(-from_string(TEXT.substr(i + 1, end - i - 1)));
-}
-
-void parse(int parent = -1, bool isLeft = true){
- int cur = tripInit.nodes[part].size();
- tripInit.nodes[part].emplace_back();
- tripInit.nodes[part][cur].up = parent;
- if (parent != -1 && isLeft) tripInit.nodes[part][parent].small = cur;
- if (parent != -1 && !isLeft) tripInit.nodes[part][parent].large = cur;
-
- if (TEXT[pos] == '(') {
- pos++;
- parse(cur, true);
- pos++;
- parse(cur, false);
- vector<int> lst;
- lst.push_back(cur);
- tripInit.nodes[part][cur].weight = max(0.0, (defaultv - minv) / (maxv - minv));
- tripInit.nodes[part][cur].length = 1;
- while (TEXT[pos] != ')'){
- int left = lst[rand() % lst.size()];
- int up = tripInit.nodes[part].size();
- tripInit.nodes[part].emplace_back();
- lst.push_back(up);
- if (cur == left) cur = up;
- tripInit.nodes[part][up].weight = max(0.0, (defaultv - minv) / (maxv - minv));
- tripInit.nodes[part][up].length = 1;
- int g = tripInit.nodes[part][left].up;
- if (g != -1){
- if (tripInit.nodes[part][g].small == left) tripInit.nodes[part][g].small = up;
- else tripInit.nodes[part][g].large = up;
- }
- tripInit.nodes[part][up].up = g;
- tripInit.nodes[part][left].up = up;
- tripInit.nodes[part][up].small = left;
- pos++;
- parse(up, false);
- }
- int i = ++pos;
- while (TEXT[pos] != ')' && TEXT[pos] != ',' && TEXT[pos] != ';') pos++;
- tripInit.nodes[part][cur].weight = WEIGHT_S(i, pos);
- tripInit.nodes[part][cur].length = WEIGHT_L(i, pos);
- }
- else {
- int i = pos;
- while (TEXT[pos] != ')' && TEXT[pos] != ',') pos++;
- tripInit.leafParent[part][MAPPING(i, pos)].push_back(cur);
- tripInit.nodes[part][cur].weight = 1;
- tripInit.nodes[part][cur].length = WEIGHT_L(i, pos);
- }
-}
-
-void readInputTrees(string input, string mapping) {
- if (mapping != ""){
- ifstream fmap(mapping);
- string gname, sname;
- while (fmap >> gname){
- fmap >> sname;
- leafname_mapping[gname] = sname;
- }
- }
- ifstream fin(input);
- string line;
- while (getline(fin, line)) TEXT += line;
- while (pos < TEXT.size()){
- while (pos < TEXT.size() && TEXT[pos] != '(') pos++;
- if (pos < TEXT.size()) {
- part = K % tripInit.nodes.size();
- parse();
- K++;
- }
- }
-}
-
-string HELP = " -a taxonNameMaps -x maxWeight -n minWeight -d defaultWeight";
-string HELP_TEXT = R"V0G0N(-a a list of gene name to taxon name maps, each line contains one gene name followed by one taxon name separated by a space or tab
--x max possible weight in weight scale (default: 100)
--n min possible weight in weight scale (default: 0)
--d min default weight when weight not provided (default: 0)
-inputGeneTrees: the path to a file containing all gene trees in Newick format
-)V0G0N";
-
-int main(int argc, char** argv){
- string mappingFile;
- meta.initialize(argc, argv, HELP, HELP_TEXT);
-
- for (int i = 1; i < argc; i += 2){
- if (strcmp(argv[i], "-a") == 0) mappingFile = argv[i + 1];
- if (strcmp(argv[i], "-x") == 0) maxv = from_string(argv[i + 1]);
- if (strcmp(argv[i], "-n") == 0) minv = from_string(argv[i + 1]);
- if (strcmp(argv[i], "-d") == 0) defaultv = from_string(argv[i + 1]);
- }
-
- for (int i = 0; i < meta.nThread2; i++){
- tripInit.nodes.emplace_back();
- tripInit.leafParent.emplace_back();
- }
- for (int i = 0; i < meta.nBatch; i++){
- batchInit[i].nodes.emplace_back();
- batchInit[i].leafParent.emplace_back();
- }
- readInputTrees(argv[argc - 1], mappingFile);
-
- cerr << "#Genetrees: " << K << endl;
-
- score_t score = meta.run().first;
- cerr << "Score: " << score << endl;
- return 0;
-}
diff --git a/addons/ASTER/astral-lengthweighted.cpp b/addons/ASTER/astral-lengthweighted.cpp
deleted file mode 100644
index cf028b3797be654689c050dc99cc1c3b06471375..0000000000000000000000000000000000000000
--- a/addons/ASTER/astral-lengthweighted.cpp
+++ /dev/null
@@ -1,168 +0,0 @@
-#include<iostream>
-#include<fstream>
-#include<unordered_map>
-#include<cstdio>
-#include<cstdlib>
-#include<cstring>
-#include<string>
-
-using namespace std;
-
-//#define LARGE_DATA
-#ifdef LARGE_DATA
-typedef long double score_t;
-
-string to_string(long double x){
- return to_string((double) x);
-}
-
-score_t from_string(const string s){
- return stold(s);
-}
-
-ostream& operator<<(ostream& cout, long double x){
- return cout << to_string(x);
-}
-#else
-typedef double score_t;
-
-score_t from_string(const string s){
- return stod(s);
-}
-#endif
-
-#include "genetreewithlength.hpp"
-#include "algorithms.hpp"
-
-
-MetaAlgorithm meta;
-TripartitionInitializer &tripInit = meta.tripInit;
-vector<TripartitionInitializer> &batchInit = meta.batchInit;
-
-unordered_map<string, string> leafname_mapping;
-string TEXT;
-int pos = 0;
-int K = 0;
-int part = 0, iBatch = 0;
-vector<string> &names = meta.names;
-unordered_map<string, int> &name2id = meta.name2id;
-
-
-int MAPPING(int begin, int end){
- string s;
- for (int i = begin; i < end && TEXT[i] != ':'; i++){
- if (TEXT[i] != '\"' && TEXT[i] != '\'') s += TEXT[i];
- }
- if (leafname_mapping.count(s)) s = leafname_mapping[s];
- if (name2id.count(s) == 0){
- name2id[s] = names.size();
- names.push_back(s);
- for (int i = 0; i < meta.nThread2; i++){
- tripInit.leafParent[i].emplace_back();
- }
- }
- return name2id[s];
-}
-
-score_t WEIGHT(int begin, int end){
- int i = begin;
- while (i < end && TEXT[i] != ':') i++;
- if (i == end) return 1;
- else return exp(-from_string(TEXT.substr(i + 1, end - i - 1)));
-}
-
-void parse(int parent = -1, bool isLeft = true){
- int cur = tripInit.nodes[part].size();
- tripInit.nodes[part].emplace_back();
- tripInit.nodes[part][cur].up = parent;
- if (parent != -1 && isLeft) tripInit.nodes[part][parent].small = cur;
- if (parent != -1 && !isLeft) tripInit.nodes[part][parent].large = cur;
-
- if (TEXT[pos] == '(') {
- pos++;
- parse(cur, true);
- pos++;
- parse(cur, false);
- vector<int> lst;
- lst.push_back(cur);
- tripInit.nodes[part][cur].weight = 1;
- while (TEXT[pos] != ')'){
- int left = lst[rand() % lst.size()];
- int up = tripInit.nodes[part].size();
- tripInit.nodes[part].emplace_back();
- lst.push_back(up);
- if (cur == left) cur = up;
- tripInit.nodes[part][up].weight = 1;
- int g = tripInit.nodes[part][left].up;
- if (g != -1){
- if (tripInit.nodes[part][g].small == left) tripInit.nodes[part][g].small = up;
- else tripInit.nodes[part][g].large = up;
- }
- tripInit.nodes[part][up].up = g;
- tripInit.nodes[part][left].up = up;
- tripInit.nodes[part][up].small = left;
- pos++;
- parse(up, false);
- }
- int i = ++pos;
- while (TEXT[pos] != ')' && TEXT[pos] != ',' && TEXT[pos] != ';') pos++;
- tripInit.nodes[part][cur].weight = WEIGHT(i, pos);
- }
- else {
- int i = pos;
- while (TEXT[pos] != ')' && TEXT[pos] != ',') pos++;
- tripInit.leafParent[part][MAPPING(i, pos)].push_back(cur);
- tripInit.nodes[part][cur].weight = WEIGHT(i, pos);
- }
-}
-
-void readInputTrees(string input, string mapping) {
- if (mapping != ""){
- ifstream fmap(mapping);
- string gname, sname;
- while (fmap >> gname){
- fmap >> sname;
- leafname_mapping[gname] = sname;
- }
- }
- ifstream fin(input);
- string line;
- while (getline(fin, line)) TEXT += line;
- while (pos < TEXT.size()){
- while (pos < TEXT.size() && TEXT[pos] != '(') pos++;
- if (pos < TEXT.size()) {
- part = K % tripInit.nodes.size();
- parse();
- K++;
- }
- }
-}
-
-string HELP_TEXT = R"V0G0N(-a a list of gene name to taxon name maps, each line contains one gene name followed by one taxon name separated by a space or tab
-inputGeneTrees: the path to a file containing all gene trees in Newick format
-)V0G0N";
-
-int main(int argc, char** argv){
- string mappingFile;
- meta.initialize(argc, argv, " -a taxonNameMaps", HELP_TEXT);
-
- for (int i = 1; i < argc; i += 2){
- if (strcmp(argv[i], "-a") == 0) mappingFile = argv[i + 1];
- }
-
- for (int i = 0; i < meta.nThread2; i++){
- tripInit.nodes.emplace_back();
- tripInit.leafParent.emplace_back();
- }
- for (int i = 0; i < meta.nBatch; i++){
- batchInit[i].nodes.emplace_back();
- batchInit[i].leafParent.emplace_back();
- }
- readInputTrees(argv[argc - 1], mappingFile);
-
- cerr << "#Genetrees: " << K << endl;
-
- score_t score = meta.run().first;
- cerr << "Score: " << score << endl;
- return 0;
-}
diff --git a/addons/ASTER/astral-pro b/addons/ASTER/astral-pro
deleted file mode 100755
index 5034d9e8d4ea3bd92e96163d1ae7446fe4c39a64..0000000000000000000000000000000000000000
Binary files a/addons/ASTER/astral-pro and /dev/null differ
diff --git a/addons/ASTER/astral-pro.cpp b/addons/ASTER/astral-pro.cpp
deleted file mode 100644
index 6731490ad5a571f2ea830af1b520a803ae6033d5..0000000000000000000000000000000000000000
--- a/addons/ASTER/astral-pro.cpp
+++ /dev/null
@@ -1,413 +0,0 @@
-#include<iostream>
-#include<fstream>
-#include<unordered_map>
-#include<cstdio>
-#include<cstdlib>
-#include<cstring>
-#include<string>
-
-using namespace std;
-
-//#define LARGE_DATA
-#ifdef LARGE_DATA
-typedef __int128 score_t;
-
-string to_string(const __int128 x){
- return to_string((double) x);
-}
-
-ostream& operator<<(ostream& cout, __int128 x){
- return cout << to_string(x);
-}
-#else
-typedef long long score_t;
-#endif
-
-#include "multitree.hpp"
-#include "algorithms.hpp"
-
-const bool VERBOSE = true;
-
-MetaAlgorithm meta;
-TripartitionInitializer &tripInit = meta.tripInit;
-vector<TripartitionInitializer> &batchInit = meta.batchInit;
-
-unordered_map<string, string> leafname_mapping;
-string TEXT;
-int duploss = 0;
-int nodecnt = 0;
-int pos = 0;
-int K = 0;
-vector<string> &id2name = meta.names;
-unordered_map<string, int> &name2id = meta.name2id;
-
-class DynamicBitset{
- int size = 0;
- vector<uint64_t> vec;
-
-public:
- DynamicBitset(){}
- DynamicBitset(int sz): size(sz), vec((sz + 63) / 64){}
-
- void set(int i){
- if (i >= size){
- size = i + 1;
- if ((size + 63) / 64 > vec.size()){
- vec.resize((size + 63) / 64);
- }
- }
- vec[i / 64] |= (1LL << (i % 64));
- }
-
- DynamicBitset operator|(const DynamicBitset &b) const{
- if (size < b.size) return b | *this;
- DynamicBitset res(size);
- for (int i = 0; i < b.vec.size(); i++){
- res.vec[i] = vec[i] | b.vec[i];
- }
- for (int i = b.vec.size(); i < vec.size(); i++){
- res.vec[i] = vec[i];
- }
- return res;
- }
-
- DynamicBitset operator&(const DynamicBitset &b) const{
- if (size < b.size) return b & *this;
- DynamicBitset res(b.size);
- for (int i = 0; i < b.vec.size(); i++){
- res.vec[i] = vec[i] & b.vec[i];
- }
- return res;
- }
-
- DynamicBitset operator^(const DynamicBitset &b) const{
- if (size < b.size) return b ^ *this;
- DynamicBitset res(size);
- for (int i = 0; i < b.vec.size(); i++){
- res.vec[i] = vec[i] ^ b.vec[i];
- }
- for (int i = b.vec.size(); i < vec.size(); i++){
- res.vec[i] = vec[i];
- }
- return res;
- }
-
- DynamicBitset operator-(const DynamicBitset &b) const{
- DynamicBitset res(size);
- for (int i = 0; i < vec.size(); i++){
- if (i < b.vec.size()) res.vec[i] = vec[i] & ~b.vec[i];
- else res.vec[i] = vec[i];
- }
- return res;
- }
-
- bool operator==(const DynamicBitset &b) const{
- if (size < b.size) return b == *this;
- for (int i = 0; i < b.vec.size(); i++){
- if (vec[i] != b.vec[i]) return false;
- }
- for (int i = b.vec.size(); i < vec.size(); i++){
- if (vec[i] != 0) return false;
- }
- return true;
- }
-
- bool operator!=(const DynamicBitset &b) const{
- return !(*this == b);
- }
-
- bool isDisjointTo(const DynamicBitset &b) const{
- if (size < b.size) return b.isDisjointTo(*this);
- for (int i = 0; i < b.vec.size(); i++){
- if ((vec[i] & b.vec[i]) != 0) return false;
- }
- return true;
- }
-
- vector<int> setBits() const{
- vector<int> res;
- for (int i = 0; i < vec.size(); i++){
- for (int j = 0; j < 64; j++){
- if (vec[i] & (1LL << j)) res.push_back(64 * i + j);
- }
- }
- return res;
- }
-};
-
-class GenetreeAnnotator{
-private:
- struct Node{
- int leftChildId = -1, rightChildId = -1;
- DynamicBitset label;
- bool isDuplication = false;
- bool isLeaf = false;
- int score = -1;
- int leafId = -1;
- };
-
- vector<Node> node;
-
- tuple<int, int, int> createSubtree(const unordered_map<long long, string> &leafname, const unordered_map<long long, pair<long long, long long> > &children, const long long cur, vector<int> &rootId){
- if (children.count(cur) == 0){
- int curId = node.size();
- node.emplace_back();
- node[curId].isLeaf = true;
- node[curId].score = 0;
- if (name2id.count(leafname.at(cur)) == 0){
- name2id[leafname.at(cur)] = id2name.size();
- id2name.push_back(leafname.at(cur));
- for (int p = 0; p < tripInit.nodes.size(); p++){
- tripInit.leafParent[p].emplace_back();
- }
- }
- node[curId].leafId = name2id[leafname.at(cur)];
- node[curId].label.set(name2id[leafname.at(cur)]);
- return make_tuple(curId, -1, -1);
- }
-
- tuple<int, int, int> left = createSubtree(leafname, children, children.at(cur).first, rootId), right = createSubtree(leafname, children, children.at(cur).second, rootId);
- int cur0 = node.size();
- node.emplace_back();
- int cur1 = node.size();
- node.emplace_back();
- int cur2 = node.size();
- node.emplace_back();
- node[cur0].leftChildId = get<0>(left);
- node[cur0].rightChildId = get<0>(right);
-
- node[cur1].leftChildId = get<0>(left);
- node[cur2].leftChildId = get<0>(right);
- if (get<1>(left) != -1) node[get<1>(left)].rightChildId = cur2;
- if (get<2>(left) != -1) node[get<2>(left)].rightChildId = cur2;
- if (get<1>(right) != -1) node[get<1>(right)].rightChildId = cur1;
- if (get<2>(right) != -1) node[get<2>(right)].rightChildId = cur1;
-
- int root1 = node.size();
- node.emplace_back();
- node[root1].leftChildId = get<0>(left);
- node[root1].rightChildId = cur2;
- rootId.push_back(root1);
- int root2 = node.size();
- node.emplace_back();
- node[root2].leftChildId = get<0>(right);
- node[root2].rightChildId = cur1;
- rootId.push_back(root2);
-
- return make_tuple(cur0, cur1, cur2);
- }
-
- int scoreSubtree(int cur){
- if (node[cur].score != -1) return node[cur].score;
- node[cur].score = scoreSubtree(node[cur].leftChildId) + scoreSubtree(node[cur].rightChildId);
- node[cur].label = node[node[cur].leftChildId].label | node[node[cur].rightChildId].label;
- if (!node[node[cur].leftChildId].label.isDisjointTo(node[node[cur].rightChildId].label)){
- node[cur].score++;
- node[cur].isDuplication = true;
- if (node[cur].label != node[node[cur].leftChildId].label) node[cur].score++;
- if (node[cur].label != node[node[cur].rightChildId].label) node[cur].score++;
- }
- return node[cur].score;
- }
-
-public:
- const vector<string> &leafnames() const{
- return id2name;
- }
-
- int annotateTree(const unordered_map<long long, string> &leafname, const unordered_map<long long, pair<long long, long long> > &children, const long long root){
- vector<int> rootId;
- tuple<int, int, int> left = createSubtree(leafname, children, children.at(root).first, rootId), right = createSubtree(leafname, children, children.at(root).second, rootId);
- if (get<1>(left) != -1) node[get<1>(left)].rightChildId = get<0>(right);
- if (get<2>(left) != -1) node[get<2>(left)].rightChildId = get<0>(right);
- if (get<1>(right) != -1) node[get<1>(right)].rightChildId = get<0>(left);
- if (get<2>(right) != -1) node[get<2>(right)].rightChildId = get<0>(left);
-
- int curId = node.size();
- node.emplace_back();
- node[curId].leftChildId = get<0>(left);
- node[curId].rightChildId = get<0>(right);
- rootId.push_back(curId);
-
- int bestscore = 999999, bestroot = -1;
- for (int root: rootId){
- int score = scoreSubtree(root);
- if (score < bestscore){
- bestscore = score;
- bestroot = root;
- }
- }
- duploss += bestscore;
- return bestroot;
- }
-
- int buildTree(int cur, int p) const{
- int w = tripInit.nodes[p].size();
- tripInit.nodes[p].emplace_back();
-
- if (node[cur].isLeaf){
- tripInit.leafParent[p][node[cur].leafId].push_back(w);
- //cerr << id2name[node[cur].leafId];
- return w;
- }
- int left = node[cur].leftChildId, right = node[cur].rightChildId;
- int large, small;
- if (node[left].label.setBits().size() > node[right].label.setBits().size()){
- large = left;
- small = right;
- }
- else {
- large = right;
- small = left;
- }
- //cerr << "(";
- int u = buildTree(small, p);
- //cerr << ",";
- int v = buildTree(large, p);
- //cerr << ")";
- tripInit.nodes[p][w].small = u;
- tripInit.nodes[p][w].large = v;
- tripInit.nodes[p][u].up = w;
- tripInit.nodes[p][v].up = w;
- if (node[cur].isDuplication){
- tripInit.nodes[p][w].dup = true;
- for (int i: (node[cur].label - node[large].label).setBits()){
- tripInit.leafParent[p][i].push_back(w);
- } //cerr << "+";
- }
- else {
- tripInit.nodes[p][w].dup = false;
- }
- return w;
- }
-};
-
-string MAPPING(int begin, int end){
- string s;
- for (int i = begin; i < end && TEXT[i] != ':'; i++){
- if (TEXT[i] != '\"' && TEXT[i] != '\'') s += TEXT[i];
- }
- if (leafname_mapping.count(s)) return leafname_mapping[s];
- else return s;
-}
-
-long long parse(unordered_map<long long, string> &leafname, unordered_map<long long, pair<long long, long long> > &children){
- int i = pos;
- long long cur;
- while (TEXT[pos] != '(' && TEXT[pos] != ',') pos++;
- if (TEXT[pos] == '(') {
- pos++;
- cur = parse(leafname, children);
- while (TEXT[pos] != ',') pos++;
- }
- else {
- cur = nodecnt++;
- leafname[cur] = MAPPING(i, pos);
- }
- vector<long long> lst;
- lst.push_back(cur);
- while (TEXT[pos] != ')'){
- i = ++pos;
- while (TEXT[pos] != ')' && TEXT[pos] != '(' && TEXT[pos] != ',') pos++;
- /*
- if (TEXT[pos] == '(') {
- pos++;
- long long left = cur, right = parse(leafname, children);
- cur = nodecnt++;
- children[cur] = {left, right};
- while (TEXT[pos] != ',' && TEXT[pos] != ')') pos++;
- }
- else {
- long long left = cur, right = nodecnt++;
- leafname[right] = MAPPING(i, pos);
- cur = nodecnt++;
- children[cur] = {left, right};
- }
- */
- long long temp = lst[rand() % lst.size()];
- if (TEXT[pos] == '(') {
- pos++;
- long long left = nodecnt++, right = parse(leafname, children);
- while (TEXT[pos] != ',' && TEXT[pos] != ')') pos++;
- if (leafname.count(temp)) {
- leafname[left] = leafname[temp];
- leafname.erase(temp);
- }
- else children[left] = children[temp];
- children[temp] = {left, right};
- lst.push_back(left);
- lst.push_back(right);
- }
- else {
- long long left = nodecnt++, right = nodecnt++;
- leafname[right] = MAPPING(i, pos);
- if (leafname.count(temp)) {
- leafname[left] = leafname[temp];
- leafname.erase(temp);
- }
- else children[left] = children[temp];
- children[temp] = {left, right};
- lst.push_back(left);
- lst.push_back(right);
- }
- }
- pos++;
- return cur;
-}
-
-void annotate(string input, string mapping){
- if (mapping != ""){
- ifstream fmap(mapping);
- string gname, sname;
- while (fmap >> gname){
- fmap >> sname;
- leafname_mapping[gname] = sname;
- }
- }
- ifstream fin(input);
- string line;
- while (getline(fin, line)) TEXT += line;
- while (pos < TEXT.size()){
- while (pos < TEXT.size() && TEXT[pos] != '(') pos++;
- if (pos < TEXT.size()) {
- pos++;
- unordered_map<long long, string> leafname;
- unordered_map<long long, pair<long long, long long> > children;
- long long root = parse(leafname, children);
- GenetreeAnnotator ga;
- int iroot = ga.annotateTree(leafname, children, root);
- ga.buildTree(iroot, K % tripInit.nodes.size());
- K++;
- if (VERBOSE && (K & 511) == 0) cerr << "Read " << K << " genetrees and found " << id2name.size() << " species.\n";
- }
- }
-}
-
-string HELP_TEXT = R"V0G0N(-a a list of gene name to taxon name maps, each line contains one gene name followed by one taxon name separated by a space or tab
-inputGeneTrees: the path to a file containing all gene trees in Newick format
-)V0G0N";
-
-int main(int argc, char** argv){
- string mappingFile;
- meta.initialize(argc, argv, " -a taxonNameMaps", HELP_TEXT);
-
- for (int i = 1; i < argc; i += 2){
- if (strcmp(argv[i], "-y") == 0) {i--; continue;}
-
- if (strcmp(argv[i], "-a") == 0) mappingFile = argv[i + 1];
- }
-
- for (int i = 0; i < meta.nThread2; i++){
- tripInit.nodes.emplace_back();
- tripInit.leafParent.emplace_back();
- }
- annotate(argv[argc - 1], mappingFile);
-
- cerr << "#Genetrees: " << K << endl;
- cerr << "#Duploss: " << duploss << endl;
-
- score_t score = meta.run().first;
- cerr << "#EqQuartets: " << NUM_EQ_CLASSES << endl;
- cerr << "Score: " << score << endl;
- return 0;
-}
diff --git a/addons/ASTER/astral-pro.exe b/addons/ASTER/astral-pro.exe
deleted file mode 100644
index 763c1ae8d61203cf3c497f1d9dfa598982d5c83d..0000000000000000000000000000000000000000
Binary files a/addons/ASTER/astral-pro.exe and /dev/null differ
diff --git a/addons/ASTER/astral-weighted-p.cpp b/addons/ASTER/astral-weighted-p.cpp
deleted file mode 100644
index 9e2182cf4e9def104122418c8f4e0d7b1f7ee5c2..0000000000000000000000000000000000000000
--- a/addons/ASTER/astral-weighted-p.cpp
+++ /dev/null
@@ -1,159 +0,0 @@
-#include<iostream>
-#include<fstream>
-#include<unordered_map>
-#include<cstdio>
-#include<cstdlib>
-#include<cstring>
-#include<string>
-
-using namespace std;
-
-//#define LARGE_DATA
-#ifdef LARGE_DATA
-typedef long double score_t;
-
-string to_string(long double x){
- return to_string((double) x);
-}
-
-score_t from_string(const string s){
- return stold(s);
-}
-
-ostream& operator<<(ostream& cout, long double x){
- return cout << to_string(x);
-}
-#else
-typedef double score_t;
-
-score_t from_string(const string s){
- return stod(s);
-}
-#endif
-
-#include "genetreewithweight.hpp"
-#include "algorithms.hpp"
-
-
-MetaAlgorithm meta;
-TripartitionInitializer &tripInit = meta.tripInit;
-vector<TripartitionInitializer> &batchInit = meta.batchInit;
-
-unordered_map<string, string> leafname_mapping;
-string TEXT;
-int pos = 0;
-int K = 0;
-int part = 0, iBatch = 0;
-vector<string> &names = meta.names;
-unordered_map<string, int> &name2id = meta.name2id;
-
-
-int MAPPING(int begin, int end){
- string s;
- for (int i = begin; i < end && TEXT[i] != ':'; i++){
- if (TEXT[i] != '\"' && TEXT[i] != '\'') s += TEXT[i];
- }
- if (leafname_mapping.count(s)) s = leafname_mapping[s];
- if (name2id.count(s) == 0){
- name2id[s] = names.size();
- names.push_back(s);
- for (int i = 0; i < meta.nThread2; i++){
- tripInit.leafParent[i].emplace_back();
- }
- }
- return name2id[s];
-}
-
-score_t WEIGHT(int begin, int end){
- int i = begin;
- while (i < end && TEXT[i] != ':') i++;
- if (i == begin || i == end) return 1;
- else return max(0.0, 1.5 * from_string(TEXT.substr(begin, i - begin)) - 0.5);
-}
-
-void parse(int parent = -1, bool isLeft = true){
- int cur = tripInit.nodes[part].size();
- tripInit.nodes[part].emplace_back();
- tripInit.nodes[part][cur].up = parent;
- if (parent != -1 && isLeft) tripInit.nodes[part][parent].small = cur;
- if (parent != -1 && !isLeft) tripInit.nodes[part][parent].large = cur;
-
- if (TEXT[pos] == '(') {
- pos++;
- parse(cur, true);
- pos++;
- parse(cur, false);
- while (TEXT[pos] != ')'){
- int next = tripInit.nodes[part].size();
- tripInit.nodes[part].emplace_back();
- tripInit.nodes[part][cur].up = next;
- tripInit.nodes[part][next].small = cur;
- cur = next;
- tripInit.nodes[part][cur].up = parent;
- if (parent != -1 && isLeft) tripInit.nodes[part][parent].small = cur;
- if (parent != -1 && !isLeft) tripInit.nodes[part][parent].large = cur;
- pos++;
- parse(cur, false);
- }
- int i = ++pos;
- while (TEXT[pos] != ')' && TEXT[pos] != ',' && TEXT[pos] != ';') pos++;
- tripInit.nodes[part][cur].weight = WEIGHT(i, pos);
- }
- else {
- int i = pos;
- while (TEXT[pos] != ')' && TEXT[pos] != ',') pos++;
- tripInit.leafParent[part][MAPPING(i, pos)].push_back(cur);
- tripInit.nodes[part][cur].weight = 1;
- }
-}
-
-void readInputTrees(string input, string mapping) {
- if (mapping != ""){
- ifstream fmap(mapping);
- string gname, sname;
- while (fmap >> gname){
- fmap >> sname;
- leafname_mapping[gname] = sname;
- }
- }
- ifstream fin(input);
- string line;
- while (getline(fin, line)) TEXT += line;
- while (pos < TEXT.size()){
- while (pos < TEXT.size() && TEXT[pos] != '(') pos++;
- if (pos < TEXT.size()) {
- part = K % tripInit.nodes.size();
- parse();
- K++;
- }
- }
-}
-
-string HELP_TEXT = R"V0G0N(-a a list of gene name to taxon name maps, each line contains one gene name followed by one taxon name separated by a space or tab
-inputGeneTrees: the path to a file containing all gene trees in Newick format
-)V0G0N";
-
-int main(int argc, char** argv){
- string mappingFile;
- meta.initialize(argc, argv, " -a taxonNameMaps", HELP_TEXT);
-
- for (int i = 1; i < argc; i += 2){
- if (strcmp(argv[i], "-a") == 0) mappingFile = argv[i + 1];
- }
-
- for (int i = 0; i < meta.nThread2; i++){
- tripInit.nodes.emplace_back();
- tripInit.leafParent.emplace_back();
- }
- for (int i = 0; i < meta.nBatch; i++){
- batchInit[i].nodes.emplace_back();
- batchInit[i].leafParent.emplace_back();
- }
- readInputTrees(argv[argc - 1], mappingFile);
-
- cerr << "#Genetrees: " << K << endl;
-
- score_t score = meta.run().first / 2;
- cerr << "Score: " << score << endl;
- return 0;
-}
diff --git a/addons/ASTER/astral-weighted.cpp b/addons/ASTER/astral-weighted.cpp
deleted file mode 100644
index 6a9a3353ffab18f3734abc68565c43be671f05ed..0000000000000000000000000000000000000000
--- a/addons/ASTER/astral-weighted.cpp
+++ /dev/null
@@ -1,175 +0,0 @@
-#include<iostream>
-#include<fstream>
-#include<unordered_map>
-#include<cstdio>
-#include<cstdlib>
-#include<cstring>
-#include<string>
-
-using namespace std;
-
-//#define LARGE_DATA
-#ifdef LARGE_DATA
-typedef long double score_t;
-
-string to_string(long double x){
- return to_string((double) x);
-}
-
-score_t from_string(const string s){
- return stold(s);
-}
-
-ostream& operator<<(ostream& cout, long double x){
- return cout << to_string(x);
-}
-#else
-typedef double score_t;
-
-score_t from_string(const string s){
- return stod(s);
-}
-#endif
-
-#include "genetreewithweight.hpp"
-#include "algorithms.hpp"
-
-
-MetaAlgorithm meta;
-TripartitionInitializer &tripInit = meta.tripInit;
-vector<TripartitionInitializer> &batchInit = meta.batchInit;
-
-unordered_map<string, string> leafname_mapping;
-string TEXT;
-int pos = 0;
-int K = 0;
-int part = 0, iBatch = 0;
-vector<string> &names = meta.names;
-unordered_map<string, int> &name2id = meta.name2id;
-score_t maxv = 100, minv = 0, defaultv = 0;
-
-int MAPPING(int begin, int end){
- string s;
- for (int i = begin; i < end && TEXT[i] != ':'; i++){
- if (TEXT[i] != '\"' && TEXT[i] != '\'') s += TEXT[i];
- }
- if (leafname_mapping.count(s)) s = leafname_mapping[s];
- if (name2id.count(s) == 0){
- name2id[s] = names.size();
- names.push_back(s);
- for (int i = 0; i < meta.nThread2; i++){
- tripInit.leafParent[i].emplace_back();
- }
- }
- return name2id[s];
-}
-
-score_t WEIGHT(int begin, int end){
- int i = begin;
- while (i < end && TEXT[i] != ':') i++;
- if (i == begin || i == end) return max(0.0, (defaultv - minv) / (maxv - minv));
- else return max(0.0, (from_string(TEXT.substr(begin, i - begin)) - minv) / (maxv - minv));
-}
-
-void parse(int parent = -1, bool isLeft = true){
- int cur = tripInit.nodes[part].size();
- tripInit.nodes[part].emplace_back();
- tripInit.nodes[part][cur].up = parent;
- if (parent != -1 && isLeft) tripInit.nodes[part][parent].small = cur;
- if (parent != -1 && !isLeft) tripInit.nodes[part][parent].large = cur;
-
- if (TEXT[pos] == '(') {
- pos++;
- parse(cur, true);
- pos++;
- parse(cur, false);
- vector<int> lst;
- lst.push_back(cur);
- tripInit.nodes[part][cur].weight = max(0.0, (defaultv - minv) / (maxv - minv));
- while (TEXT[pos] != ')'){
- int left = lst[rand() % lst.size()];
- int up = tripInit.nodes[part].size();
- tripInit.nodes[part].emplace_back();
- lst.push_back(up);
- if (cur == left) cur = up;
- tripInit.nodes[part][up].weight = max(0.0, (defaultv - minv) / (maxv - minv));
- int g = tripInit.nodes[part][left].up;
- if (g != -1){
- if (tripInit.nodes[part][g].small == left) tripInit.nodes[part][g].small = up;
- else tripInit.nodes[part][g].large = up;
- }
- tripInit.nodes[part][up].up = g;
- tripInit.nodes[part][left].up = up;
- tripInit.nodes[part][up].small = left;
- pos++;
- parse(up, false);
- }
- int i = ++pos;
- while (TEXT[pos] != ')' && TEXT[pos] != ',' && TEXT[pos] != ';') pos++;
- tripInit.nodes[part][cur].weight = WEIGHT(i, pos);
- }
- else {
- int i = pos;
- while (TEXT[pos] != ')' && TEXT[pos] != ',') pos++;
- tripInit.leafParent[part][MAPPING(i, pos)].push_back(cur);
- tripInit.nodes[part][cur].weight = 1;
- }
-}
-
-void readInputTrees(string input, string mapping) {
- if (mapping != ""){
- ifstream fmap(mapping);
- string gname, sname;
- while (fmap >> gname){
- fmap >> sname;
- leafname_mapping[gname] = sname;
- }
- }
- ifstream fin(input);
- string line;
- while (getline(fin, line)) TEXT += line;
- while (pos < TEXT.size()){
- while (pos < TEXT.size() && TEXT[pos] != '(') pos++;
- if (pos < TEXT.size()) {
- part = K % tripInit.nodes.size();
- parse();
- K++;
- }
- }
-}
-
-string HELP = " -a taxonNameMaps -x maxWeight -n minWeight -d defaultWeight";
-string HELP_TEXT = R"V0G0N(-a a list of gene name to taxon name maps, each line contains one gene name followed by one taxon name separated by a space or tab
--x max possible weight in weight scale (default: 100)
--n min possible weight in weight scale (default: 0)
--d min default weight when weight not provided (default: 0)
-inputGeneTrees: the path to a file containing all gene trees in Newick format
-)V0G0N";
-
-int main(int argc, char** argv){
- string mappingFile;
- meta.initialize(argc, argv, HELP, HELP_TEXT);
-
- for (int i = 1; i < argc; i += 2){
- if (strcmp(argv[i], "-a") == 0) mappingFile = argv[i + 1];
- if (strcmp(argv[i], "-x") == 0) maxv = from_string(argv[i + 1]);
- if (strcmp(argv[i], "-n") == 0) minv = from_string(argv[i + 1]);
- if (strcmp(argv[i], "-d") == 0) defaultv = from_string(argv[i + 1]);
- }
-
- for (int i = 0; i < meta.nThread2; i++){
- tripInit.nodes.emplace_back();
- tripInit.leafParent.emplace_back();
- }
- for (int i = 0; i < meta.nBatch; i++){
- batchInit[i].nodes.emplace_back();
- batchInit[i].leafParent.emplace_back();
- }
- readInputTrees(argv[argc - 1], mappingFile);
-
- cerr << "#Genetrees: " << K << endl;
-
- score_t score = meta.run().first;
- cerr << "Score: " << score << endl;
- return 0;
-}
diff --git a/addons/ASTER/astral.cpp b/addons/ASTER/astral.cpp
deleted file mode 100644
index 50936d44ecc562e54577fb5975aba7b69abd33a6..0000000000000000000000000000000000000000
--- a/addons/ASTER/astral.cpp
+++ /dev/null
@@ -1,154 +0,0 @@
-#include<iostream>
-#include<fstream>
-#include<unordered_map>
-#include<cstdio>
-#include<cstdlib>
-#include<cstring>
-#include<string>
-
-using namespace std;
-
-//#define LARGE_DATA
-#ifdef LARGE_DATA
-typedef __int128 score_t;
-
-string to_string(const __int128 x){
- return to_string((double) x);
-}
-
-ostream& operator<<(ostream& cout, __int128 x){
- return cout << to_string(x);
-}
-#else
-typedef long long score_t;
-#endif
-
-#include "genetree.hpp"
-#include "algorithms.hpp"
-
-MetaAlgorithm meta;
-TripartitionInitializer &tripInit = meta.tripInit;
-vector<TripartitionInitializer> &batchInit = meta.batchInit;
-
-unordered_map<string, string> leafname_mapping;
-string TEXT;
-int nodecnt = 0;
-int pos = 0;
-int K = 0;
-int part = 0, iBatch = 0;
-vector<string> &names = meta.names;
-unordered_map<string, int> &name2id = meta.name2id;
-
-
-string MAPPING(int begin, int end){
- string s;
- for (int i = begin; i < end && TEXT[i] != ':'; i++){
- if (TEXT[i] != '\"' && TEXT[i] != '\'') s += TEXT[i];
- }
- if (leafname_mapping.count(s)) return leafname_mapping[s];
- else return s;
-}
-
-void parseTaxa(){
- int i = pos;
- while (TEXT[pos] != '(' && TEXT[pos] != ',' && TEXT[pos] != ')') pos++;
-
- if (TEXT[pos] == '(') {
- while (TEXT[pos] != ')'){
- pos++;
- parseTaxa();
- while (TEXT[pos] != ')' && TEXT[pos] != ',') pos++;
- }
- pos++;
- }
- else {
- string name = MAPPING(i, pos);
- if (name2id.count(name) == 0){
- name2id[name] = names.size();
- names.push_back(name);
- }
- }
-}
-
-void parse(int parent = -1){
- int i = pos, cur;
- while (TEXT[pos] != '(' && TEXT[pos] != ',' && TEXT[pos] != ')') pos++;
-
- if (TEXT[pos] == '(') {
- cur = nodecnt++;
- while (TEXT[pos] != ')'){
- pos++;
- parse(cur);
- while (TEXT[pos] != ')' && TEXT[pos] != ',') pos++;
- }
- pos++;
- }
- else cur = name2id[MAPPING(i, pos)];
- if (parent != -1) tripInit.parentChild[part].back().push_back({parent, cur});
- else tripInit.roots[part].push_back(cur);
- if (parent != -1) batchInit[iBatch].parentChild[0].back().push_back({parent, cur});
- else batchInit[iBatch].roots[0].push_back(cur);
-}
-
-void readInputTrees(string input, string mapping) {
- if (mapping != ""){
- ifstream fmap(mapping);
- string gname, sname;
- while (fmap >> gname){
- fmap >> sname;
- leafname_mapping[gname] = sname;
- }
- }
- ifstream fin(input);
- string line;
- while (getline(fin, line)) TEXT += line;
-
- while (pos < TEXT.size()){
- parseTaxa();
- while (pos < TEXT.size() && TEXT[pos] != '(') pos++;
- }
- tripInit.nTaxa = names.size();
- for (int i = 0; i < meta.nBatch; i++){
- batchInit[i].nTaxa = names.size();
- }
- pos = 0;
- while (pos < TEXT.size()){
- part = K % tripInit.roots.size();
- tripInit.parentChild[part].emplace_back();
- iBatch = K % meta.nBatch;
- batchInit[iBatch].parentChild[0].emplace_back();
- nodecnt = names.size();
- parse();
- while (pos < TEXT.size() && TEXT[pos] != '(') pos++;
- K++;
- }
-}
-
-string HELP_TEXT = R"V0G0N(-a a list of gene name to taxon name maps, each line contains one gene name followed by one taxon name separated by a space or tab
-inputGeneTrees: the path to a file containing all gene trees in Newick format
-)V0G0N";
-
-int main(int argc, char** argv){
- string mappingFile;
- meta.initialize(argc, argv, " -a taxonNameMaps", HELP_TEXT);
-
- for (int i = 1; i < argc; i += 2){
- if (strcmp(argv[i], "-a") == 0) mappingFile = argv[i + 1];
- }
-
- for (int i = 0; i < meta.nThread2; i++){
- tripInit.roots.emplace_back();
- tripInit.parentChild.emplace_back();
- }
- for (int i = 0; i < meta.nBatch; i++){
- batchInit[i].roots.emplace_back();
- batchInit[i].parentChild.emplace_back();
- }
- readInputTrees(argv[argc - 1], mappingFile);
-
- cerr << "#Genetrees: " << K << endl;
-
- score_t score = meta.run().first / 2;
- cerr << "Score: " << score << endl;
- return 0;
-}
diff --git a/addons/ASTER/astral.exe b/addons/ASTER/astral.exe
deleted file mode 100644
index e225084cd63c0434a54cf6a6a2cfb5b5ac3a4f79..0000000000000000000000000000000000000000
Binary files a/addons/ASTER/astral.exe and /dev/null differ
diff --git a/addons/ASTER/binary.hpp b/addons/ASTER/binary.hpp
deleted file mode 100644
index 92933b396577538d2f4f31b9e631b8f17083a0f9..0000000000000000000000000000000000000000
--- a/addons/ASTER/binary.hpp
+++ /dev/null
@@ -1,147 +0,0 @@
-#include<vector>
-#include<array>
-#include<thread>
-
-using namespace std;
-
-score_t scoreGene(const vector<array<array<int, 2>, 3> > &cnt, const score_t R){
- long long rryy0 = 0, rrnn0 = 0, nnyy0 = 0, nnnn0 = 0;
- long long rryy1 = 0, rrnn1 = 0, nnyy1 = 0, nnnn1 = 0;
- long long rryy2 = 0, rrnn2 = 0, nnyy2 = 0, nnnn2 = 0;
- for (const array<array<int, 2>, 3> &c: cnt){
- const long long r0 = c[0][0], y0 = c[0][1], n0 = r0 + y0;
- const long long r1 = c[1][0], y1 = c[1][1], n1 = r1 + y1;
- const long long r2 = c[2][0], y2 = c[2][1], n2 = r2 + y2;
- rryy0 += r0 * (r0 - 1) * y1 * y2; rrnn0 += r0 * (r0 - 1) * n1 * n2; nnyy0 += n0 * (n0 - 1) * y1 * y2; nnnn0 += n0 * (n0 - 1) * n1 * n2;
- rryy1 += r1 * (r1 - 1) * y2 * y0; rrnn1 += r1 * (r1 - 1) * n2 * n0; nnyy1 += n1 * (n1 - 1) * y2 * y0; nnnn1 += n1 * (n1 - 1) * n2 * n0;
- rryy2 += r2 * (r2 - 1) * y0 * y1; rrnn2 += r2 * (r2 - 1) * n0 * n1; nnyy2 += n2 * (n2 - 1) * y0 * y1; nnnn2 += n2 * (n2 - 1) * n0 * n1;
- }
- return (((nnnn0 != 0) ? ((score_t) rrnn0) * ((score_t) nnyy0) / ((score_t) nnnn0) : 0)
- + ((nnnn1 != 0) ? ((score_t) rrnn1) * ((score_t) nnyy1) / ((score_t) nnnn1) : 0)
- + ((nnnn2 != 0) ? ((score_t) rrnn2) * ((score_t) nnyy2) / ((score_t) nnnn2) : 0)) - (rryy0 + rryy1 + rryy2) * (1 - 2 * R + 2 * R * R);
-}
-
-struct TripartitionInitializer{
- int nThreads = 1;
- vector<score_t> pi;
- vector<vector<vector<int> > > seq;
-};
-
-struct Tripartition{
- int nThreads, n = 0;
- vector<vector<array<array<int, 2>, 3> > > cnt; // gene * pos * part * letter
- vector<vector<array<int, 2> > > total; // gene * pos * letter
- const vector<score_t> pi; // gene
- const vector<vector<vector<int> > > seq; // gene * taxon * pos -> letter
- // i, j, k -> taxon; p, q, r -> pos; x, y, z -> part; a, b, c -> letter; g -> gene
-
- Tripartition(const TripartitionInitializer &init): nThreads(init.nThreads), seq(init.seq), pi(init.pi){
- for (const vector<vector<int> > s: seq){
- cnt.emplace_back(s[0].size());
- total.emplace_back(s[0].size());
- }
- }
-
- void resetWork(int start, int end){
- for (int g = start; g < end; g++){
- for (int p = 0; p < total[g].size(); p++){
- for (int a = 0; a < 2; a++){
- cnt[g][p][0][a] = total[g][p][a];
- cnt[g][p][1][a] = 0;
- cnt[g][p][2][a] = 0;
- }
- }
- }
- }
-
- void addTotalWork(int i, int start, int end){
- for (int g = start; g < end; g++){
- for (int p = 0; p < total[g].size(); p++){
- int a = seq[g][i][p];
- if (a != -1) total[g][p][a]++;
- }
- }
- }
-
- void rmvTotalWork(int i, int start, int end){
- for (int g = start; g < end; g++){
- for (int p = 0; p < total[g].size(); p++){
- int a = seq[g][i][p];
- if (a != -1) total[g][p][a]--;
- }
- }
- }
-
- void addWork(int x, int i, int start, int end){
- for (int g = start; g < end; g++){
- for (int p = 0; p < total[g].size(); p++){
- int a = seq[g][i][p];
- if (a != -1) cnt[g][p][x][a]++;
- }
- }
- }
-
- void rmvWork(int x, int i, int start, int end){
- for (int g = start; g < end; g++){
- for (int p = 0; p < total[g].size(); p++){
- int a = seq[g][i][p];
- if (a != -1) cnt[g][p][x][a]--;
- }
- }
- }
-
- void scoreWork(score_t &res, int start, int end){
- score_t temp = 0;
- for (int g = start; g < end; g++){
- temp += scoreGene(cnt[g], pi[g]);
- }
- res = temp;
- }
-
- void reset(){
- vector<thread> thrds;
- for (int t = 1; t < nThreads; t++) thrds.emplace_back(&Tripartition::resetWork, this, pi.size() * t / nThreads, pi.size() * (t + 1) / nThreads);
- resetWork(0, pi.size() / nThreads);
- for (thread &t: thrds) t.join();
- }
-
- void addTotal(int i){
- n++;
- vector<thread> thrds;
- for (int t = 1; t < nThreads; t++) thrds.emplace_back(&Tripartition::addTotalWork, this, i, pi.size() * t / nThreads, pi.size() * (t + 1) / nThreads);
- addTotalWork(i, 0, pi.size() / nThreads);
- for (thread &t: thrds) t.join();
- }
-
- void rmvTotal(int i){
- n--;
- vector<thread> thrds;
- for (int t = 1; t < nThreads; t++) thrds.emplace_back(&Tripartition::rmvTotalWork, this, i, pi.size() * t / nThreads, pi.size() * (t + 1) / nThreads);
- rmvTotalWork(i, 0, pi.size() / nThreads);
- for (thread &t: thrds) t.join();
- }
-
- void add(int x, int i){
- vector<thread> thrds;
- for (int t = 1; t < nThreads; t++) thrds.emplace_back(&Tripartition::addWork, this, x, i, pi.size() * t / nThreads, pi.size() * (t + 1) / nThreads);
- addWork(x, i, 0, pi.size() / nThreads);
- for (thread &t: thrds) t.join();
- }
-
- void rmv(int x, int i){
- vector<thread> thrds;
- for (int t = 1; t < nThreads; t++) thrds.emplace_back(&Tripartition::rmvWork, this, x, i, pi.size() * t / nThreads, pi.size() * (t + 1) / nThreads);
- rmvWork(x, i, 0, pi.size() / nThreads);
- for (thread &t: thrds) t.join();
- }
-
- score_t score(){
- vector<score_t> res(nThreads);
- vector<thread> thrds;
- for (int t = 1; t < nThreads; t++) thrds.emplace_back(&Tripartition::scoreWork, this, ref(res[t]), pi.size() * t / nThreads, pi.size() * (t + 1) / nThreads);
- scoreWork(res[0], 0, pi.size() / nThreads);
- for (thread &t: thrds) t.join();
- for (int t = 1; t < nThreads; t++) res[0] += res[t];
- return res[0];
- }
-};
diff --git a/addons/ASTER/example/example.phylip b/addons/ASTER/example/example.phylip
deleted file mode 100644
index a3bc38fde21e4c2175eb75c2bba076c7bc67063d..0000000000000000000000000000000000000000
--- a/addons/ASTER/example/example.phylip
+++ /dev/null
@@ -1,306 +0,0 @@
-101 367
-0 AATACTAGCGCAGCGGCCTGGTGGTTACAGGCAGCATCTCACACAGTTATCTGACTAGATAAACAGGTCCAGTCATAACAAGCAGGTGTAAGAGAGTACACTTTTATGATAGGCCTTACAAATAGCGCAGATAAAGAGCGACCAAAGGTATGTAGATCGAGTGATAAAAAGGCAGGAAAGCGAGGATCTGGAGGGTCCTAGCGACAGTGATAGAGTACCGAGCCCGTTCTAAACCGATACATCGCGAAGTGGACCTTTGCCAGGCCGGAGCGCACGTTGGTATCTGTTTCAGCACCCTGTGAGGTAGTACAAGAGGTTACATCCAGTGGTAAATGCGCAGCGATCGGTTCGCGCAGATGCGGTGTCG
-98 GTTGCTCTCGAGGATCGACGCGGGTTGCGAGCAGTATCCCACGGAGTTCTCTAATTCGAAAAAGCGGTGCGGCGATGCGAACTAGACGTGGAGAAGTACATGCGTCCCATGCGCCTTACAATCAGCGTATCTAAGCACCGATCAGTGAAATATGTCATACAAAACAATAGTGCAAGACGACAGCGAATGAGAGGCTACTGACGGCAGTGGGGGGTCAGGGAATACGTTGTAAACCAATGACTCACGAGGTGGACGGTCTACGTAGGCGGGCATGGGACTTTATCGCTGTCAACGCCTTTTCTATTGATACCAAAGGCTAAATGCAATGGCCAGTGATGGCCGATCGTTGTGGACATATAGGACACCG
-17 GTTGCTATCGAGGATCGGTGCTGATTGCGAGCAGTATCCTACAAGGTTCTCTAGTTCGAGAAAATGGTACGGCCATGCCAACCAGGCGTGGGCAGTCACATGCTTGCTATGGGCCCGACAATTAGCGTATGTAAGTACTGATCAGCGAAGTGTGTCGTACAAAACAATAGTGCAGGATGACGACGAATGAGAGACCACTGACGGCAGTGGAGGGCCAGAAAATGCTTTGTAAACCGATGGCTCGCGGAGTGGACAGTCCACGTAGGCGGACATTGGTCGTTATCGCTCTCGACACCCTTTCTCTTGATACAAAGGGCTAAATTCAATGGACAGGAATGACCGATCGTTGTGGACATATAGGACACCA
-14 GTTGCTGTCGAGGATCGGTGCGGGTTGCGAGCGATATCCTACGCAGTTCTTTAAGTCGAGAAAGTGGTGCGGCGATGCGAATCAGGCGTGAAAGAGTACATGCTTGCCATACGCCTGACAATCAGCCTATCTAAGTACTAAACGACGGAGTATGTCATATAAAACAATAGTGCAGGACGACGGCGAATGAGAGGCTACTGACGTCAGTGGGGGGGCAAGAAATGCGTTGTAAACCAATGGCTCACGAAGTAACCGGTCCACGTAGGCGGGCATAGGACGTTATCGCTTCAAACGCCCTTTCTGTTGATACCAAAGGCTAAATTCAATGACCGGTGATGGCCGACCGTTGTGGACATATAGGACACCA
-33 GGTGCTATCGAAGGTCGGTGCGGGTTGCGAGCAATATCCTACGGAGTTCCTTGACTCGAAAGAGGGGTGCGGCTATGTGAACCAGGCGTGGAAAAGGATATGCTTGGCATACGCCTGACGATCAGCCTATCTGAGTACTAATCACCAAAGTATGCCATATAAGATGATAGTGCAAGACGACAGCGAATGAGAGACTACTGGCGCTAGTGGGGGGGCATGGAACACGTTGGAAACCAATGATTCACGAAGTGGTCGCTCCACGTAGGTGGGCATAAGAGTTTATTTCTTTCGACGCCCTTTCTGTTGATACCAAAGACTAAATTCAATGACTGGTGATGTCCGATCGGTGTGGACATGTGAGAGACCA
-6 GTTGCTATCGAAGATCGGTGCAGGTTGCGAGCGATATCCGACGAAGTTCTTTGATTCGAGAAAGGGGTGCGGCGATGTGAGACAGGCGTGAAAAAGGACATGCTTTCCATACACCTGACGATCAGCTTATCTAAGGACTAATCGACGAAGTACGTCATATAAGATAATAGTGTGAGACGACGGCGAATGAGAGGCTGCTGGCGCTAGTGGGGGGTCAGGGAATACGTTGGAAACCAATGACTCACGAAGCGATCGCTCCACGTAGGCGGGCATAGGAGTTTATCTCTTTCGGCGCCCTTTCTGTTGATACCAAAGGCTTAATTCAATGACTAGTGATGGGCGGTCGGTATGGACATATAGGAAACCG
-22 GTTGCTATCGAAGATCGGGGCAGGTTGCGGGCAATATCCTACGGAGTTCCTTAATTCGACAAAGCGGCGCGGCGATGTGAAGCAGGCGTGGAAAAGGACACGCTTGGCATATGCCTAACTATCAGCCTATCTAAGGACTAAGCAACGAAGTATGTCGTAGAAGATAGTAGTGCAGAATGACAGGAAATCAGAGGCCACTGGCGTTAGCGGGGGGTCAGGCAATGCGTTGAAAACCAATGACTCACAAAGTGATCGTTCTGCGTAGGCGGACATGGGGCCTTATCCCTTTCGACGCCCTTTCCGTTAGTACCGAAGCCTAAATTCAATGACCAGTGATGGCCCATCGGTGTGGACATATAGCAAACCA
-84 GTTACTATCAAAGATCGGGGCAGGTCACGGGTAATATCCTACGGAGTTCCTTAATTCGACAAAGAGGTGCGGCGATGAGAACCAGGGGTGGAAAACCACATGCTTGCCATATGCCTGACTATCAGCCTATCTACGGACTAACCAACAAAGTATGTCGTAGAAGAGAGTAGTACAAGACGACGGCGAATGAGAGGCTACTGGTGCTAGTGGGGGGTCAGGCAATGCGTTGGAAACCAATGACTCACGAAGTGATCGTTCCACGTAGGCGGACATAGGACCTTATCTCTTTCAACGCCCTTTCCGTTGGTACCGAAGCCTAAATTCAATGACCGGTAATGGCCGATCGGTGTGGACATATAGTAAACCA
-54 GTTGCTATCGAAGATCGGGGCAGGTTGCGGGCAATATCCTACGGAGTTCTTCAATTCGATAGAGCGGTGCGGCGATGTGAACCAGGCGTGAAAAACAACATGCTTGCCACATACCTAACTATCAGCCTATCTAAGTACTAATCAACGATGTATGTCGTAAGAGACAGTAGTGGAAGATGACCGCGAATGAGAGGCTACTGGCGGTAGTGGAGGGTCAGGCAATGCGTTGGGAACCAATGGCTCACGAAGTGATCGTTTCACGTAGGCGGATATAGGACCTTGTCTGTTTCAACGCCCTCTTCGTTAGTACCAAAGCCTAAATGCAATGACCGGTAATGGCCGATCGGTATGGACATATAGTAAACCG
-19 GTTGCTATCGAAGATCGGGGCAGGTTGCGGGCAATATCCTACGGAGTTCCTCAATTCGATAGAGCAGTGCGGCGATGTGAACCAGGCGTGAAAAAGGACATGCTTGCCACATGCCTGACTATCAGCCTATTTAAGGACTAATCAACGAAGTATGTCGTAAGAGACAGTAGTGAAAGATGACGGCGAATGAGAGGCTACTGGCGCTAGTGGGGGGTCAGGCAATGCGTTGGGAACCAATGACTCACGAAGTGATCGTTTTACGTAGGCGGACATAGGACCTTATCTGTTCCAACGCCCTTTCCGTTGGTACCAAAGCCTAAATTCAATGACCTGTAATGGCCGATCGGTGTGAACATATAGTAAACCT
-47 GTAGCTATTGAAGATCGAAGCGGGTTGCGGGCAGTATCCTACGGAGTTCCTTAGTTTGACAGAGCGGTACGGCGATGTGAGCCAGGCGTGAACGAGCAGAAGCTTCCCATATGCCTAACTACCAGCCTGTCTAAGAACTAACCAACAAGGTATGTCGTAAAAGATAATAGTACAAAACGACGGCGAATAGGAGGCTACTGGCCCTAGTGGTGGGTCAGGCGATGCGTTGGAAACCTATGCTTCACGAAGGAATCGTTTCGGGTAGGTGAACATAGAGCCTTATCTCTCTCAACGCCCTTTCCGCTTGTACCAAGGCCTAAACTCAATGACAGGTAATGCCCGATCGTTGCGGACATATAGTAAACCA
-50 GTTGCTATCGAAGATCGAAGTAGGTTGCGGGCAACATCCTACGGAGTGCCTTAATTCGATAAAGCGGTACGGCGATGTGAACCAGACGTGAAAAAGCACATGCTTACCATATGCCTAACTATTAGCCTATCTAACGACTAACCAAGGAGGTATGTCGTAAAAGATAATAGTGCAAGACGACAGCAAATGGGAGGCTACTGGCGCTAGTGGGGGGTCAGGCAGTGCGTTGGAAACCCATGCCTCACCAAGTGATCGTTCCGGGTAGGTGGACATAGGGCGTTATCTCTCTCGACGCCCTTTTCGTTTGTACGCAGGCCTAGATTCAATGACCGGTAATGGCCGATCGTTGTGGACATATGGTAAATCA
-77 GCTGCTACCGAAGATCGAAGCAGGTTACGGGCAATATCCTACGGAGTTCCTTAATTTGATAGAGCGGTACGGCGATGCGAACCAGGCGTGAAAAAGCACATGCTTACCATATACCTAACTATCAGCCTATCTAAGGACTAACCAACAAAGTATGTCGTAAAAGACAATAGTGCAGGACGACAGCGAATGGGAAGCTACTGGCACTAGTGGGGGGCCAAGCAGTGCGTTGGAAACCCATGGTTTACGGAGTGATCCTTCCGGATAGGTGGACATAGTACCTTATCTCTCTCCACGCCCTTTCCGTTTGTACTAAAGCCTAGATTCAATGACCGGTAATGGCCGATCGTTGTGGACATATAGTAAACCA
-21 AATACTAGCATATGGGGCTGGCGGTTACGGCCAACATCTCACACAGCTCCATCAGTCGAAAAACGGGTCCAGTCATCACAACCAGGCGTAGAAAAGGACACTTTTATCACAAACCCCACAACCAGCCCAAGTGAATACCCATCGAAAAAATGTAACATAAAGGATAGCGACGCAAGAGGGCAAGGATCGAGAAGCCCCTGGAGGCAGTGAGAGAGCAGCGAGTTCAGTGTGGACCCATACGTCCCTAAGTAAACCTTTGACGAACTAGGGCATGAAAAAGTATCTGTTTCGACACTCTGTAAGGTCGTGCAAAGGGTTGAATTCAGCGGCCGATAAGGACCGATCGCTTCGCACGAAGGAAGCGTCA
-92 AATACTAGCACATGGGGCTGGCGGTTACGGCTAACATCTCACACAGCTCCGTCAGTCGAAAAACGGGTCCAGTTATCACAACCAGGCGTGGAAAAGCGCACTTTTATCACAAACCCCACAACCAGCCCAAGTAAATACCGATCGAAAAAATGTAACATAGAGGACAGCAATGCAAGAGGGCAAAGATCGAGAAGCCCCTGGAGACATTGAGGGAGCAGCGAGTTCGGTGGGGACCCATACGTCCCTAAGTAAGCCTTTGACGAACTAGGACATAAAGGGGTATCTGTGTCGACACTCTGTAGGGTCGTGCAGAAGGTTGAATTCAGCGGCCGATAAGGACCGATCGCTTCGCACGGAGGAAGTGTCA
-2 AATACTAGCACATGGGGCTGGCGGTTACGGCCAACATCTCACACAGCTCCGTGGGTCGAAAAACGGGTCCAGTCAGCACAACCAGGCGTGGAAGAGGACACTTTTATCACAAACCCCACAACCAGCCCAAGTGAATACCGATCGAAAAAATGTAACATAGAGGATAGCAACGCAAGAGGGCAAGAATCGAGAAGCCCCTGGAGACAGTGAGAGGGCAGCGAGTTCGGTGTGGACCCATACGTCCCTAAGTAAGCCTTTGACGAACTAGGACATAAAAGGGTATCTGTTTCGACACTCCGTAAGGTCGTGCAAAGGGTTGAATTCAGCGGCGGATAAGGACCGATCGCTTCGCACGGAGGAAGTGTCA
-64 AATACTAACACAGGGGGCTGGCGGTTACGGCCAACATCTCACACAGCTCTGTCAGTCGAAAAACGGGTCCAGTCATCACAACCAGGCGTGGAAAAGGACACTTTTATAACAAACCCCACAACCAGCCTAGGTGAAGACCGATCGAAAAAATGTAACATAAAGGATAGCAACGTAAGAGGGCAATGATCGAGAGGCCCCTAGAGCCAGTGAGAGATCAGCGAGTTCGGTGTGGACCCATACGTCCCTAAGTAAACCTTTGACGAACTAGGACATAAGCGAGTATCTCTTTCGACACTCTGTAAGGTCGTGCAAAGGGTTGAATTCAGTGGCCGATAAGGACCGATCGCTTCGCACGGAGAAAGCGTCG
-81 AATACTAACACAGGGGACTGGCGGTTACGGCCAGCATCTTACACAGCTCTGTCAGTCGAAAAACGGGTCCAGTCATCACAACCAGGCGTGGAAAAGGACACTTTTATAACAAACCCCACAACCAGCCTAGGTGAAGACCGATCGAAAAAATGTAACATAAAGGACAGCAACGTAAGAGGGCAAGGATCGAGAGGCCCCTAGAGCCAGTGAAAGATCAGCGAGTCCGGTGTGGACCCATACGTCCCTAAGTAAACCTTTGACGAACTAGGACATAAACGAGTATCTCTTTCGACACTCTGTAAGGTCGTGCAAAGGGTTGAATTCAGTGGCCGATGAGGACCGATCGCTTCGCACGGAGAAAGCGTCG
-100 AATACTAACACAGGGGGCTGGCGGTTACGGCCAACATCTCACACAGCTCTGTCAGTCGAAAAACGGGTACAGTCATCACAACCAGGTGTGGAAAAGGACACTTTTACAACAAACCCCACAACCAGCCTAGGTGAAGACCGATCGAAAAAATGTAACATAAAGGATAGCAACGTAAGAGGGCAAGGATCGAGAGGCCCCTAGAGCCAGTGAGAGATCAGCGAGTTCGGTGTGGACCCATACGTCCCTAAGTAAACGTTTGACGAACTAGGACATAAACGAGTATCTCTTTCGACACTCTGTAAGGTCGTGCAAAGGGTTGAATTCAGTGGCCGATAAGGACCGATCGCTTCGCACGGAGAAAGCGTCG
-34 AATACTGGCACAGGGAGCCGGCAGTTACGGGCAACATCTCACACAGCTCTGTCGCTCGAAAAACAGGTCCAGTTATCACAACCAGGCGTGGGAAAGGACACTTTTATCACAAACCTTACAACCAGCCCAACTGAAGACCCATCGAGAAGATGTAACATAAAGGATAGCAACGCAAGAGGGCGAGGATCGGGAGGCCCCTGGCGCCAGTGAGAGAGTAGCGAGTTCGGTGTGAACCGATACATCCCTAAGTAAACCTTTGACGAACTAGGACATAAACGAGTATCTCTTTCGACACCCTATAAGGTCGTGCAGACGGTTAAATTCAGTGGCTGATAAGGACCGATCGCTTCGCACGGAGAAAGTGTCG
-58 AATACTGGCACAGGGGGCCGGCTGTTACGGGCAACATCTCACACAGCTCTGTTGCTCGAAAAACAGGTCCAGTCATCACAACCAGGCGTGGGAAAGGACACTCTTATCACAAACCTCACAACCAGCCCAAGTGAAGACCGATCGAGAAAATGTAACATAAAGGATAGCAACGCAAGAGGGCAAGGATCGGGAGGCCCCTGGCGCCAGTGAGAGAGCAGCGAGTTCGGTGTGAACCCATACATCCCTAAGTAAACCTTTGACGAACTAGGACAGAAACGAGTATCTCTTTCGACACCCTGTAAGGTCGTGCAAAGGGTTAAATTCAGTGGCTGATAAGGACCGATCGCTTCGCACGGAGAAAGTGTCA
-37 GATACTCACACGGGGGGCCGGCGGTCGCGAGCAACATCTAACGCAGCTTTATATTTCAATAGACGGGTCCAGTCATCGCAAGCAGGCGTGAGAAAGTACACTCTTATCACAAACCGCACAAACAGCCCAGGTGAAGACCAATCGAGGAAGTGTGATATAGATGATAGCAACGTAGGAGGGCAAGAATCGGGACGCTCCTGGCGTCAGTGAGCGACTAGCGGGTACGGTGTGAACCTAGACATCCCTAAGTAAACGTTTGACGGACCAGGACATAAATGAGTATCTCTTTCAACACCCCGTAAGGTCGTGCAGAGGGTTAGATCCAGTGATTTATGAGGGCCCATCGCTGCGCACGAAGGAAGCGTCC
-88 AAAACTAGCACAGGAGGCCGGCGGTTACGGGCGGCATCTCACACAGTTGTGTGGCTCGAAAAACAGGCCCAGTCATCACAACCAGGCGTGGGAAGGAACATTCTTGTCACAAACCTCACAACCAGCCCGAGTGGAGACCGATCGAGCAAATGTGACATAAAGGATAGTAACGCAAGAGGGCAAGAATCCGGAGGCTCCTGGCGTCAGTGAGAGAACAGCGAGTTCGGTGTGAACCCATACATCCCTAAGTGCGCCTTTGACGGACCAGGACATAAAGGAGTATCTGTTTCGACACCCTGTAAGGTCGTGCAAAGGGTTAAATCCAGTGGTTGATTAGGATCGATCTCTTCGGACGGAGAAAGCGTCA
-53 GAGACTACCACAGGAGGCCGGCGGTTACGGGCAGCATCTCACACAGTTGTGTGGCTCGACAAACAGGTCCAGTCATCACAACCAGGCGTGAGAAGGGTCATTCTTGGCACAAACCTCACGACCAGCCCAAGTGGAGACCGATCGAGCAAATGTGACATAAAGGATAGCAACGCAAGAGGGCAAGAATCCGGAGGCTCCTGGCGTCAGTGAGAGAACAGCGAGTTCGGTGTGAACCCATACATCCCTAAGTAGGCCTTTGACGGACCAAGACATAAACGAGTATCTGTTTCGACACCCTGTAAGGTCGTGCAAAGGGTTAAGTCCAGTGGTTGATGAGGACCGATCTCTTCGGACGGAGGAAGCGTCA
-42 ACAACTAGCACAGGGGGCCGAAGGGTACGGGCAGCATCTCACATAGTCCTTTCGTTCAGGAGACAGGTCCAGTCATTATAACCAGGCGTGAGAAGGGACATTCTTTTCACAAACCCCACAACCAGCCCAAGTAGAGACCGATCAAACAAATGTGATATAAAAGACAGCAATGCACAATGGTAAGAATGCGGAGGTTACTGGCGACAGTGAAAGAACAACGAGTTCACTGTGATTCCATGCATCCCTAAGTGAACCTTTTACTGATCGTGACATGAAGGAGTCTCTGTTTCGACGCCCTGTAAGGTCATGCGGGTGGTTAAATCCAGTGGTTAATTAGGGCCGATCTCTTTGGACGGAGGAAGCGTCA
-46 ACAACTAGCACAGGGGGCCGAAGGGTACGGGCAGCATCTCACATGGTCCTTTCGTTCAGGAGACAGGTCCAGTCATTATAACTAGGCGTGAGAAGGGACATTCTTCTCACAAACCCTACAACCAGCCCAAGTAGAAACCGATCAAACAAATGTGGTATAGAAGACAGCAATGCAGAATGGCAAGGATCCGGAGGTTACTGGCGACAGTGAGAGAACAACGAGTTCACTGTGACTCCATGCATCCCTAAGTGGACCTTTTACTAACCGTGACATGAAGGAGTCTCTGTTTCGACGCCCTGTAAGGTCATGCGGGAGGTTAAATGCAGTGGTTAATTAGGGCCGATCTCTTTGGATGGAGGAAGCGTCA
-90 AGTACTGGCACAGGGAGCCGGGGGTTAGAAGCAACATCTAACACAGCTCTGTGACTGGAAAAACAGGCCCAGTCATCCCAACCAGACGTAAGGAAGGACACTTCTGCGACAGACCTTACAACAGGCCCAAGTCAAGACTGATCGAAACAATGTGACATAAAAGACAGCGACGGAAGAGGGCAAGGATCGGGAGGCTCCTGGCGACAGCGAAAGAACAGTAAATTCGGTGTGAACCCATACATCCCTAAGTAGGCCTTTAAAGGACCAGGGCATGAATAAGTATCTCTTTCGACACCGTATGAGGTCGTGCAAAGGGTTAAATTCAGTGATTGATAAGGGTCGATCGCTTCGCACGTAGGAGGTGCCA
-85 AGTACTGGCACAGGGAGTGGGGGGTTACAAGCAACATCTAACAGAGCTCTGTGGCTGGAAAAACAGGCCCAGTCATCCCAACCAGACGTAAGGGAGGACACTTCTGCGGCAGACCTTACAACAAGCCCAAGTCAAAACTAATCGAAATAATGTGAAATAGAAGACAGCGACGTAAGGGGGCAAGGATCCGGAGGCTCCTGGCGACAGCGAAAGAACAGTAAATCCGGTGTGAACCTATAGATCCCTGAGTGGGCATTTAAGGGACCAGGGCATAAATAAGTATCTCTTTCGACACGGTATGAGGTCGTGCAGAGGGTTAAAGTCAGTGATTAATAAGGATCGATCGCTTCGCACGTAGGAAGTGCCA
-82 AATGCTGGCACAGGCAGCCGGGGGTTACAAGCAATATCTAACACAGCTCTGTGACTGGAAAAACGAGCCCAGTGATCTCAACCAGAGGTAAGGAAGGACACTTCTACGACAGACCTTACAACAAGCCCAAGTCAAAACTGATCGAAGCAGTGTGACATAAAAGACAGAGACGGAGGGGGGCAAGGATCGGGAGGCTCCTGGCGGCAGGGAAAGAACGGTAAATTCAATGTGGACCCATATATCCCTAAGTAGGCCTTTAAGGTACCAGGGCATAGAGGAGTATCTCTTTCGGCACCGTATGGGGTCGTGCAAAGGGTTAAATTCAGTGATTAATAAGGGTCGATCGCTTCGCACGTAAGAAGTGCCA
-62 AATGCTAGCACAGATAGCCGTGGGTCGCAATCAACATCTAACAGAGCTTCATGGCTGGTAAGACGGGCCCAGTCATCCCAGCCAAACGTAGGGAAGAACACGTCTTCAACGAACCTTACAACAAGCCCAATTTAACACCGATCACGACGATGGGACACAGAGGACACCGACGAAAGAGGGCCAGAACTTGGAGGCTTCCGGCCTCAGCGAAAGAACAGTAAATCCGGTGTGGACCCATACCTCCACGAGTAATCGAGTAAGAGACCCGGGCATGAATGAGCATCTCTTTCGACACCGTATGGGGTCGTGCGGAAGCCTGAATTCAGTGATTGAAAAAGGTCGACCGCTTCGCACGCGGAAAGTGCCG
-57 GACACTGGCACAGAGAGCCGGGGGTTACAAGCAGCATCTAACATAGCTCTGTAGCTGGAAAAACGGGCCCAGACATCTCAAGCAGACGTACGAAAGGACACCTCTGCGACAGACCTTACAACGAGCCCAAGTCAAGACTGATCGACACAATGTGGCAAAAAAAACAGCGACGGAAGAGGGCGAGGATCGAGGGGCTCCTCGTGGCAGCGAAAGAACAGTAAATTCGGTGTGAACCTATACATCCCTAAGTGGGCCTTTAAAGGACCAGGGCATAAAAGAGTATCTCTTTCAACACCGTATGAGGTTGTGCAAAGGGTTAAACTCAGTGATTAATAAAGGTCGATCGCTTCGCACGTAGAAAGTGCCA
-13 AATACTGCCGCAAGAAGCGGGGGGTTGCAGGCAACATCTAAAATAGTTCTGTGGCTAGAAAAACCCGCCCAGTCATCTCAACCAGACGTAGGGAAGGACACTTCTCCGACACGCCGTACCGCAAGCCCAAGTCAAAACTGATCGACACAATCTGACATAAAAGACAGCGACGGAAGATGACAAGGATCGTGAGGCTCCTGGCGACAGCGAAAGAACAATAAGTTCGGTGGGAGCCCATACATCGCTAAGTGGGCCTTTGAGTGACCCGGGCATAAACGAGTATCTCTCGCGACACCGTATGAGGTCGTGCAAAGGGTTAAATTCAGTGATTAATAAAAGTCAAGCGCTCCGCACGTAGGAAGTGCCC
-59 GATACTAGCGCAGGAAGCGAGGGGTTGCAGGCAACATCTAAAATAGTTGTGTGGCTAGAGAAACACGCCCAGTTATCTCAACCAGAGGTAAGGAAGGAAACTTCTGCGACAGGCCGTACTACAAGCCCAAGTCAAGACTGATCGACACAATCTAACATAAAAGACAGCGACGTAAGAGGACAAGGATCGTGAGGCTCCTGGCGACAGCGAAAGAACAGTAAGTTCAGTGGGAGCCCATACGTCGCTAAATAGGCCTTTAAGGGACCCGGGCATAAACGAGTATCTCTTGCGACACCGTATGAGGTCGTGCAAAGGGTTAAATTCAGTGATTAATAAGGTTCAAGCGCTCCGCACGTAGGAAGCGCCG
-18 AATACTTTCACAGGAAGCAGGGAGTTGCAAGCAACATCTAACACAGCTCTGTGACTGGAAAGACAGATCCAGTCATCTCAACCAGACGTAGGGAAGAACATTTCTGCGACAGACCTTACAACAGGCCCGAGTCAAAACTGATCGAGACAATCTGACATAAAAGACAGCGACGGAAGAGGGCAAGGAGCGTGAGGCTCCTGGCGGCAGCGAAAGAACAGTAAATTCGGTGAGAACCGATAAACCGCTAAGTAGGCCTTTGAGGGACCATGGCATAAGTGACTATCTCTTTCCACACCGTATGAGGTCGTGCAAAGGGTTAAATTCAGTGATTAATAAGGATCGATCGCTCCGCACGTAGGAAGTGCCA
-67 AGTGCTGGCACAGGAAGGCGGCGGCTACAAGCAACATTTCACACGGCTCTGTAACTGGAGAAACAGGTCCAATCATCGCAACCAGGCGTGGGTAAGTACACTTTCGCGACAGACCTTACAAGAAGCCCAAGTCAACACCTATCAAGAAGATGTGACGTAGGGGAAAGTGACGGAAAAGTGCAAGGATCGGGAGGCGCTTGGCGTCAGCGAAAGGACGGTAAATTCGGTGTGAACCAATACATCCCTAAGCGAACCTTCCAGGAACCAGGGCACAAAGGAGTATCTCTTTCAACACTGTGTGGAGTCGTGCAACGGGTTGAATCCAGTGGTTGATGAGGGTCGATCGGTTCGCACGGAGGAAGTTTCG
-69 AATACTGGCACAGGAAGGCGGCGGCTACAAGCAACATTTCACACGGCTTTGTAACTGGAAAAACAGGTCCAATCATCACAACCAGACGTGGGTAAGCATACTTTCGCAACAGACCTTACAAGAAGCCCAAGTCAACACCTATCGAGAAGATGTGACGTAGGGGAAAGTGACGGAAAAGTGCCAGGATCGGGAGGCGCTTGGCGTTAGCGAAAGGACAGTGAATGCAGTGTAAACCAATATGTCCCTAAGCGAACCTTACAGGAACCAGGGCATAAAGGGGTATCTCTTTCAACACTGTGTGGAGTCGTTCGACGGGTTGAATCCAGTGGTTGATTAGGGGCGATCGGTTCGCACGGAGGAAGTGTCG
-8 AATGCTGGCACAGCAAGCTGGCGGTTACAAGCAACATTTCACACAGCTCTACGGCTGGAGAAACAGGTTCAGTCATCGCAACCAGGCGTGAGGGAGAACACTTTCGCTACAGACCTTACAGCAAGCCCAAGTCAAGACCTATCGAGGAAATGTGACGTAGAGGACAGTGACGGAAGACGGCAAGGATCGGGAGCCTCCTAGCGGCAACGAAAGAACGGTAAATTCGGTGTGAACCAATACATCCCTAAGCAGACCTTTGAGGGACCAGGGCATCAGGGAGTATCTCTTTCAACACCGTATGAGGTCGTGCAAAGGGTTGAATCCAGTGGTTAATAAGGGTCGATCGCTTCGCACGGAGGAAGTGTCG
-16 GACGCTGGCACAGGAAGCCGGCGGTTGCAAGCAGCATCGTACATAGCTCCGTGCCTGGGCAAACAGTTTCAGTCATCGTAACCAGGCGTGAGGAAAGACACTTTTATCGCACACCTGACAACAAGCCCAATTCAAGACCGACCGAGAAAATGTGACCTAAAAGAGAGCAACGTAAGAGGGCAAGAATCGGGAGGCTCCTGGCGTCAGCGGAAGAACAGCAAATTCGGTGTGAGCCTATATGTCTCCAAGTAGACCTTTAGGAGACTAGGGCATAAACGAGTGTCTCTGCCGACACGGTATGAGGTCGTGTGGAAGGTTAAATCCAGTGGTTGATAAGGGTCGATCGCTTTGCACGTAGGAAGCGCCA
-70 GACGCTGGCACAGGAAGCCGGCGGTTGCAAGCAGCATCGTACATAGCTCCGTGCCTGGGCAAACAGTTTCAGTCATCGTAACCAGGCGTGAGGAAAGACACTTTTATCACACACCTGACAACAAGCCCAATTCAAGACCGACCGAGAAAATGTGACCTAAAAGATAGCAACGTAAGAGGGCAAGAATCGGGAGGCTCCTGGCGTCAGCGGAAGAACAGCAAATTCGGTGTGAGCCTATATGTCTCCAAGTAGACCTTTAGGAGACTAGGGCATAAACGAGTGTCTCTGCCGACACGGTATGAGGTCGTGTGGAAGGTTAAATCCAGTGGTTGATAAGGGTCGATCGCTTTGCACGTAGGAAGCGCCA
-7 AATACTGGCACAGGAAGCCGGCAGTTGCAAGCAGCATCGCACACAGCTCCGTGGCTGGGTAGACAGTTCCAGTCATCAGAACCAGGCGTGAGGAAGGACACTTTTGCCACACACCTGACAACAAGCCCAATTCAAAACCGATCGAGAAAATGTGATCTAAAGAAGAGCAACGTAAGAGGGCAAGAATCGGGAGGCTCCTGGCGCCAGCGGAAGAACGGCAAATTCGGTATGAACCCATATGTCTCTAAGTAGACCTTTAAGGGACCAGGGCATAGACGAGTATCTCTTTCGACACCGTATGAGGTCGTGTGAAAGGTTAAATCCAGTGGTTAATAAGGGTCGATCGCTTTGCACGTAGGAAGTGCCA
-35 AATACTGACACAGGAAGCCCGTGGGTGGAAGCAGCATCGCGCACAGGTCCGTGGTTGGAAAGACAGTTCCAGTCATCTCACCCAGACGTCAGTAGGGACACTTTTGCCACACACCCGACAACGAGCGCAAGTCAAGACCAATCGAGAAGATGTCGCCTAGAGGATAGCAACGGAAGAGGGCAAACACCAAGAGGCTCCTGGCGTTAGCGGCAGAACGGTAAGTTCAGTGTGAACCGATACGGCCCTTAGTAACCCTTTAAAGGACTAGGGCATAGGTGCGTATCTCTTTCAACACAGTATGAGGTGGTGTAAAGGGTTAAATCCAGTGGCTAATAAGGGCCGATCGTTTTGCACGTAGGAAGTGCCG
-9 AATACTGGCACAGGAAGCCCGCGGGTGCAAGCAGCATCGCACACAGCTCCGTGGTTGGAAAGACAGTTCCAGTCATCGCACCCAGGCGTGAGGAGGGACACTTTTACCACACACCCGACAACAAGCGCAAGTCAAGACCGATCGAGAAGATGTGACCTAAAGGATAGCAACGGAAGAGGGCAAGTATCAGGAGGCTCCTGGCGTTAGCGGCAGAACAGTAAATTCAGTGTGAACCCATATGTCCCTGAGTAGACCTTTAAAGGACTAGGGCATAGATGAGTATCTCTTTCGACACCGTATGAGGTGGTGTAAAGGGTTAAATCCAGTGGTTAATGAGGGTCGATCGTTTTGCACGTAGGAAGTGCCG
-93 AACACTGGCACAGGAAGCCGGCGGTTGCAAGCTGCATCGCACACAGCTCCGTGACTGGAAAGACAGTTCCAGTCATCGCAACCAGGCGTGAGGGAGGACACTTTTGCCACACACCTGACAACAAGCCCAAGTTAAGACCGATCGAGAAAATGTGAGCTAAAGGATAGTAACGGAAGAGGGCAAGAATCGGGAGGCTCCTAGCGGCAGCGGAAGAACAGTAAATTCGGTGTGAACCAATATGTCCCTAAGTAGACCTTTAAGGGACTAGGACATAGATGAGTATCTTTTTCGACACCGTATGACGTCGTGTGAAGGGTTAAATCCAGTGGTTAATAAGGGTCGATCGCTTTGCACGTGGGAAGTGCCA
-56 AACAGTAGCATAGGAAGCCGGAAGTTGGAAGCGGCATCTAATCCAAGAGAATAACTGTGGAGACTGACCCAGTGATCGCAATCAGATGTGAGGAAGCAGAGTTCTGCTATAGACCCAACGATGAGTCCGGATAGAAACCGATCTAAGGAATGTGGCATAAACAACAACAACAGAGCAGGGCAAAGACCGCGAGGCTCCTGGTGTCAGGGATGGAACAATAAACCCGGAGTACGGCTATACCTCCCTAGACAAACTTTTAAGGGACCACAGCACGAACGTGTATCGCTCGCTACGCTGTATGAGGTCATGCAAAAGGTTAAATCCAGTGGCTCACGATTGTCGATCGTTTAGCGGGATGGACGGGCCA
-51 AATACTGGCATCGGAGGCAGCCGCTTACAAGCAACATCTCACACAGCTCTATTGCTGGAGAAACAGGTGCAGTCATCACAACGAGGCGTGGGAAAGCACAATTTTACCACAGACCCGACAACAAGCCCCAGTCAACACCGATCAAGGCTATGTGATGTATACGACAGCAACGGAAGAGGGCAAGAATCGGGAGGCTTCTGGCGACATCGAAAGAACAATAAAATTGGTGGGAGCCCATACGTCCCTAAGTATACCTTTAAGGGACCGGGGCATAAACGGGTACCTCTTTCGACACCGTATGAGGTCGTGCAAAAGGTTAGATCCAGTGGCTTATAAGTGTCGATCGCTTCGCACAGAGGAGGTGCCA
-87 GACACTAGCACAGGGAGCTGGGGTTTACAAGGGACATCATACACAGCTCTGTTACTGGAAAAATGGGTCCAGTCATCCCAGCCAGGCGCGTGGAAGTGCACTTTCACAGCACACCTGACAACAGGCCCCAGTCAAGACCGACCGCCGACATGTGGCATAGAAGACAGCAACGGAAGAGGGCGAGGATCGAGAGGCTCCTAGTGGCAGCGAAAGAACAATAAACTCGATGTGAGCCGATAGGTCCCTAAGTATACCATTAAGGGACCAACACATGACTGCGTAGCTCTTTCAACGCCGTATGAGGTCGTGCAAAAGGTTAAACCCAGGGGCGAGTAACTATCAATCGCTTCGCACGTGATGGGCGCTG
-1 AACACTAGCACAGGGCGCAGGGGGTTGCAAGGGACATCATACACAGTTCTGTTCCTGGAGAAACAGATCCAGTCATCGCAACCAGGCGTGAGGAAGGACACTTTTACTGCACACCTGACAACGAGCCCCCGTCAAGACCGACCGCGAACATGTGGCATAGAAGACAGCAACGGGAAAGGGCAAGGATCGAGAGGCTCCTGGTGGCAGCGAAAGAACAATAAATTCAATGTGAGCCCATACATCCCTAAGTATACCCTTAAGGGACCAGCACATGATGGCGTATCTCTTGCGACACGGTATAAGGTCGTGCAAAAGGTTAAATCCAGTGGCCAGTAAGTATCGATCGCTTCGCACGTAGTGAGTGCGA
-79 AACACTGGCACAGGAAGCAGGCGGTTACAAGGAACATCTAACACAGCTCTGTTGCTGGAAAAACAGGTCCAGTCATCGCAACCAGGTGTGAGAAAGGACAGTTTTACCGCAGACCTGACAACAAGCCCCGGTCAAGACCGATCGAGAAAATGTGCCGTAAAGGACAGCAACGGAAGAGGGCAAGGATCGAGAGGCTTCTGGCGTCGGCGAAAGAACGGTAAATTCGATGTGAACCCATACATCCCTAAGTATACGGTTAAGGGACCAGGGCATGAACGCGTATGTCTTTTGACACCGTATGAGGTCGTGCAAAGGGTTAAATCCAGTGGTTAATAAGTGTCGATCGCTTCGCACGGAGGAGGCGCCG
-61 AAGTCTGGCACAGGAAGCAGGTGGTTACAAGCAACATCTCACACAGCTCTGTTGTTGAAGAAACTGGCTCAGTTATCGCAAGCAGGCGTGGAGAAGGACAGTTTTACCGCAGCCCCGACAACAAGCTCCGGTCAATACCGATCGAGAAAATGCGGTATAAAGGACAGCAACGGAACAGGGCGAGGATCGGGAGGCTATTGGCGGCAGAGAAAGAACAGTAAATTCGATGTGAAGCCATACATCTCTAAGTAGACCTTTAAGGGACCAGGGTAGAAACGCGTATCTCTTTCGACACTGTATGAGGTCGTGCAAAGGGTTAAATCCAGTGGCTAATAAATGCCGATCGCTTCGCACGGAGGAGGTGCCA
-4 AAGTCTGGCACAGGAAGCAGGCGGTTACAAGCAACATCTCACACAGCTCTGTTGTTGAAGAAACAGGCTCAGTCATCACAAGCAGGCGTGGGGAAGGACAGTTTTACCGCAGCCCTGACAACAAGCTCCGGTCAATACCGATCGAGAAAATGTGGTATAAAGGACAGCAACGGAGCAGGGCGAGGATCGGGAGGCTACTGGCGCCAGAGAAAGAACAGTAAACTCGATGTGAACCCATACATCTCTAAGTACACCTTTAAGGGACCAGGGTAGAAACGTGTATCTCTTTCGACACTGTGTGAGGTCGTGCAAAGGGTTAAATCCAGTGGCTAATAAATGCCGATCGCTTCGCACGGAGGAGGTGCCA
-72 AAGACTGGCAAAGGAAGCAGGCGGTAAGAAGCAACATCCCACACAGCTCTATTGCTGAAGAGACGGGTTCAGTTATCGCAACCAGGCGTGAGGAGGGACGGTTTTGCCGCAACCCTGACAACAAGCTCCGGTCGAGACCGATCAAAGAAATGTGGTATAAATGACAGCGACGGAGCAGGGCGAGAACCCGGAGGCCGTTGGCGGCAGGGAAAGAATAGTAAATTCAATGTGAACCCATACATCTCTAAGTAGGCGTTCAATGGACCAGGGTAGGAAAGGGTATCTTTTTCGACACTGTGTAAGGTCGTGCAGAGGGTTGAATTCAGTGGCGGACAAATGGCGATCGCTTCGCACGGAAATAATGTGA
-29 GACGCTTGCGGAGGATTCGAAGGGTTGCAACCAGCGTGCAACTCAGTTGTGTCCTCGGGTAAACAAATCCAGTCATCGGAGCCAGGCGTACGACAGAACACTGTAAGCGTAGACCTTACCACAGGCCGCGGTAAAAACTAAGCGGAAAAATCTGCCGTAAGAGATGAAAACGGAACACGGCAAACATCTAGAGGCCCCTGGCGTCAGCGGAGGATTAGAAGACCTCGTGTTGACCGATAGGTTGCTGTATAGCCGTTTGGCTGAACAGAACATGAGCGAGTATTTCTCTCAATACCATATACAGTCCTCCAAATAGTTTAATCCAGTGTGTCACGAGTGTCAGGCGTTCCGCACACGGTAAGTGCCC
-3 GACGCTCGCGAAGGATTCGAAGGGTTGCAACCAGCGTGCAACTCAGTTGTGTTCTGGGGTAAACAAATCCAGTCATCGCAGCCAGGCGTACGACAGAACACTGTAAGCGCAGACCTGACCACAGGCCGCGGTAAAAACTAAGCGGGAAAATCTGCCGTAAGAGATGAAAACGGAACGCGGCAAACATCTAGAGGCTCCTGGCGCCAGTGGAGGATTAGAAGACCTCGTGTTGACCGATAGGTTGCTGTATAGCCGTTTGACTGAACAGAACCTGAGCGAGTATTTCTTTCAATACCATATACAGTCCTCCAAAGAGTTTAATCCAGTGTGTCACCAGTGTCAGGCGTTCCGCACACGGTAAGTGCCG
-27 GACGCTCGCGGAGGATTCGAAGGGTTGCAACCAGCGTGCAACTCAGTTGTGTTCTAGGGTAAACAAATCCAGTCATCGGAGCCAGGCGTACGACAGAACACTGTAAGCGTAGACCTGACCACAGGCCGCGGTAAAAACTAAGCGGGAAAATCTGCCGTGAGAGATGAAAACGGAATACGGCAGACATCTAGAGGCTCCTGGCGCCAGCGGAGGATTAGAAGAGCTCGTGTTGACCGATAGGTTGCTGTATAGCCGTTTGGCTGAACAGAACCTGAGCGAGTATTTCTTTCAATACCATATACAGTTCTCCAAAGAGTTTAATCCAGTGTGTCACGAGTGTCAGGCGTTCCGCACACGGTAAGTGCCG
-75 GACGCTTGCGGAGGATTCGAAGGGTTGCAGCCAGCGTGCGACTCAGTTGTATTCTGGGGTAAACAAATCCAGTCATCGGAGCCAGGCGTACGACGGAACATTGTAAGCGTAGACCTGACCACAGGCGGAGGTAAAAACTAAGCGGGAAAATCTGCCGTAAGGGATGAAAACGGAACACGGCAAACATCTAGAGGCCCCTGGCGTCAGCGGAGGATTAGAAGACCTCGTGTTGACCCATAGGTTACTGTATAGCCGTTTGGCTGAACAGAACCTGAGCGAGTATTTCTTTCAATACCATATACAGTCCTCCGAAGAGTTTAATCCAGTGTGTCACGAGTGTCAGGCGTTCCGCACACGGTAAGTGCCG
-78 AATACTGGCATAGGAGGCAGGCGGTTACAAACAACATCTCACCCAGCTCTGTTCCTGGGGAAACGGGTCCAGTCATCGCAACCAGGCGTGGGGAAGGACATTTTCACCACAGACCTGACAACGAGCCCCAGTGAAGACCGATCGAAAAAATCTGACGTAAAGGACAGGAACGGAAGAGGGCGAGGATCGAGAGGCTTCTGGCGGCAGCGAAAGAACAGTAGATTCGATGTAAACCCATACATCCCTAAATAGGCCTTTAGGGGACCAGGGCATGAACGCGTATCTCTCTCGACACCCTATGAGGTCGTGCAAAGGGTTAAAGCCAGTGGCTAAGAAGTGTCGATCGCTTCGCACAGAGGAGTTGCCA
-31 AACACTGGCAGGGGGGGCAGGGGTTTACAAGCAACATCTCACCCAGGTGCCGGACTTAGTAAAGCAGTGCAATCATCACAGACAGGGGTGAGGAAGTATACCTTTAGTGCAATCCTAACAGCGGGCCCCCATGAAAACTGAGCGAGAGGATGTGGCACAGAGAAAATGAGCGGGAGATGGCGTAAATCCAGAGGCTTCTTGCGGCAGCGTGGGAACGGTGCATTCAATGTAAACCTATATGTCCCGAAGTGTACTGTTAAGGTACCCGGCCATGAATGCGTACTTCTTCCGACTCTGTGTAAGTTTTTGCAAAAGGGTAAATCCAGTGGCTGATAAATATCGATCGTTTCGCGCAAAGAAGGAGGCT
-95 AACACTGGCAGAGGAAGCCGGGGTTTACAAGCAGCATTTCAACCAGGTGTCTTAGTTAGCAAAGGAGTACAATTATCACAGACAGGGGTGAGTAAGCATACCTTTAGTGTGAACCTAACAGCGAGGCCCCATAGAGACTAAGCAAGAGAATATGCCACAAAAAACGGGAACGAAGCATGGCCTAGATCCGGAGGCTTCTTGCGGCAACGCGGGAGCGGTGCATGCGATGGAAACCCATATATCCCGAAGTGAACTGTTAGGGCACCCAGCCATGAGTAAGTAGCTCTGTCGACTCCGTGTAAGTTCTTGCAAAAGGGTAAATCCAGTGGCTAATGAATATCGATCGTTTCGCACACAGAAAGGGCCT
-86 AATACTTGCACAGAAAGTCAGCGGTTAGAAGCAACATCTTACACAGATCTGTAGCTAGACAAACGGGGCCAGTGATCACAACCAGACGTGAGCAAGTACACTTTTAGCATAGACCTTACAACAAGCCCAAGTCAAGACAGACCGAAGAAATACGACATAGGGGACAGCAACGGAAGAGGGCAAGGATCGGGAGGCTCCCGGCGTCAATGAAAGAATAATAAATTCGGTGTGGACCCATACATCCCGAAGTACGCCTTTAATGGACTAGGCCGTGAATAAGTATCTTTTGCGACACAGTATCAGATCGTGCAGAGGGTTGAATCCAGTGGTTGACAAGGGTCGATCGCTTCGCACCGAAGAAACGCCT
-11 AATGCTTGCACAGAAAGTCAGCGGTTAGAAGCAACATCTTACACAGATCTGTAGCTAGACAAACGGGGCCAGTTATCACAACCAGACGTGAGCAAGTACACTTTTAGCATAGACCTTACAACAAGCCCAAGTCAAGACAGACCGAAGAAATACGACATAGGGGACAGCAACGGAAGAGGGCAAGGATCGGGAGGCTCCCGGCGTCAATGAAAGAATAATAAATTCGGTGTGGACCCATACATCCCGAAGTACTCCTTTAATGGACTAGGGCGTGAATAAGTATCTTTTGCGACACAGTATCAGATCGTGCAGAGGGTTGAATCCAGTGGTTAACAAGGGCCGATCGCTTCGCACCGAAGAAACGCCT
-24 CATACCGGCACAGGAAGCCAGCGATTACAAACAACATGTTACACAGATCTGTGGCTGGTCAAACGGGTCCAGTGACCACAACCAGGCGTGAGTAACTACACTCTTAGCATAGGCCTTACGATAAGCCCAAGTCAAAACAGATCGAAAAAATACGACATAGAGGACAGCAACGTAAGAGGGCGAAGATCGAGAGGCTCCTGGCGGCGATGAAAGAATAGTAAATTCGGTGTGGACCTATACATCCCAAAGTAGGCCTTTAAGGGACTAGGGCGTAAAGAAGCATCTGTTTCGACACTGTATCGGGTCGTGCAGAGGGTTGGATTCAGTGGTTGACAGGGGTCGATCGCTTCGCACGGAAGGAACGCCC
-40 AGTACTCGCACAGGAAGCCAGAGGTTATAGGCAACATCTCACAAAGGTCTGTGGCTAGATAAACCGGGCCAGTTGTCGCAACCAGGCGTTGACAACTACAATTTTGGTACAAACCTTACAACGAGCCCAACTCAAGACGGATCGAGGAAATACGACATAGAGGAGAGTAACGGAGAAAGGCCAGAATCGTGAGGCTCCTGGTACCAATGAAAGAATAGTAAATTCGGTGTGGACCCATAAGTCCCAGAATGAGCTTTTAAGGGACTCGGACCTACATAGGTATCTTTAGCCACACTGTATCTGATCGTGCGGACGGTTGAACCCAGTGGTTCGGGAAGGTCGATCGCTTCGCACGGCGAAAGAGCGC
-45 AGTACTCGCACAGGAAGCCAGAGGTTATAGGCAACATCTCACAAAGGTCTGTGGATAAATAAACCGGGCCAGTTGTCACAACCAGACGTTGACAACGACAATTTTGGCACAAACCTTACAACAAGCCCAACTCAAGACGGACCGAACAAGTACGACATAGAGGAGAGTGACGGAGAAAGGCCAGAATCGTGAGGCTCCTGGTCCCAATGAAAGAATAGTAAATTCTGTGTGGATCCATAAATCCCAGAATGAGCTTTTAATGGACTCGGGCCTACATACGTATCTTTAGCCACACTGTATCCGATCGTGCAAACGGTTGAACCCAGTGGTTCGTGAAGGTCGATCGCTTCGCACGCCGGAAGGGCGT
-94 GATACTGGCATAGGGGGCCGGCGGTTACGAGCAACATTTCACAAAAGTGTGTGGCTGGAAAAACAGGTGCAGTGATCACAACCAGGCGTGAGAAAGGATATTCTTTCCACAATCCTCACAACCAGCCCAAGTGAAAACCGATCAAGGAGATGTGGCATAAAAGACACCAATGCAAGAGGGCCAGAATTGGGAGGCCCCTGGCGGCAGTAAGAGAACAGCGAGTTCGGTGTGAACCAATACATCCCTAAGTAGGCCTTTGACGGACCGGGACACTAGCGGGTATCTCTTTCTACACCCTGTAAGGTCGTGCAAAGGGTTAAATCCAGTGGTTGGTAAGGACCGATCGTTTCGCACGAAGGAAGTGTCA
-91 AGGACTTGCATAGGGGGCTGGCGATTACGGGCAACATCCTACAAAACCATGTGGCTAGAAAAACAGGTCCAGTCATCGCAACGAGGCGTGAGAGAGAATACTCTTTCCATAATCCTCACAACCAGCCCAAATGAAAATTTATCGAAGAGATATGGTATAGAGGACACTAAACCAAGAGGGCCATGATTAGGAGGCCCCTGGCAGCAGTAAGAGAACAGCGAGTTCGGTGTGAACCGATACATCCCCAAGTCGGCCTTTGACGAGCCGGGACACGGACGAGTATCTCTGTCTACACCTTGTAAGATGGCGCAAAAGGTTAAAGCCAGTGGTGAGCAAGGACCGATCGCTTCGCACGAAGGAAGCGCCA
-25 AATGCTAGCATAGGGGTCCGGCAGTTACGGGCAACATCTTACAAAACTGCGTAGCTAAAAAAACAGGTCCGGTCATCACAACTAGGCGTGAGGAAGGACACGGTTTCCGCACACCTCACAACCAGCCCAAGTGGACACAGATCAAGAAGGTGTGACATATAGGACAGAAACGCAAGAGGGCAAGGATTGGGAGGCTCCTGGCGCCAGTAAGAGAGGAGCGAGTTCGGTGTGAACCAATACATCGCTAAGTAGGCCCTTAACGGACCAGGACATAATCGGCTACCTCTTTCAACACACTGTAGGGTCGTGCAGAGGGTTAAATCCAGTATTCGTTAAGGACCGATCGCTGCGCACGGAGAAAGTGTCA
-63 AGTGCTAGCATAGGGGTCCGGCGGTTACGGGCAACATCTCACAAGACTGCGCAGCTAAAAAAACAGGTCCCGTCATCACAACTAGGCGTGAGGAAGTAGACGGTTGCCACACACCTCACAACCAGCCCAAGTGGAGACAGATCAAGAAGGTGTGACATATAGGACAGAAACGCAAGAGGGCAAAGATTGGGAGGCCCCTGGCGGCAGTAAGAGAGGAGCGAGTTCGGTGTGAACCGATACATCGCTAAGTAGGCCCTTAACGGACCAGGACATAATTGGCTATCTCTGTCAACACACTGTAGGGTCGTGCAGAGGGTTAAATACAGTATACGTTAAGGACCAATCTCTGCGCACGGAGAAAGTGTCA
-60 AATGCTAGCATAGGGGTCCGGCAGTTACGGGCAACATCTCACAAAACTGCGTAGCTAAAAAAACAGGTCCGGTCATCACAACTAGGCGTGAGGAAGGACACGGTTTCCACACACCTCACAGCCAGCCCAAGTGGACACATATCAAGGAGGTGTGACATATAGGACAGAAACGCAAGAGGGCAAGGATTGGGAGGCTCCTGGCGACAGTAAGAGAGGAGCGAGTTCGGTGTGAACCAATACATCGCTAAGTAGGCCCTTAACGGACCAGGACATAATCGGCTATCTCTTTCAACACACTGTAGGGTCGTGCAGAGGGTTAAATCCAGTATTCGTTAAGGACCGATCGCTGCGCACGGAGAAAGTGTCA
-48 AATGCTAGCATAGGGGTCCGGCAGTTACGGGCAACATCTCACAAAACTGCGTAGCTAAAGAAACAGGTCCGGTCATCACAACTAGGCGTGAGGAAGGACACGGTTTCCACACACCTCACAACCAGCCCAAGTGGACACAGATCAAGAAGGTGTGACATATAGGACAGAAACGCAAGAGGGCAAGAATTGCGAGGCTCCTGGCGACAGTAAGAGAGGAGCGAGTTCGGTGTGAACCAATACGTCGCTAAGTAGGCCCTTAACGGACCGGGACATAATCGGCTATCTCTTCCCACACACTGTAGGGTCGTACAGAGGGTTAACTCCAGTATTCATTAAGGACCAAGCGCTGCGCACGGAGAAAGTGTCA
-26 AATGCTAGCATAGGGGTCCGGCAGTTACGGGCAACATCTCACAAAACTGCGTAGCTAAAAAAACAGGTCCGGTCATCACAACTAGGCGTGAGGAAGGACACGGTTTCCACACACCTCACAACCAGCCCAAGTGGACACAGATCAAGAAGGTGTGACATATAGGACAGAAACGCAAGAGGGCAAGGATTGCGAGGCTCCTGGCGACAGTAAGAGAGGAGCGAGTTCGGTGTGAACCAATACATCGCTAAGTAGGCCCTTAACGGACCGGGACATAATCGGCTATCTCTTTCCACACACTGTAGGGTCGTGCAGAGGGTTAAATCCAGTATTCGTTAAGGACCGATCGCTGCGCACGGAGAAAGTGTCA
-66 AATACTAGCATAGATGGCTGGACGTTACGGGCAACATTTTACAGAGGTGTGTGGCTAGAAAGGCAAATTCAGCCATCACACCCAGGCGTAAGAAAGAACCCTCTTGCCACAGACCACACAATCAGCCCAGATCAAAACTGACCAAAGAAATGTGGCATAGAAGATAGCAATGCAAGAGGACGAGAATTTGGAGGCCCCTGGGGACAGTAAGAGGACGGTGAGTTCTGTGTGAACCGATAAGTCCCTAAGTAGGTGTTTGGCAGACGAGGACATAACTGAGTACCTTTGTCAGCACCCTCTAGGGTCGTGCAGACGGTTAAACCTAGTGGGTGGCAAGGACCGATCGATTCGCACGGAAAAGGCGTCG
-44 AGGACTCGCGTATGAGGCCGGCTGTTACGGGCAACATCTTACATAGCTCTTGAGCTAGAGAAACGGGTTCAGTCATCGCAGCCAGGCGTGAGAAAGGACATTCTTACCACAGACCTCCCAACCAGCCCAAGTAAAAACCGATCTATAACATGTGACATAAAGGAGGGCAATGCAACACGGCGAGAATCGGGAGGCTCCTAGCGTCAGTGAGAGAACGGCGAGTTCGGTGTGAACCCATGCATCGCTAAGTAACCCTTCGATAGACCAGGGCCTGAGCGAGTATCTTTTTCCACACCCTGTAAGGTCGTGCAAGGGGTTAAATCCAGTGGTTGATACGGATCGATCGCTTCGCACGGAGGAACTGTTA
-73 AGGACTTGCGTATGAGGCCGGCTGTTACGGGCAACATCTTACATAGCTCTTGGGCCGGACAAACGGGTTCAGTCATCGCAACCAGGCGTGAGAAAGAACATTCTTACCACAGACCTCCCAACCAGCCCAAGTAAAGACCGATCTACAACATGTGACATAAAGGATGGCAATGCAGCACGGCGAGAATCGGGAGGCTGCTGGCATCAGTGAGAGAACGGCGAGTCCGGTGTGAACCTATACATCGCTAAGTAACCCTGCGATAGACCAGGGCCTAAGCGAGTATTTTTTTCCACACCCTGTAAGGTCGTGCAAGGGGTTAAATGCAGTGGTTGATACGGACCGATCACTTGGCACGGAGGAACTGTTA
-96 AGGACTCGCGTATGAGGCCGGTTGTTCCGAGCAACGTGTTACACAGCTCTTGGGCCGGGAAAACGGGTTCAGTCATCCCAACCAGGCGTGAGAAGGAACATTTTTACCACAGGCCTTCCAATCAGCCCAAGTAAAGACCGATCTACTACATGCGGCATAAAGGACGGCAATGCACCACGGCAATAATTAAGAGGCTCCTGGCATCAGTGAGAGAACGGCGAGTTCAGTGTGAGCCCATACATCGCTCGGTAATCCTTCGATAGACCAGGGCCTAAGTGCGTATCTTTTTCCACACCCTGTAACGTTGTGCAAGGGGTTAAATGCAGTGGTTCATACAGACCGATCACTCCGCACGGAGAAACTGTTA
-65 AAAACTAGCGTATGACACCGGTACTCACGAGTGAAATCCAACCTAGTTTTGGGAGTGGATAGACAGTTCCGGTCATCACATTCAGATGTGGGAGGGCACACTGCTCAAAGATACCTGACAACCGGCACAGGTCGACACGCACCTAAAGGATGTAGCGTAGATGACAGGAATGCATGGGAGCAAGAATTGAGAACCTTCTGGCGGCAGTGAGAGAGCAACAAGTTCAAAGTCAACTGATAAGTCGCTAAGTAAGCGATTAATAGACGGTCGCGTTGCGAAGTATATCTCTCCACACTCTATATGGTTGTGTAAGCGCTTAAATGCAGTGGTTCACGCGAACCGATCGCTTCGCACTAAGGAAATATCC
-5 AAAACTAGCGTATGACACCGGTACTCACGAGTGAAATCCAACCTAGTTTTTGGAGTGGATAGACAGTTCCGGTCATCACACTCAGATGTGGGAGGGCACACTGCTCAAAGATACCTTACAACCGGCACAGGTCGACACGCACCTAAGGGATGTAGCGTAGATGACAGGAATGCATGGGAGCAAGAATTGAGAACCTTCTGGCGGCAGTGAGAGAGCAACAAGTTCAAAGTCAACTGATAAGTCGCTAAGTAAGCGATTAATAGACGGTCGCGTTGCGAAGTATATCTCTCCACACTCTATATGGTTGTGTAAGCGCTTAAATGCAGTGGTTCACGCGAACCGATCGCTCCGCACTAAGGAAATATCC
-99 AAGACTCGCGAATGAGGCCGGCTCTTACGGGTAACATCTTACGTAGGTCTTGAGGCGGAGAAACAGTTTCAGTCATCGCAACCAGACGTGGGAAAGTGCACTCCTACCATAGACCTCACAACCAGCCCAAGTAAAGACCGATCTAGCAAATGTGACATAAGGGATAGGAATGCAACAAGGCAACAATCCGGAGGCTCCAGGCGGCAGTGAGAGAACGCCGAATTCGGTGTGAACCCATAGATCGCTAAGGAACCCTTCGATAGATCGGAGCCTGGGCGAGTGCGTTTGTCCACACCTTGTACGGTCGTGCAAGGGGTTAAATACAGTGGTTTATACGGGCCGATCGCTTCGCACGGAGGAAGCGTCA
-80 AACACTCGCGTATGAGACCGGCTGTTACGGGTAACATCTTACATAGGTCTTGAGCCGGAGAAACAGGTTCAGTCATCACAACCAGGCGTGAGAAAGAATAGTCCTACCGCAAACCTCACGACCAGCCCAAGTAAAGACCGATCCAGAACATGTGCCGTAGAGGATAGCAATGGAACAAGGCAAGAATCAGGAGGCTCCTGGCGACGGTGAGAGAACGGTGAGTGCGGTGTGGGCCAATACATCGCTAAGTAAGCTTTCGATAGATCGGAGCCTGAAGCAGTATATTTTTCCACACCCTGTAGGTTCATGCAAGGGGTTAAATGCAGTGGTCCATACGGGCCGATCGCTTCGCACGCAGGAAGCGTCG
-23 ACCACTAGCGTATGCGACCGGCCGTTATGGGCAACATCTTACATAGGTCTCCAGCCGGAGAGACAGGTCCGGTTATCAAAACCAGACGTGAGAGAGAACAATTCTGCTTGATACCTCACGACCAGCCCAAGTGAAAACTCAGCTAGTATGTGAGGCATAGAGGATAACAATGCAACAAGGCGAAGATCAAGAGGCCCCTGGGGACAGTGAAAGAACGGTGAGCCCCATGCGAGCCGATACATCGCTAAGTAAGCTTTCGATAGATCGTCGCCTGAGCCAGTACATTTATATACACCCCGTAGGTTCGTGCATGGGATTAAATGCAGTGGTCAATGCGGACCGATCGATTCGCACGCAGAAAGCGTCA
-20 AGTACTGGCATATGGGGCCGGCTGTTGCGGGTAACATCTTACACAGGTCTTCGGCTGCACAAACAGGTTCAGTCATCGCAACCAGTTGTGAGAGAGGACACTCTTATGACAAACCTCACAACCACCCCGGGTGAGAATGCATCGACACCCTGTAGCATAAAAGATGGTAAGGCAGCAGGACAAGCATCGCGACGCTCCCGGCGGCAGCGGTAGAGAGGCAAGTTCGGTGTGAACCCATACGTCGCTGAATAACCCATCGATTCACTATGGCATGAGCGGGTACCTCTTTCCTCACGCTGTAATGTCGTGCGGAAGCCTAGAGCCAGTGGTTGACGCGGATCAATCGCTTCGCACGACAGAAAGGTCC
-30 AGTACTGGCATATGGGGCCGGCTGTTGCGGGTAACATCTTACACAGGTCTTCGGCTGCACAAACAGGTTCAGTCATCGCAACCAGTTGTGAGAGAGGACACTCTTATGACAAACCTTACAACCACCCCGGGTGAGAAGGCATCGACACCCTGTAGCATAAAAGATAGTAAGGCAGCAGGACAAGCATCGCGACGCTCCTGGCGTCAGCGGTAGAGAGGCAAGTTCGGTGTGAACCCATACGTCGCTGAATAATCCATCGATTCACTATGGCATAAGCGGGTACCTCTTTCCTCACGCTGTAATGTCGTGCGGAAGCCTAGAGCCAGTGGTTGACGCGGATCAATCGCTTCGCACGACAGAAAGGTCC
-89 AGTACTGGCATATGGGGCCGGCTGTTGCGGGTAACATCTTACACAGGTCTTCGGCTGCACAAACAGGTTCAGTCATCGCAACCAGTTGTGAGAGAGGACACTCTTATGACAAACCTTACAACCACCCCGGGTGAGAAGGCATCGACACCCTGTAGCATAAAAGATAGTAAGGCAGCAGGACAAGCATCGCGACGCTCCTGGCGTCAGCGGTAGAGAGGCAAGTTCGGTGTGAACCCATACGTCGCTGAATAATCCATCGATTCACTATGGCATGAGCGGATACCTCTTTCCTCACGCTGTAATGTCGTGCGGAAGCCTAGAGCCAGTGGTTGACGCGGATCAATCGCTTCGCACGACAGAAAGGTCC
-38 AGTACTGGCATATGGGGCCGGCTGTTACGGGTAACATCTTACACAGTTCTTTGGCTGCACAAACAGGTTCAGTCATCACAACCAGTTGTGAGAGAGGACACTCTTACGACAGACCTTACAACCACCCCAAGTGAGGAGGCATCGAGAACCTATAGCATAAAAGATAGTAAGGCAACAGGACAAGCATCGCGACGCTCCTGGCGTCAGCGGTAGAGTGGCAAGTTCGGTGTGAACCCATACCTCGCTGAATAAGCCATCGATCCACCATGGCATGAGTGGGTACCTCTTTCCTCACCCTGTAATGTCGTGCAAAGGCTTAGAGCCAGTGCTTGACACGGATCGATCGCTTCGCACGACAAAAAGGTCC
-83 AGTACTGGCATATGGGGCCGGCTGTTACGGGTAACATCTTACACAGTTCTTCGGCTGCACAAACAGGTTCAGTCATCACAACCAGTTGTGAGAGAGCACACTCTTACGACAGACCTTACAACCACCCCAAGTGAGGAGGCATCGAGAACCTGTAGCATAAAAGATAGTAAGGCAGCAAGACAAGCATCGCGACGCTCCTGGCGTCAGCGGTAGAGCGGCAAGTTCGGTGTGAACCCATACCTCGCGGAATAAGCCATCGACTCACCATGGCATGAGTGGGTACCTCTTTCCTCACCCTGTAATGTCGTGCAGACGCTTAGAGCCAGTGGTTGACGCGGATCGATCGCTTCGCACGACAGAAATGTCC
-68 AGTACTGGCATATGGGGCCGGCTGTTACGGGTAACATCGTACACAGTTCTCCGGCTGCACAAACAGGTTCAGTCATCGCAACCAGTTGTGAGAGAGGACACTCTTACGACAAACCTTACAACCACCCCAAGTGAGGAGGCACCGAAAACCTGTAGCATAAAAGATGGTAAGGCAGCAGGACAAGCATCGCGACGCTCCTGGCATCAGCGCTAGAGCAACAAGTTGGGTGTGAAGCTATATGTCGCTGAATAAGCCATCAATTGACCATGGCATGAGTGGGTACCTTTTTCTTCACCTTGTACTGTCGTGCAGAGGCTTAGAGCCAGTGGTTGACGCGGATCGATCGCTTCGCACGACAGAAAGGTCC
-55 ACTACTAGTAAATTGGCCGGGCCGTTGCGCTCGACATCTCACTCAGTTTCTCAACTACATAAACAGTTCCAGTAATCGCAAGCAGTAGTGAGAAGAAACACTCTTCCGATACGCTGTACACCAACCCCAAGTGAAGAGGAATCTGATAACTAAAACATGCAACATGGTAAAGCAGTAGGACAAATAGCTCGACGCCCCTCGCGTCAGCGACAGAACCGCAGGTCCAGTGTGAAACGATGTATCACGCATTAAACGGTCGACTCATCATGACATCGGCTCTTACCTCTTGCACCACCCTTTGATGTCGTTCAGAAGCTTGGAGGCAGTGGGTGGGTCCAATCAGTCGCTTCGGTCGGCGGAAAGATCG
-28 GGTACTGGCATATGGGGCCGGCCGTTCCGGGTGACATGTTACATAGGTCCTTGGCTGGAAAAACCGATTCACTCATCACAAGCAGGTGTCAGAAAGCACACTCCTACAACAGACCTTACAACAAGCCCAAGTAAGCACCGATCGAGAACATGTGGCATATAGGATAGCAATGTAACAGGGCAAGTATCGGGAGGCTCCTGGCGACAGTGGGAGAAGGGCGAATCCGGTGTGAACCGATACATCCCTAAGTAGACCTTCGGTTGACCACGTCATGATTGGGTATCTGTTTCCGCACCCTGTAAGGTCGTTCAAGCGGTTAAAACCAGTGGTTGACACGGGCGGATCGCTTCGCACAGAGCAAATGTAA
-76 AGGACTCGCATATGCGGCCGGCTATTACGGACAACATGTCACATAGGTCCATTGCTGGGGAAACCGGTTCAGTCATCACAACCAGGTGTGAGGGAGGACACTCTAACTACAAACCTTACGACCGGCCCAAGTAATGACCAATCGAGAAGGTGTGGTATAAAGAATAAAAATGTAACAGGGCAAAAATCGGGAGGCTTCTGGTGGCAGTTAGAGGACAACGAAGTCGGTGCGAGCCCATACACCGCTGGATCAGCGTTTGGTAGACCATGACATGACGGAGTGTCTTTCTCCGCACGTTGTAAGGTCGTTCAAGGGATTAAAGGTGGTGGGCGAGACAGGCCAATCGCTCCGTACGAAATAAACGTCC
-71 AGCACTGGCATATCGGGCCGGCTGTTACGGGCAACATGTTACACAGGTCTTTAGCTGGACAAACAGGTTCAGTGATCGCAACCAGGTGTGAGAGAGGACACGCTTACGAGAAACCTTACAACCAGCCCAAGTGAGCACCGACCGAGAACATGTATCGTAAAAGATAGCAATGCAACAAGGCAAGGATCGGGAGGCTCCTGGCGACAGTGAGAGAACGGGGAATTCGATGTGAACCCATACGTCGCTGAGTAGACCCTCGGTAGACCATGACATGACCGAGTATCTCTCTCCGCACCCTGTAAGATCGTTCAAGGGGTTAAAGCCAGTGACTAAGGCGGGCCGATCGCTTCGCACAAAGAAAACGTTA
-52 AGTACTAGCATATGGGGCCGGCTGCTACGGGCAATATCTTACACAGTTCTTTGGCTGGACAAACAGGTTCAGTCATCACAACTAGGTGTGAGAGAGGACACTCTTACGAGAAACCTTACGACCAGCTCAAGTGAGGACCGATCGAGAACATGTGACATAAAGGATAGCAATGCAACAGGGCAAGGATCGTGAGGCTTCTAGCGTCAGTGAGAGAACGGCGGATTCGGTGTGAACCCATACATCGCTGAGTAGGCCTTCGGTACACCATGACACGAACGAGTATCTCTTTCCGCACCCTGTAAGGTCGTTCAAGGGGTTAAAGCCAGTGGTTAACGCGGGCCGATCGCTTCGCACAAAGGAAGTGTCG
-43 AGTACTAGCATATGGGGCCGGCTGTTACGGGCAACATCTTACACAGCTCTATAACTGGAAAAACAGGTTCAGTCATCGCAACCAGGCGTGAGAAAGCACACTCTTGCCACAAACCTCACAACCAGCCCAACTGAGGACTGATCGAGAACATGTGACATAAAGGACAGCAATGCAAGAAGGCGAGGATCGGGAGGCTCCTGGCGTCAGTGAGAGAACAGCGAGTTCGGTGTGAACCCATACATCGCTAAGTAGGCCGTCGATAGACCAGGGCATTAATGAGTATCTCTTTCCACACCCTGTAAGGTCGTGCAAAGGGTTAAATCCAGTGGTTCATACGAACCGATCGCTTCGCACGGAGGAAGTGTCA
-15 AGTACTAGCCTATGGGGCCGGCTGTTATGTGAAACATCTTACACAGCTCTGTGGCTTGAAAAACAGGTTCGGTCATCACAACCAGGTGTGAGGAAGGACACTCTTTCCACAAACCCCACAGCCAGCCCGAGTAAGAATCAACCAAAAACATGTGGCAGAAAGGATAGTAATGCAAGAGGGCAAGGATCGGGAGGCTCGTGACGACGGTGAGAGAACAGCGAGTTCGACCTGAACCGATATATCGCGAAGTAAACTGTCGACAGATCAGGGCATCGGTGAGTATCTAGCTCCACACCCTGTAAAGTCCTACGAAGGGTTGAATCCAGTGGTTCATACGAGCCGGTCGCTTCGCACGGAGACACTGTCA
-49 AGTACTAGCCTATGGGGCCGGCTGTTATGTGGAACATCTTACACAGTTGCGTGGCTTGAGAAACAGGTTCGGTCATCACAACCAGGTGTGAGGAAGCACACTCTTTCCACAGACCCTACAGCCAGCCCGAGTAAGAATCAACCAAGAACATGTGACAGAAAGGATAGTAATGCAGGAGGGCAAGGATCGGGAGGCTCGTGACGACAGTGAGAGAACAGCGAGTTCGATCTGAACCGATATATCGCGAAGTAGACTGCCGACAGATCAGGGCATCGTTGAGTATCTGGTTCCACACCCTGTAAAGTCCTGCGAAGGGTTGAATCCAGTGGTTTATACGAGCCGGTCGCTTTGCACGAAGACACTGTCA
-32 AGGACTGGCACATGGGGCCGGCTGTTACGGGAAACATCTTATACAGTTGTGTAGCCTGAAAAACAGGTTCGGTCATCGCAACCAGGCGTGAGGAAGCACACTCTTCCCACAAACCCCACAGACAGCCCAAGTAAGAACCAATCGAGAACATGTGAGAGAAAAGATAGCAATGTAAGAGGGCAGGGATCGGGAGGCTCGTGACGTCGATGGGAGAATAGCGAGTTCGATCTGAACCAATATATCGCGAAGTAGACTATCGATAGACCAGGGCAGTAGTGGGTATCTATTTCAACACCCTGTAAAGTCGTGCAAAAGGTTAAATCCAGTGGTTTATACGAGCCGGTCGCTTTGCACGGAGAAGCCGTCA
-74 AGTACTGGCATATGGGGCGGGATGTCACAGGCAACATCTTACACAGTTCTGTAGCTGGAAAAACGGGTTCAGTCATCCCAACCAGGTGTGAGGAAGAACACTATTGCCGCAAACCCAACAACTAGCCGAAGTAAGGACTGATCGAGGACATGTGGCGGAGAGGATAGCAATGCAGGAGGGCAAAGATCGTGAGGCCCATGACGGCAGTGGGAGAACAGCGAGTTCGGTGTGAACCAATAAATCGCGAAGTAGGCCGTCGGTAGACCAGGGCACTATGGAGTATCTGTTTCCACACCCTGTAAGGTCGTGCCAAAGGTTAAATCCAGTGGTTTGTCCGAGTCGGTCGCTTTGCAGGGAGAAACTATCA
-39 AGTACTAGGATATGGCGCCCGTTGTTACGACCAACATCTCACATGGCTCCTTGAATGGATAGACGAGTACAGTAATCGAAACCAGGTTTGAGAAAGTACACTCTTACCGCAAACCTCGCTGCCAGCCCAAGTCAGGACCGATCGAAAACATGTGGCATAAAAGACACCAATAAAAGAAGGCATACATCGAGAGCCTCAGGGGGTCAATGGGAGAATAGCAAGTTCATTGTGAGTCGATAGATCGCTAGGGGACCCCTCGATAGACCAGGCCATAAATAGGTATCTTTTTCCACACTCTGTATGGTCGTGGGAGTGACTAAACCCAGTGGTGGATGCGAGTCGATCGTTTCACACGAAGAAAGTGTCG
-41 AGTACTAGGATATGACGCCTGTTGTTACGACCAACATCTCACATGGCTCCTTGAATAGAAAGACGGGTACAGTAATCGAAACCAGGTTTGAGAAAGCACACTCTTACCACAAACCTCGCGACCAGCCCAAGTCAGGACCGATCGAGAACATGTAACATAAAAGACACCAATAAAAGAAGGCCTGCATCGGGAGCCTCAGGGGGTCAATGGGAGAACAGCAAGTTCATTGTGAGTCGATATATCGCTAGGGGACCCCTCGATAGACCAGGCCATAAATAGGTATCTTTTTCCACACCCTATAAGGTCGTGGCAAGGATTGAACCCAGTGGTGGATGCAAGTCGATCGTTTAGCACGAAGAAAGTGTCG
-12 AGTACTAGGATATGGCGCCTGTTGTTACGACCAACATCTCACATGGCTCCTTGAATGGAGAGACGGGTACAGTAATCGAAACCAGGTTTGAGAAAGCACACTCTTACCACAAACCTCGCGACCAGCCCAAGTCAGGACCGATCGAGAACATGTAACATAAAAGACACCAATAAAAGAAGGCCTACATCGGGAGCCTCAGGGGGTCAATGGGAGAACAGCAAGTTCATTGTGAGCCGATATATCGCTAGGGGACCCCTCGATAGACCAGGCCATAAATAGGTATCTTTTTCCACACCCTGTAAGGTCGTGGCAGGGATTAAACCCAGTGGTGAATGCGAGTCGATCGTTTAGCACGAAGAAAGTGTCG
-36 AGTACTAGGATATGGCGCCTGTTGTTACGACCAACATCTCACGTGGCTCCTTGAATGGAAAGACGGGTACAGTAATCAAAACCAGGTTTGAAAAGGCACACTCTTACCACAAACCTCGCGACCAGCCCAAGTCAGGACCGATCGAGAACATGTAACATAAAAGACACCAATAAAAGAAGGCCTACATCGGGAGCCTCAGGGAGTCAATGGGGGAACAGCAAGTTCATTGTGAGTCGATACATCGCTAGGGAAGCCCTCGGTAGACCAGGCCATAAGTAGGTATCTTTTTCGACACCCTGTAAGGTCGTGGCAGGGATTAAACCCAGTGGTCCACGCGAGTCGATCGTTTAGCACGAAGAAAGTGTCG
-97 AGTACTAACATATAGGGCCTGCTGTTACGAGCGACATCTCACAGAGGTCCTTGAATGGATAGACGGGTACAGTCATCGCAACCAGGTGTGAGAAAGCGTACGCTTACTACAGACCTCGCGACAAGCCCAAGTTAGGACCGATCGAGAACATGTGACATAGAAGACACCAATAAAAGAAGACTTACATCGGGAGCCCCAGGGCGTCAATGAGAGAACAGCGAGTTCGTTGTGGATCAATATATCGCTAGGGGACCCGTCGATGGACCAGGCCTTAAAGGAGTATTTTTTTCCACGCCCTATAAGATTGTGGAGAGGATTAGACCCAATGGTTAGTACGAGTCGATCGTTCCGCACGAAGCAAGTGGCA
-10 AGGACTGACATATAGGGCCTGTTGTTACGAGCGACATCTCACAGGGCTCCATTAATGGATAGGCGGGTACAGTCATCGCAACCAGGTGTGAGAAAGCGTACGCTTACCACAAACCTCGCGACAAGCCCAAGTTAGGACCGATCGAAAAAATGTGGTATAGAAGACACCAATAAAGGAAGACTTACATCGGGAGCCCCAGGGTGCCAATGAGAGAACAGCGAGTCCGTTGTAAATCGATATATCGCTAGGGGATTCATCGATGGACCAGGCCATAAAAGATTATTTTTTTCCACACCCTATCAGATTGTGGGGAGGATTGGACCCAATGATTGATACAAGTCGATCGTTTCGCACGAAGCAAGTTTCG
-101 387
-73 CCGTTTGTTGTATTAATTAACGGTCTCAAATGTCTTAACTGTATGCGTAAATTAGACTAGCTAAGTAGACAGTTGACGGAAGTTGACCTAACTTCTGTCCTAAGTAGTACCGAACGTTTGCTTTGATAGCAGCGAGGTAAAGTTGTAGGGCATCGCTGCAAGCAGTATGGGACTTATTTCTGAGTTAAGAGTTTCCTATTATGGGTATACTTAATTGAGGTGGCTTGGAGCGGTGTAGGGTAGACTACTGCATGCAGAGACTAAAGATATCCAGTAAGGGGCTTTCGTTATTCAGCCACTCTGATAGGGATGTTGTAGCCAAGTTGGTAATGATGGTTGTAGTAAGTCCTATATTATTTGGCACGAGGTCATATAGAAACCTTGGAG
-96 CCGTTTGTTGTAGTAATTATTGGTCTCAATTGTTTTAACTGTATGCGGAAATTATGCTGGCGCAGGAGACAGTTGACGGAAGTTCACCCAGCTTCTGTCCTAAGTTGTACCAAACGTTTGCTTTGATAGCAGCGATGCGAAGTTGTGGAGCAGCACGGTAATCAGTTTGGGGCTTAATTCTGCGTTTAGAGTTTTCTATTATGGTTATAGGTAGGTGAGGTGGCTTGAAGCGGTGTATGTTTGACTACTGCAATCAGAGACTAAAGGTATCCAGTAAGGGGCTTTCGTTATTCAGCCACTCTAGTAGGGATGTTGTAGGCTAATTGGTAATGGTGGTGGTAGTAAGTCCTTTATGATTTGGCGCGAGGGCTTAACGAAACCGAGGAG
-44 TCGTTGATGAATGTAAGTAATGGTCGTAAATGGCTTAACTGTATGCGTAGGTTATTCTAGCTAAGAAGATAGTCGACGGCGGTTCGCTAAACTACTATCTTAAGTAGTACCGGACTTTTGCTTTGACATCAGCGAGGCACGGTTGTTGTGGAACGTTGTAGGCAGTATGGGGCGTATTTCTTAGTTAAGAATTTTTTACCATGGGGGTGATTACATGAGAGGGCTTGAAGCGGTTTGGGGGTGACTACTGTACTCGGAGACTAAAGATATCTAGTATGGGTCTTTCGTTATTCAGCAACCGTTAAAGGGATGTTGTAGTCAAAAGGGTAATGCCGGTGGGAGTAGGTCTAATATTATCGAGCACGATGGCATATATAAGCCTTGGAG
-23 CCGGTGGTTGGAGTGATTATTTGTCTTTAGTGGCTTAACTGTATACGTAGTTTAAGCTAGCCACGGATACAGATTACGGGGGTTTACGTAATTACTGTCCTAAGCTGTATTAAACGTATGCTTGGACATCAGCGGGGTAAGGTTATTTTGCAATTTTGTGGGCAGTAGGTAGCTTGGTCCTCAATTAAGTACTTTCTATTATGGGGGTAATTATGTGAGGTTTTTCGCAGCGGTGCGTTGTTGACCACCGTAATCATAGACTAAAGATATCCAGTAAGGGACTTTCGTAATTCAGCAAACTTAATGGGTTTGTTGAAGCCGAATGGGTAATGCTGCTAGAAGTTAGTTTCGTATTATTTGGCTCGAGGGCATACTGAAGTACGGGAG
-80 CCGTTGGTTGGAGTGATAATCTGTCTTCAATGTCTTAACTGTATGCGTAGTTCAGATTAGCCACGTAGATAGCTGATGGCTGTTTACGTAACTTTTTCCCTAAGCGGTATTGAACGTGTGTTTGGAAATCAGCGAGGTAAGGTTGTTTTGCGGCGTTGCGGGCAGTTGGTGACGTAATTCTGGAGTAAGTACTTTCTAGTATGGGGGTAGTTAGGTGAGGTGTCTCTTAGCGGTGTATTGTTGATCACCGTAATCATGGACTAAGGATACCTAGGAAGTGTCTTTCGTAATTCAGCAAACTGAATAGGTTTGTTGAAGTTGAGCTGGTAATGCTGGTGGAAGTTAGTGTTCTATTATTTGACTCGAGGGCATACTGAAGTACGGGAG
-99 CCGGTGTTTGTAGTGATAAATTGTCATCAATGGCTGAACTGTATATGTAGTTTAGCCTAGCCACGTAGATAGATGATGGGGGTTCACGGGATTACTTTCCTAAGCAGTATCGGACGCATGTTTGGACATCAGCGGTGTAGGGTTGTTTTGCGACTTTGTGGGCAGTAGGCGGGGTGGTTCTGAATTAAGTACTTTCTATTATGGAGATAAGTAGGTGAGGTGTTTTGTAGCGGTGTGTTGATGACCACCGTATTCAGGGTCTAAAGATATCTGGTAAGAGTCGTTCGTAATTCAGCAAACTGAATAGGTTTGTTGAAGCTGATTGGGTAATGCTGGTGGATGTGAGTTTCTTATTAGTTGACTCGAAGGTATACAGAAGTACAGGAG
-5 CCGTTGGTTGTAGTGATTAATTGTCTAGAATGGTTAAACTGGATAAGTATTTAAAGCTAGTCAGGTAGACGGATGGCGGGGGTTCACGTACTTTCTTCCCTAGGCGGTAACGATCGTATGGTCGGACACCAGCGGGGCAAGGTTTCCTTGCAGCATTGTAGGCAGTGGGTGGCGTAGTTCCATATTAAGTGCTTTGTATTATGGAGGTAAGTACACGAGGTGTTTCGTAGCGGTGTGGTGTTGATCACCTTATGTGGTGTCTAAAGATATCCCGGACGGGCCTTTCGTAACTCAGCAAACTCCGTTGGTTTGTTGGAGGTAATGTGGTAATGCTGTGTGAAGTGGGTTTTGTACTAGTTTACTCGAGGGCACACTGAAGTAGAGGAG
-65 CCGTTGGTTGTAGTGATTAGTTGTCTTTAATGGCTAAACTGGATAAGTATTTAAGGCTAGCCACGCAGACAGATGGCGGGGGTTTACGTAATTGCTTTCCTAGGCTGTATCGATCGTATGGTCGGACATCAGCGAGGTAAGGTTTTCTTGCAACTTTGTAGGCAGTAGGTGGCGTAATTCTAAATTAAGTGCTTTTTATTATGTAAGTAATTATATGAGGTGTTTCGTAGCGGTGTGGTGTTGACCACCGTACTTAGGGTCTAAAGGTATCCAGTAGGGGCCTTTCGTAACTCAGCAAACTTAGTAGGTTTGTTGGAGCAAATTTGGTAATGCTGACTGAAGTGAGTTTTGTACTAGTTCACGCGAAGGCGTACAGAAGTATAGGAG
-53 CCGTTGGGTGTAGTTATTATTAGTCTTAAATGACTCAACTTTATACGTAAGTAAGACTATCTATGCAGACATATGACGGTGGTCTACTAGGGTTTTGTCTTAAGCGGTGCCGAGCGCATGAGTTGAAAACAGCGCTGTAAGGTTAGAGCGCATCATTGTAAGCAATAAGTGGCGTTTTTCGGAGTTAATATCTTCCTATTAGGGGAGTAATTAAGAGGGGTGGTTCGGAGCGGCATGGGTCTGACTACTATAGAGAGAGACTAAAGATATCAAGTATGGTGCATTCGTCATTCAGCAAACGTGATAGGGATGTTGGAGTTTAGCTGGTAAGGCTGCTTGAAGTAAGTCTTACATTATTCAACACGATGGAATATAGAAGTATGGGAG
-88 CCGTTGGGGGTAGTTATTATTAGTCTTAAATGACTCAACTTTATACGTAGGTAAGACTATCTATGCAGACATATGACGGTGGTTTACTAGGGTTTTGTCTTAAGCGGTGCCGAGCGCATGGGTTGAAAACAGCGCTGTAAGGTTGGAGCGCATCATTGGAAGCAATAAGTGGCGTTTTTCGGAGTTAATATCTTTCTATTAGGGGAGTAATTAAGAGGGGTGGTTCGGAGCGGCATGGGTCTGACTACTGTAAAGAGAGACTAAAGATATCAAGTATGGTGCATTCGTCATTCAGCAAACGTGATAGGGATGTTGGAGTTGAGCTGGTAAGGCTGCTTGAAGTAAGTTTTACATTATTCAACACGATGGAATATAGAAGTATGGGAG
-42 CCGTTGGAGATGTTTATTATTAGTCATAAATGACTCAACTTTATACGTATGTAAGACTATCTATGCAGACATATGACGGCGGTCTACTATAGTTCTGTCATAAGCGGTACCGAGCGCATGAGTTGAAACCAGCGCTGAAGAGTTGGATCGCAACATCGTAAGCAATAAGTGGCGTTGTTCGGAGTTAATATCTATCTATTAGGGGAGTAATTACTAGGGGTGGTTCGGAGCGGCATGGGTCTGAATACTATAAGGAGGGACTAAAGATATAAAGTATTGTGCATTCGTCATTCAGCAAACTTGATAGGGTTGTTGAAGCTCAGGTGGTAAGGCTGATTGAAGTAAGTCTGGTATTATTGAGTACGATTGAATCTAGAAGTTTGGGAG
-46 CCGTTGGGGAGGTTTATTATGAGTCTTAAATGACTCAACTTTATACGTATGTAAGACTATCTATGCAGACATATGACGGTGGTCTACTCGAGTTTTGTCATAATCGGTGTCGAGCGCATCAGTTGAAACCAGCGGTGAAGGGTTGGAGCGCAACATTGAAAGCAATAAGTGGCGTTTTTCGGAGTTAATTTCTATCTATTAGGGGAGCAATTAAAAGGGGTGGTTCGTAGCGGCATGGGTCTGAAGACTATAAAGAGGGACTAAAGATATACAGTATGGTGCATTCGTCATTCAGCAAACGTGATATGGATGCTGGAGTTCAGGTGGTAAGGCTGATTGAAGTAAGTCTGCTATCATTGAGTACGATTGAGTATAGAATTTTGGGAG
-37 CCGTTGATGGTACGAATTATTGGTCTTAAATAACTCAACTGTATCCGTAGGTAATACTATCTAAGCAGACGTATGACGGTGGTCCACAAAGGTGTTGTCTTAAATAGTGCCGGTCGCATGATTTAATAGCAGAGTCGTCAGGTTTAATGGCACCGTTGTAAAAAATGAGTGGTGGTTTTCGGAGTTAATTCCTTTCTATTGGGGTAGTTATTAGGAGGGGTGGTTTGTAGCGGCATGGATCTGACCACTGTATACAGAGACTAAAGATATCGGGCAGGGTGCATTCGTCATTCAGCGAACTTTATGGGGATGTTGGAGTCTATTTGGTAATGCTGGATGAAGTAAGTCTTGCATTATTTTTCACAAAGGCCTATGGAAGTGAGGGTG
-100 CCGTTGGTGGCAATAAGTACGGGTCTTAAATGTCTCAACTGTATACGTAGTTAATGCTAGCTAAGCATACATATGATGGTGGTCCACTTAGGTTTTGCCTTAAATAGTGCCGAGCGCATGCTTTGACAACAGCGAAGAAAGGATTAAATGCTACATTGGAGGCAAGAAGAGGCGTTCTTCGAGGTTAATATCTTCCTATTAGGAAAGTAATGAAAAGGGGTAGTTTGCAGCGGCACGAATTTTACTACTGTATAGAAAGTCCAAATATACCTAGTATGGTGCATTCGTCATTCAGCGAACTTAATAGAGATGTTGAAGTTTAGTGGGTAGGGTTGTAGGGAGTCAGTTTAACTCTATTTTATACGAAAGCATGTAGCAGTGTGGGAG
-64 CCGTTGGTGGCAATAAGTACGGGTCTTAAATGTCTCAACTGTATACGTAGTTAATGCTAGCTAAGCATACATATGATGGTGGTCCACTTAGGTTTTGCCTTAAATAGTGCCGAGCGCATGCTTTGACAACAGCGAAGAAAGGATTAAATGCTACATTGGAGGCAAGAAGAGGCGTTCTTCGAGGTTAATATCTTCCTATTAGGAAAGTAATGAAAAGGGGTAGTTTGCAGCGGCACGAATTTTACTACTGTATAGAAAGTCCAAATATACCTAGTATGGTGCATTCGTCATTCAGCGAACTTAATAGAGATGTTGAAGTTTAGTGGGTAGGGTTGTAGGGAGTCAGTTTAACTCTATTTTATACGAAAGCATGTATCAGTGTGGGAG
-81 CCGTTGGTGGCAATAAGTACGGGTCTTAAATGTCTCAACTGTATACGTAGTTAATGCTAGCTAAGCATACATATGATGGTGGTCCACTTAGGTTTTGCCTTAAATAGTGCCGAGCGCATGCTGTGACAACAGCGAAGAAAGGATTAAATGCTACATTGGAGGCAAGAAGAGGCGTTCTTCGAGGTTAATATCTTCCTATTAGGAAAGTAATGAAAAGGGGTGGTTTGCAGCGGCACGAATTTTACTACTGTATAGAAAGTCCAAATATACCTAGTATGGTGCATTCGTCATTCAGCGAACTTAATAGGGATGTTGAAGTTTAGTGGGTAGGGTTGTAGGGAGTCAGTTTAACTCTATTTTATACAAAGGCATGTAGCAGTGTGGGAG
-34 CCGTTGGTGGAAATAAGTACGAGTCTTAAATGTCTCAACTGTATGCGTAGTTAATGCTAGTTTAGAATACATATGATGGTGGTCCACTTAGGTGCTGCCGTAAATAGTGTCGAGCGTGTGCTTTGACAGCAGCGAAGAAAGGATTAAATGCGACGTTGGAGACAAGAAGAGGCGTTCTTCGAGGTTAATATCCACCTATTAGGAGGGCAATGAAAAGGGGTGTTTTGTAGCGGTACGATTTTTACGGCTGTATAGGAAGGGCAAATATACCTAGTAAGGTGCATTCGTCATTCAGCGAACGTAACGGGAATGTTGAAGTTAAATGGGTAGGGTTGCAAGGGGTCAGTGTAGCTTTATTTTGTACAAGGGTACATAGCAGTGGGGGAG
-92 CCGTTGGTGGACTTAAGTACTGGTCTTAAATGCCCCAACTGTATACGTAGTTGATACTAGCTAAGCAAACATATGACGGTAGTCTACTTGGGTCTTGCCCTAAGTAGTGCCGATCGCATGTTTTGACATCAGCGTCGTTAGGTTTAATAGCTGCATTGAAGGCAGGAAGAGGCGGGGTTCTAGGTTAATGTCTTCCCATTAGGAAAGTAATGAAGAGTGGTGGTTTGCAGCGGCACGAATTTTACTACCGTAAAGAATGTCCAAATATACCTAGTATGGTGCATTCGTCATTCAGCGAACTTAAGAGGGATGTTGAAGTTCAGCGGGTAGGGTTGATGGGGGTGAGTTTTGCTCTATTTTATACAAAGGCGTGTAGCAGTGTGGGAG
-2 CCGTTGGTGGGCATAAGTACTGGTCTTAAATGCCCCAACTGTATACGTAGTTAATACTAGCTAAGCATACATATGACGGTAGTCTACTTTGGTCTTGCCTTAAGTAGTGCCGATCGCATGTTTTGACAACAGCGTCGTTAGGTTTAATCGCTGCATTGAAGGCAGGAAGAGGCGGGGTTCTAGGTTAATATCTTCCCATTAGGAAAGTAATGAAGAGGGGTGGTTTGCAGCGGCACGAATTTTACTACCGTAAAGAATGTCCAAATATACCTAGTATGGTGCATTCGTCATTCAGCGAACTTAAGAGGGATGTTGAAGTTCAGTGGGTAGGGTTGTAGGGAGTGAGTTTCGCTCTATTTTATACAAAGGCGTGTAGCAGTGTGGGAG
-21 CCGTTGATGGTCATAAGAATTAGTCTTAAAGGTCTCAACTGTATTCGTAGTTAATACTAGCTAAGCATTCATATCACGGTAGTCCACTTTGGTCTTGGCTTAAGTGGTGTCGATCGCATGTGTTGACAACAGCGTCGTTTGGTTTAGTCGCAGCATTGAAGGCAGGAAGAGGTGGGTTTTTAGGTTAATATCTCCCCATTAGGACAGTAATTATGAGGGGTGGTTTGCAGCGGCACGCATGATACTGCCGTAAAGAAGGTCCAAATATACCTAGTACGGTACATTCGTCATTCAGCGATCATAAGAGGGGTGTTGAAGTGCAGTGGGTAGGGTTGTGGGGAATGAATTTCGCTCTATTTTATACAAAGGCGTTTAGCATTGTGGGAG
-58 TCGGTGGTGGCGCCAAGTATTGGTCGTAAATGCCTCAACTGAATACGTAGGTAACACTATCTAAGTAGACATATGGCGGTGGTCCTCTTAGGTTTTGTCATAAGCAGTGCGGAGCGCATGAATTAACAACAGCGGCGTAAGGTTGAAGTGCAGCGTTGTAAGCAGTAAATGGCGTTGTTCGCGGTTAATACCTTTCTATTAGGGAGGTAATGAAGATGGGTTGTTGGGAGCGGCATGGGTCCGACTTCTGTAGACAGAGACTAGAGGTATCTAGTATGGTGCATTCGTCATTCAACGAACTTAAGAGGGATGTTGGAGTTTAGGGTGTAAAGCTGAATGGAGTAAGTCTGACATTATTTGAAGCGAGGGCGTATATAAGTGGGGGAG
-97 TCGTTGGTTGAATGGAGCAATGGTCTTTAGTTACTTCACCGTATACGTAGGTTAGACTAACTAGGGACATAAGTTATGGTGGTCTTCCAGAGTTATAATTTAAGCCGTATTACCTTTACGCTGCGATATAAGCGGTGTGAAGTGAGTAGGCAGAGCTGGGCGCATTAGTCGCCGTATTCGCGAGTTGATAATGGGTGAGTGTGGGCGTAAATAGTAATGGTGTGTTGAAGCGGGATGCATGCAAGTTCCGTATTTAGGGAGTAAAGAGGCTGGGTAAGAGGCATTCGTCATTCTGCTAACTTCTTTGTTATGGCGGAGTTCAATTGGTAATGGCGTGGAAAGTGAGTGTATTATTATTTTACACGAAAGGATGTTGAAGTTTGAGAG
-10 TCGTTGGTTGAATGGAGCAATGGTCTTTAGTGTCTTCACCGTATACGTAGGTTAAACTAACTAGGTACATAGGTTATGGTAGTCTTCTAGAGTTATAATTTAAGCCGTATTACTTTTACGCTGCGATATTAGCGTTGTAAAGTGATTAGGCAGAGCTGGGTGCATTAGTCGCCGTGGTCGCGAGTTGACAATGGGTGATTGTGAGTGTAAATAGTAGTGGTGTGTTGGAGCGGGATGCAGGCAATGTCCGTATTTAGGGAGTAAAGAGGCTTGGTAAGAGACCTTCGTCATTCTGCTAACTTTTTTGTTACGGCGGAGGTCAATTGGTAATGACGTGTAAAGTGAGTTTGTTATTATTTTCCACGAGAGGATGTTGAAGTTTGAGAG
-12 TCGATGGTTGAAGGAATCATTGGTCTTTAATTTCATAACTGTATGCGTAGGTTAGACTAACTGGGCATATAGGTTACGGTGGTCCACTATATTCATAATCTAAGCAGTACTGAATGTACGCGGCGATACTAGCGATGTGAGGTGAACAAGCATCGTTGGGAGCAGTTGGGGGCGTAATCCTAAGTTAATACCTTCTTATTATGAGCGTAAGGATGAGTGGTATTTTGAAGCGGTGTTGGGTCGGCTACAGTATTCAGTGTGTAATTATGTTTGGTAAGGGGCGTTCGTTATTCAGCAAACTTCAGGGGTATGTTGGAGACGAGACGGTAATGCTGTAAAAAGTGTGTTTTGTATTATTTGTCACGGAGGCATTTAGAAGCGGGGGAG
-41 TCGATGGTTGAAGGAATCATTGGTCTGTAATTTCATAACTGTATGCGTAGGTTAGACTAACTGGGCATATAGGTTACGGTGGTCCACTATATTCATAATCTAAGCAGTACTGAATGTACGCGGCGATACTAGCGATGTGAGGTGAACAAGCTACGTTGGGAGCAGTTGGGGGCGTAGTCCTAAGTTAATACCTTCTTATTATGTGCGTAAGTAGTAGAGGTTTTTTGAAGCGGTGTTCGGTCGGCTACAGTATTCAGTGTGTAATGATGTTTGGTAAGGGGCGTTCGTTATTCAGCAAACTTCAGTGGTATGTTGGAGACGAGACGGTAATGCTGTAAAAAGTGTGTCTTGTATTATTTGTCACGGAGGCATATAGAAGCGAGGGAG
-36 TCGATGGTTGGGGGAAGCAATGGTCTGTAATTCCGTAACTGTATGCGTAGGTTAAACTAATTATGCAGACAGGTTACTGTAGTGCACTACAATTATATTCTAAGCAGTAGTGAATTTACGCGGCGATATTAGCGTTGTTAGGTGAGCAAGCTTCATTGTGCGCAGGTGGTGGCGTAATCCTAAGTTGATACCTTCTTATTATGTGCGTAAGAATTAGAGGTATCTTGAAGCGGTGTTTGGTTGGTCACTGTATTTAGTGTGTAAAGATTTTCGGTAAGGGGCGTTCGTTATTCAGCAAACTTTATTGGTATGTTGGAGACTAAACGGTAATGCTGGATAAAGTGTGTTGCATATTATTTGTCGAGTTTGCATATAGAAGCGAGGGAG
-39 CCGATGGTTGAAGGAATCACTGGTCTTAAATTTCTTAACTGTATGCGTAGGTTATACTAACTAAGAATACATGTTACGGTGGTCCACTATATTCATAATCTAAGTAGTACTGAATGTACGCGGCGATATTAGCGATGCGATGTGAGCAAGCAACGTTGGGAACAGTTAGGGGCGTAATCCTTAGTTAATACCTTCTTATTATGTGCGTAAGCATTAGCGGTATTTTGGAGCGGTGTTGTGTCGACTACATTATCCTTTGTGTAAGGATGTTTGGTAGGGGGCTTTCGTTATTCAGCAAACTTCATGGGTATGTTGAAGACGAGCCGGTAATGCTGAAGAAGGTGTGTTTATTATTATTTTGCACGGAAGCATATGGAAGCGAGGGAG
-28 TCGTTGGTTGGAGGAATCAGTGGTCTTGACTTTCTTAACTGTATTCGTAGGTTATACTAACTGGGAATATTTGTCACGGTGGTTCACAATATTTATATTCTAGGTAGTACTGAATGTACGCGGCGATATTAGCGATGTAAGGTGAGAATGCAGTGTTGGGAGCAGTAGAAGGCGTAATCCTAAGTTCATGTCTTCATAGTATGGGCGTAAATACCAGTGGTATTTGGGAGCGGTGTGGCGGCGACTACCGTACTCAGTGAGTGAAGATCTTTAGTAAGTGGCGTTCGTTATTCAGCAAACTTCGTTGGTATGTTGGAGGGAAATCGGTAATGCGGTGGAAAGTGAGTCTTATATTATTTGCCACGAGGGAATATGGAAGCACGGGAG
-71 TCGTTGGTTGAAGGAATCAGTGGTCTTTAGTTTCTTAACTGTATTCGTAGGTTAGACTAACTAGGTATATTGGTCACTGTGGTTCACTATATTCATATTTTAAGCAGTACTGAATGTACGCTGCGATATTAGCGATGTGAGGTGAGAATGCAACGTTGGGAGCAGTAGAGGGCGTAGTCCTAAGTTAATACCTTCATAGTATGGGTGTAAGTATCAGTGGTATTTTGGAGCGGTGTGGTGGCGACTACCGTATTCAGTGAGTAAAGATGTTTAGTAAGTGGCGTTCGTTATTCAGCAAACTTCGTTGGGATGTTGGAGCCGTATCGGTAATGCTGGAGAAAGTGAGTCTGATACTATTTGCCACGAGGGCATATGGAAGCGCGGGAG
-76 TCGTTGGTTGAAGGAACCAGTGGTCTTCAGTTTCTTAACTGCATTCGTAGGTTAGACTAACTAGGTATATTGGTCGCTGTGGTACACTATATTTATAATTTAAGCAGTACTAAATGTACGCTACGATATTAGCGATGTATGGTGTGAATGCAACTTTGAAAGCAGTAGAAGACGTATTTCTAGGTTAATACCTGCGTAGTATGGGAGTAAGTATTAGTGGTAATTTGGAGCGGTGTTGTGGCGACGACGGTACTTGGTGAGTAAAGATGTTTAGTAAGGGGCGTTCGTTATTCAGCAAACTTCGTTGGGACGTTGGAGCTGTATCGGTAATGCTGGAGAAAGTGAGTCTGGTACTATTCGCCACGAGGGCACGTGGAAGCGCGGGAG
-52 TCGTTGATGGAAGGTAGCAGTGGTCTTGAGCTCCTTCACTGTATGCGTAGGTCAGATGAACTAGGGATATCGGTTATGGTGGTTAACGATTTTTATACTTTAAGCAGTTCTGAATGTACGTGGCGATATTAGCGTTGTAATGTGAGAATGCATCGTTGTAAGCATTAGGGGGCGTGATCTTAAGTTAATACCTTTATAGGATGGGCGTAATTATCAGTGGGTTTTTGGAGCGGGGTGTTGTCGACTGCCGTAATCGGTGAATAAAGATTTTAAGTAAATGGCGTTCGGTATTCAACGAACTGCGTAGGTATGTGGGAGTCGAAATGGTAATGCTGGATAAAGTCAGTTTGATAATATTGGGCACGAGGGCATATCGAAGTGTGGGAG
-55 TCGGTGATTGAATGAATGAATGGTCATAAGTGTCTTAGCGGTATTCGTAACTTAGACTAACTATGAATATAGGTTGCAGCAGTTCACAATATTCATATTTTAAGCAGTACTGAACGTGCGCTATGATAGTAGCGATGAGATGTGCTAATGCTCCTTAGCATACTGTAGTAGGCGTAGTTCTTAGGTAAGGACTTTACATGATGACTGCAAGTGGTAGCGGTACATAGTAGCGGTATGGGGCCGACTGCTGTAATCATTGACTAAAGATTCTTGGCGAGGGACTTTCGTTATCCAGCAAACCTAGTAGATATGCTTGAGTTAACTCTGTAATGATGGAAGAAGTGGTTCTATTACTATTAATCACAAATGCATGTGGAAGATGGGGAG
-38 TCGGTGATGGGGTCTAGGAAATGTCTTAATTGGCATGGCTGTATGCGTAACTGAGACTAACTAGGAATATGTGTTGTAGCAGTTCATCATAGTAATATTATAAGCTGTATTGAACATACGCCATGATATTAGCGGTGTGATGTACGTGCGCAGCCTAGAATGCTGTGGTAGGTGTAGTTCGCTGTTAATGGCTTTGCATCGTGTATTCCATGAACAGCGGTGCATAGAAGCGGCATGATGCCGATGTCTTTAGTTAGAGACTAAAGGTAATTTGCTATTTACTTTCGTAATCCAGCAAACTTAGTGGATATGCTTGAGTAGACTGTGTAATGGTGTTAGACGTGGTTTTCCTATTATTAAATGCAATCGCATTTTAAAGAGGGGGAA
-89 TCGGTGATGGTGTCTAGTAAATGTCCTAAGTGACTTAGCGGTATGCGTAACTGAGACTAACTGGGAATATGTGTTGCAGCAGTTCACCAGAGTAATATTATAAGCTGTATTGAACGTGTGCTATGATAGTAGGGATATGATGTGCTTGCGCTTCCTAGCAGACTGTGGTAGGTGTAGTCCACAGTTTATGGCTTTGCATTGTGACTGCAAGTAATAGCGGTGCATTGAAGCGGCATGGTGTCGGTGGCTTTAGTCATTGACTAAAGGTTGTGGGCGATTGACTTTCGTAATCCAGCAAACCTGTTTGAGACGCTTGAGTCGACTCTGTAATGCTGGCAGAAGTGGTTCTCGTACTATTAAACACAATCGCATGTTAAAGAGGGGGTA
-30 TCGGTGATGGTGTCTAGTAAATGTCCTAAGTGACTTAGCGGTATACGTAACTGAGACTAACTGTGAATATGTGTTGCAGCAGTTCACCAGAGTAATATTATAAGCTGTATTGAACGTGTGCTATGATAGTAGCGATGTGATGTGCTTGCGCCGCCTAGCAGACTGTGGTAGGTGTAGTCCACAGTTTATGGCTTTGCATTGTGACTGCAAGTAATAGCGGTGCATTGAAGCGGCATGGTGTCGGTGGCTTTAGTCATTGACTAAAGGTTATGGGCGATTGACTTTCGTAATCCAGCAAACCTACTTGAGACGCTTGAGTCGACTCTGTAATGCTGGCAGAAGTGGTTCTCGTACTATTAAACACAATCGCATGTTAAAGAGGGGGTA
-20 TCGGTGATGGTGTCTAGTAAATGTCCTAAGTGACTTAGCGGTATGCGTAACTGAGACTAACTGGGAATACGTGTTGCAGCAGTTCACTAGAGTGATATTATAAGCTGTATTGAACGTGTGCTATGATAGTAGCGATGTGATGTGCTTGCGCTTCCTAGCAGACTGTGGTAGGTGTAGTCCACAGTTTATGGCTTCGCATTGTGACTGCAAGTAATAGCGGTGCATTGAAGCGGCATGGTGTCGGTGGCTTTAGTCATTGACTAAAGGTTATGGGCGATTGACTTTCGTAATCCAGCAAACCTACTTGAGACGCTTGATTCGACTCTGTAATGCTGGCAGAAGTGGTTCTCGTACTATCAAACACAATCGCATGTTAAAGAGGGGGTA
-83 TCGGTGATTGAATGAAGAAATGGTCATGAGTGGCTTAGCGGTATTCGTAAATTAGACTAACTATTGATATAGGTTGCAGCAGTCCACCATATTTATATTTTAAGCAGTGATGAACGTGCGCTATGATAGTAGCGATGAAATGTGTTCACGCGACTTAGAAGACTGTAGTAGGCGTAGTTCTTAGGTAAGGACTCGACATGATGACTGCAAGAAGTAGCGGTACATTGTAGCGGTATGGGGCCGACTGCTGTAATCAGTGACTAAAGATTCTTGGCAAGGGACTTTCGTTATCCAGCAAACCTAGGAGATATGCTTGAGTTAACTCTGTAATGCTGAAAGAAGTGGTTCTTTTACTATTAATCACAAATGCATGTAGAAGATGAGGAG
-68 TCGGTGATTGAATGAATAAATGGTCATAAGTGGCTTAGCGGTATTCGTAAATTAGACTAACTATTGATATAGGTCGCAGCAGTTCACCATATTTGTATGTTAAGCGGTGATGAACGTGCGCTATGATAGTAGCGATGAATTGTGCTCACGCTACTTAGATGACTGTAGTAGCCGTGTTTCTTGGGTCAGGAATTGACATGATGACTGCAACTAGTAGAGGTATATGGTAGCGGTATAGGGTCGACCGCTGTAATCAGCGACTAAAGATTTTCTGCAAGGGACTATCGTTATCCAGCTAACCTATTAGATATGCTTGAGTTAACCCTGTAATGCTGTAAGAAGTGATTCTAGTACTATTAATCACAAATGCATGTAGAAGATGAGGAG
-74 GCGCTGGTGGGGTTAAGTATTGGTCATGAGTGTCTTAACTGTATACGTATGTCAAACTATCTGAAGACATATATTATGGTGGTCTGCTTCACTGATGCTTTAAGTAGTACTGAGCGTACGCTGTGATATTAGCGGTGTGATGTTACCATGCAGCGTAGGTGGCAGTGGGGTGCGTTTTCCTAAGTTAATACCTTCTTAATATGGTTGTAAGGATTAGGGGTATTTTGGAGCGGTATGAAGCAGACTACTGTACACGGTGACTAAAGGTGTACAGTACTGGGCTTTCGTTATTCAGCTAACTGGGTTGGTATGTTGGAGCGAAATCGGAAGGGTTGTATGATGTGAGTTTGATATTATTTAACACGGAGGTATATTGATATGCTGGAG
-32 TCGTTGGTTGCATTAATTAGTAGTCTTAAATGGCGTAACTGTATCCGTATGTTATGCTAGTTGTATAGAAATTTTATGGTGGTCTACTTCAGTTATGCCCTAAGCAGTTCTGAGCGTACGTTGTGACAACAGCGATGGAATGTTGCTCTGCATCGTAGGCAGCAGGGGGGGGCGTCATCCTATGGTAATAACTTTTTAAAATGGGTGTAAGCAATAGGGGTTTTTGGGAGCGGTATGCAAAGTACTACGGTAAGCAAAGACTAAAGGTTTTTAGTATTAGTCATTTGTTATTCAGCGAACTGGTTTGGTATGTTGAAGTTGAAGCGGAAAGGTTGAATGATGTGAGTCTATTATTATTTGTTACGGAGGTATATTGAAATTTGGGAT
-49 CCGTTAATAGTGAGAACTAGCTGTCGTGAGTGGTGTGACTATATCCGAATGTCAAATTAGTTTTTTAGACATGTGATGGGGGTCAACTCCTCGTGTGACACAAACGGTCTTCAAGGTATGCTGTGATTTCAGCGGGGTAAGGTTACCGTGCGCCTTAGTTACCTAGGGGAGACGTCCTCCCAAGTTAATACTTCCCTAAATTGTTAGTGAGTACAAGGGGTGTTTTGAAGCGGGATGAAAGGTATTACAGGAGCGGACGACTAAACTTCACCAGTACTAGGCATTCGTAATTCGGCTAACTGTGGAGATATGTTGAAGCAATCGCGGAAATGTCGAGAGATGTTGATCTTAAAGTATTAATTACGGAGGTATATGGAAATGGGGGAC
-15 CCGTTAGTAGTGTTAACTAGTTGTCGTAAGTGGTGTGACTGTATCCGTATGTCAAATTAGCTGTTTAGACATATTATGGGTGTCAACTCCATGTGTGACTCAAACAGTCTTGAGGGTATGCTGTAATATCAGCGATGTAATGTTACCGCGCATCCTAGTCAGCTGGGGGGGGCGTCTTTCCAAGTTAATACCTATTTAAATCGGTGGTGAGTAACAGGGGTGCTTTGAAGCGGGATGTAAAGTACTACTGTAACGGATGACTAAAGGTCTCCGGTAATGGGCATTCGTAATTCAGCTAACTGGGGAGGTATGTTGAAGTAAATACGGAAATGTTGAGTGATGTGAGTCTATGAGTATTTATTACGGGGGTATATTGAAATGGGGGAC
-43 TCGTTGGTTGGAGTAATTAGTGGTCGTAAATGTCTTAACTGTATCCGTATGTGATACTAGCTAGGTATATAGGTTATGGTGGTCAACTGTATTCATGTTTTAATCAGTATCAAACGTACACCGTGATACTGGCGTTGAGATGTTGCCTTGCAACGTAGAGAGCGGGGGGGGGCGTAGTCTCAAGGTGATAACTTCTTATAATGGGGTTGAGCATTAGGGGTATTTAGTAGCGGTGTGGTATTGACAACGATATTCGGAGACTAAAGATTTTTAGTAAGGGACCTTCGTTATTCAGCTAACTTGGGAGGTATGTTGGAGTCGAATTGGTAATGCTGTAGGAAGTGAGTCTATTATTATTTGCCACGGGGGCTTATAGAAACTTGGGCT
-72 GCGTTGGTGGAATTAATCAATGGTCAATAATGGCTTAACCGTACACGCAGGTTAGACTAGCTTAGTAGATTGTTTTCGGCGGTCCACCTTATTTATACTTTAAGCAGTATTGAACTTACGCTTTGATATTAGCGTATTGAGGTTTTTTTGCAACATTGGAAGTAGTAGGTGGCGATTTCGTTGGTTAAGAGTTTCGTATCATGGTTGTAAGTATAGGAAGTATTTTGGAGTGGTATGTTGCTGATCGCTGTACTCATAGACTAAAAATATCCAGTAAAGGGCTATCGTTATGCAGCAAACTTGATAGTGAGATTGGAGGGGGATTGGTGACTATGTAGGGAGTGAGTCTAATATTATTCGCCACCAGGGCGTGTAGTAGTACGGGAG
-4 GCGTTGTTGGGATTAATCAATGGTCAGTAATGTCTTAACCGTACGCGCAGTTTAGACTAGCTTGGAAGACTGTTTTCGGCTGTCCTCCTTATTTATACTTTAAGCAGTATTGAACATACGCTTTGATATTAGCGGATTGAGGTTGTGTTGCAACGTTGGAAGTAGTAGGTAGCGATTTCGTTGGTTAAGAGTTTCGTATCATGCTTGTAAGTATAGGAAGTATTTTGGAGTGGTATGTTATTGATTGCCGTATTCATAGACTAAAAATACCCAGCAAATGGCTATCGTTATGCAGCAAACTTGATGGTGAGATTGGAGGGGGTCTGGTGACTATGTAGGGAGTAAGTCTTGTATTATTCGCCACCAAGGCGTGTGATAGTACGGGAG
-61 GCGTTGTTGGGATTAATCAATGGTCAGTAATGTCTTAACCGTACGCGCAGTTTAGACTAGCTTGGTAGATTGTTTTCGGCGGTCCTCCTTATTCATACTTTAAGTAGTATTGAACTTACGCGTTGATATTAGCGTATTGAGGTTGTGTTGCAACGTTGGAAGTAGTAGGTAGCGATTTCGTTGGTTAAGAGTTTCGTATCATGCTTGTAAGTATAGGAAGTATTTTGGAGTGGTATGTTAGTGATCGCCGTACTCATAGACTAAAAATATCCAGCAAATGGCTATCGTTATGCAGCAAACTTGATAGTGAGATTGGAGGGGGTTTGGTGACTATGTAGGGAGTAAGTCTTGTATTATTCGCCACCAAGGCGTGTAATAGTACGGGAG
-95 TCGTTGGTGTTCTTAATCAGTGGTCTTGAATGGCTTAAATGTATACGCAGATCATACTAGCTAATTAGATTGTTTGCGGTGGTCCACCTTATTCGTAGTATAAGTAGTTCTGAACTTACGCGTTTATAGTAGCGGGTTGAGGTTGTCCTGCTTCGTTGGAAGTGGTTGGAGGCGTTCTCCTGCGTTAAAAGTTTTGTATCATGGTCCTGAGTAGATGTGGTATTTCGCAGTGGTGTGGAGGGGTCAACTGTATCGATAGACTAAAAATACCGAGTAAAGTACTGTCGTTATGCAGCTAACTTGGTGGTGAGGTTGAAGTGGGAAGGGTAATGTTGAAGGAGGTAGGTCTAATACTATTTGTCACCACGGAATGTAAAAGTGCGGGAA
-31 TCGTTGGTGGTCCTAAGCAGTGGTCTTGAATGACTTAAACGTATTCGTAGATCATTCTAGCGAATTAGATTGTTTGCGGGGGTCCACCTTGTTTTTAATATAAGCGGTTCTGAACTCACGCGTTTATAGTAGCGTGTTGAGGTTGTGTTGCTTCGTTGGAAGTGCGTGGAGGCGTTTTCCTGTGGTAAAAGTTTTGTATCATGGTTCTGAGGATATGTGGTATTTCGCAGTGGTGTGGAGTGGTCTACTGTAGCGATAGACTAAAAATATCTAGTAAAGTACCGTCGTTATGCAGCTAACTTGATGGTGAGGTTGAAGTGGGAGGGGGAATGCTGTAGGAGGTAGGTCTAAGACTATTTGCCACCACGGAATGTTAAATTGCGGGAA
-78 TCGTTGGTGGGATTAAGCATTGGTCTTGAATGACTTAACCGTATATGCAGATTAGACTAGCTAAGTAGAATGATTACGGAGGTCTACCTTATTTCTACTTTAAGCTTTAATGAACTTACGCTTTGATATTAGCGCATCTAGGTTATTTCGTGGCGTTGGGAATAGTAGGTAGCGTGTTTCTGAGTTAAAAATTCCGTATCATGGTGGTTAGGAGATCTGGTTTCTCTCAGTGGTGTGGGGTTTACGACTGTAGAGAGAGGCTAAAAATATCTGGTAAAGGACTTTCGTTATGCAGCTAACTTGATAGAGAGGTTGAAATTTGAAGGGTAGTGCTGTTGGGGGTAAGTTTAGTATTATTTGACACCATTGCATGTCAAAGTTGGGGAG
-90 TCGTTGGTGGGATTAATCAATGGTCTTGAATGGCTTAACCGTATATGCAGATTAGACTAGCTAAGTAGAGTGTTTACGGTGGTCCACCTTATTCCTACTTTAAGCAGTACTGAACTTACGCTTTGATATTAGCGTGTTGAGGTTTTCTTGCAACGTTGGAAATAGTAGGGGGCGTTCTCCTGAGTTAAGAGTTTCGTATCATGGTTGTAAGTAGATGTGGTATTTTGTAGTGGTGTGGGGCTGACTACTGTATGGATAGACTAAAAATATCTGGTAAAGGACTTTCGTTATGCAGCAAACTTGATAGTGAGGTTGAAGCTGGAATGGTAATGCTGAAGGAGGTAAGTCTAATATTATTTGCCACCAGGGCATGTAAAAGTGCGGGAG
-62 GCGTTGGTTGCGATAATCAAGGGTCTTGAATAGCACAACCAGATCTGCAAATAAATCTAGCTAAGTGGATTGTTTGCGGGTGTCCACCTTACTTCTATTTTAAGCAGTACTGAGTCGGCGCTTTGATAGTAGCGTGTTTAGGGGTGTGTGCAACTTCGGATATAGAAGGTGGCGTGATATTTTGCTAAGTTTTTTGTATCATGAACGCGAGTAACTGTGGTATCTTTTAGTGGTGTTTGTCTGGAAGCTGTATTCGTAGGCTAAAGATGACGAGTAAAAGTCCTTCGTTATGCAGCAAACTTGGCTGTTAGGTTGCAGTATGATTGGTAAGGTTGTGCAAGGTGGGTTTGCCATTATTTGTCGCCAGGGCAGTTAAAAGTACGGGAG
-57 TCGTTGGTTGGGGTAATCAATGGTCTTGAATAGCGCAACCGTATATGCAGATGAGGCTAGCTAAGTAGATTGTTTACGGGGGTCCACCTTATTCCTACTTTAAGCAGTACTGAACTGACGTTTTGATATTAGCGGGTTGAGGTGTTTTTGCAACGTTGGAAATAGTAGGGGGCGTACTCTTGAGCTAATGGTGTAGTATCATGGACGTAAGTACATGTGGTCTTTTGTAGTGGTGTTGGGCTGACTACTGTATTCGTAGACTAAAGATGTCTAGTAGAGGACTTTCGTTATGCAGCAAACTTTGCAGTGAGGTTGAAGCATGATTGGTAATGTTGAATGAGGTAAGTGTTGTATTATTTGCCACCAGGGCATGTAAAAGTGCGGGAG
-85 TCGTTGGTTGGATTAATGAATGGTCTTTAATGACTTAACCGTATATGCAGATGAGGCTAACTAAGTATTTTGTTCACTTTGGTCCACCTTATTGCTAGTTTAAGTAGTACTGAACTTGCTCTTTGATATTAGCGAGTGGAGGTGTGTTTGCAACGTTGGAGATAGTAGGCGGCGTTGTCCTTAGCTGAGGGTTCCGAATCATGTACGGAAGTACGCGTGGTTTCTCGTAATGGTGTTTGGTTGACTACTGTATCCGTGGATTAGAAATGTCTAGGAAATGGCATTCGTTATGCAGCAAACTTGGCAGGGAGGTTGAAGTTAGAATGGTAATGCTGAATTAGGTTAGTCTTTTTCTATTGGCCTCTATGGCATGAAAAAGTATGGGAG
-82 TCGTTGGTTGAATTAATTAATGGTCTTGAATGGCTTAACCGTATATGCAGATGAGGCTAGCTAAGTAGTTTGTTTACGGTGGTCCACCTTATTCCTACTTTAAGTAGTACTGAACTTGCGCTTTGATATTAGCGAGTTGAGGTGTCTGTGCAACGTTGGAAATAGTAGGTGGCGTTTTCCTGAGCTAAGGGTTTCGTATCATGTACGTAAGTACATGAGGTATTTTGTAGTGGCGTTTGGCTGACTACTGTATTCGTAGACTAAGAATGTCTAGTAAATGTCTTTCGTTATGCAGCAAACTTGGCAGTGAGGTTGAAGCTAGACTGGTAATGCTGAAGGAGGTAAGTCTTGTATTATTTGCCTCCACGGCATGTAAAAGTATGGGAG
-13 TCGTTGATTGAAATGAGCAATGGTGTTGAATGGCTTAACCGTATATGCAGGTTATGCTAGCTACGTAGATTATTGACGGTGGTTCACCTTATTTCTACTTTAAGCAGTACTGGGCTTGCGTCTTGATATTAGCGGGTTGAGGTGTTTTTGCACCGTTGGAATTATGAGGGGGCGTTGTTATGAGTTAAGGGCTTCGTATCATGGACGTAAGTATATGTGGTGTTTTGTAGTGGGCTTTGGCTGACGGCCGTAGGCGTGGACTAAAAATGTCTAGTAAGGGACTTTCGTTATGCAGCAAGCTTAAGAGTGAGGTTGAAGCTGGATTGGTAATGCTGAAAGAGGTTAGTCTTTTATTATTTGTTACCATGGCATGTAAAAGTGTGGGAG
-59 ACGTTGATTGAGATGAGCAATGGTCTTGAATGGCTTAACCGTATATGCAGGTTATGCTAGCTACGTAGATTATTGATGGTGGTTCACCTTATTTCTACTTTAAGCAGTATTGGGCTTTCGTCTTGATATTAGCGGGTTGAGGTGTTTTTGCATCGTTGGAAGTATGAGGGGGCGTTTTTCTGAGTTAAGGGCTTCGTATCATGGACGTAAGTAGATGTGGTGTTTTGTAGTGGGCTTTGGCTGACGGCCGTAGGCGTTGACTAAAAATGTCTAGTAGGGGACTTTCGTCATGCAGCCAGCTTAAGAGTGAGGTTGAAGTTGGATCGGTAATGCTGAAAGAGGTCAGTCTTGTATTATTTGTTACTATGGCATGTAAAAGTGTGGGAG
-18 ACGTTGATTGAGATGAGCAATGGTCTTGAATGGCTTAACCGTATATGCAGGTTATGCTAGCTACGTAGATTATTGACGGTGGTTCACCTTATTTCTACTTTAAGCAGTATTGGGCTTGCGTCTTGATATTAGCGGGTTGAGGTGTTTTTGCATCGTTGGAAGTATGAGGGGGCGTTTTTCTGAGTTAAGGGCTTCGTATCATGGACGTAAGTAGATGTGGTGTTTTGTAGTGGGCTTTGGCTGACGGCCGTAGGCGTTGACTAAAAATGTCTAGTAGGGGACTTTCGTCATGCAGCCAGCTTAAGAGTGAGGTTGAAGTTGGATCGGTAATGCTGAAAGAGGTCAGTCTTGTATTATTTGTTACTATGGCATGTAAAAGTGTGGGAG
-75 TCGCTGGTAGGATTAAATGATTGTCTAAAATGGCTTAACCGTATATGCAGTTAAGACTAGCTGCGTAGATTGCTTACGGTGGTCAACCTTGTTTGTGCTTTAAGCATTATTGGATTTTCGCTTTAAGACTAGCGGTTGGACGATGTGTTGCGGCTCTGTTTGTATTTCGGAGCATTGTCCTCTGTTAGGGATTTGATGTCGTGCTTGTAATTATATGGGGTGTTTTGAAGTGGGGTGAGATTGATTACTGTACGCAAGGACTAAAAGTAGCTAGTATAGGTCTATTGTTATGCAGCAAGCTTGATGGTGAGGGTGAAGTTGGATTGGTAGTGTTGAAAGATGTTAGTACCGTAGTATTTATCACCAGGGGATGGAAAAGTGCGGGAG
-3 TCGTTGGTGGGATTAAATAGTGGTCTAAAATGGCTCAACCGTATGTGCAGTTGAGACTAGCTAATCAAATTGCTTGCGGTGGTCTACGTTGTTTGTATTGTAAGTATTACGGAACTTTCGCTTTAAGATCAGCGCGTGGACGATGTTTCGCGACGCTGTTTTTATTACGGAGCACTTTCCCATGTTAGGGGTTTGATATCGTGTTTTTAAGTAGATGAGGTTTTTTAGAGTGGTGTGCGGCTGACTACAGTATTCAAAGACTAAAAGTAGCTTGTATAGGTCTGTCGTTACTCAGCAAGCTTCATAGTGAGGGTGAAGCAGGATTGGTAATGTTGTAGGATGTAAGTACTTTAGTATTTATCACCAGGGCATGGAAAAGTTTGGGAT
-27 GCGTTGGTGGGTTTAAAAAGTGGTCTAAAATTGCTCAACCGTATGTGCAGTTGAGACTAGCTAATCAAATTGTTTGCGGTGGTCTACGTTGTTTGTATTGTAAGTATTACGGAACTTTCGCTTTAAGATTAGCGTGTGGACGATGGTTCGCGGCGCTGTTTATATTACGCAGCACTGTCCCATGTTAGGGGTTAGATATCGTGTTTGTAAATAGATGAGGTTCTTTAGAGTGGTGTGTGGCTGACTACAGTATTCAAAGACTAAAAGTAGCTAGCAGAGGTCTGTCGTTACTCAGCAAGCTTCATAGCGAGGGTGAAGCAGGATCGGTAATGTTGTAGGATGTAAGTACTTTAGTATTTATCACCAGGGCATGTAAGAGTTTGGGAT
-29 TCGTTGGTGGGATTAAATAGTGGTCTAAAATGGCTCAACCGTATGTGCAATTGAGACTAGCTAAGCATATTGCTTGCGGGGGTCTACGTTGTTTGTATTTTAAGTATTACGGAACTTTCGCTTTAAGATTAGCGTGTGGACGATGTTTCGCGTCGCTGTTTTTATTACGGAGCATTTTCCCCTGTTAGGGGTTTGATATCGTGTTTGTAAGTAGATGGGGTTTTTTAGAGTGGTGTGCGGTTGACTACCGTATTCAAAGACTAAAAGTAGCTAGTATAGGTCTGTCGTTATTCAGCAAGCTTCATAGTGAGGGTGAAGCAGGAGTGGTAATGTTGTAGGATGTAAGTACTTTAGTATTTATCACCAGGGCATGGAAAAGTTTGGGAT
-51 TCGCTGGTGGGGTTAATCAATGGTCTTTAATGGCTTAAACGTATACGCAGATTAGACTAGCTAAGTAGATTGTTTACGGTGGTCTACCTTATTCCTACTTTAAGCGGTACTGAACTTACGCTTTGATATTAGCGTGTTGAGGTTTTCTTGCAACGTTGGAAGTAGTAGGTGGTGTTTTCCTGAGTTAAGAGTTTCGTATCATGGTTGTAAGTAGATGTGGTATTTTGGAGTGGTGTGGGTCGGACTACTGTATTCATGGACTAAAAATAGCTAGTATAGGCCTTTCGTTATGCAGCAGACTTGATTGCGAGGATGAAGCTGAAATGGTAAGGCTGAAGGAGGTAAGTTTGATAGTATTTGCCACCAGGGCGTGTAAAAGTGTGGGAG
-1 TCGTTGGTGGGATTAATCAATGGTCTTGAATGGCTTAACCGTATACGCAGATTAGACTAGCTAAGTAGATTGTTTACGGTGGTCCACCTTATTCCTACTTTAAGCAGTACTGAACTTACGCTTTGATATTAGCGCGTTGAGGTTTTCTTGCAACGTTGGAAGTAGTAGGGGGCGTTTTCCTGAGTTAAGAGTTTCGCATCATGGTTGTAAGTAGATGTGGTATTTTGGAGTGGTGTGGGGCGGACTACTGTATTCATAGACTAAAAATATCTAGTAAAGGACTTTCGTTATGCAGCAAACTTGATAGTGAGGTTGAAGCTGGAATGGTAAGGCTGAAGGAGGTAAGTTTAATATTATTTGCCACCAGGGCGTGTGAAAGTGCGGGAG
-79 TCGTTGGTGGGAGTAATCAATGGTCTTGAATGGCTTAACCGTATACGCAGATTAGACTAGCTAAGGAGATTGTTTACGGTGGTCCACCTTATTCCTACTTTAAGCAGTACTGAACTTACGCTTTGATATTAGCGCTTTGAGGTTGTCTTGCAACGTTGGAAGTAGTAGGGGGCGTTTTCCTGAGTTAAGAGTTTCGTATTATGGTTGTAAGTACATGTGGTATCTTGGAGTGGTGTGGGGCGGAATACTGTATTCATAGACTAAAAATATCAAGGAAAGAACTTTCGTTATGCAGCAAACTTGATGGTGAGGTTGAAGCTGGAACGGTAAGGCTGAAGGAGGTAAGTCTAATATTATTTGCCACCAGGGCGTGTAAAAGTGCGGGAG
-87 TCGTTGGTGGAGTAAATTAACCGTCTTGAATGGCTCAACCGTATACGCAGATTAGACTAGCTAAGGAGATTGCTAACGGTGGTCCACTTTATTGCTACTATAAGTAGTACCGAACTTACGCTTTGAGATTAGCGGGTTTACGTTTTCTGGCGACGTTGAAAGTAGGAAGGGGCGTTTTCCATAGTTAAGCGTTTGGTATCATGGTTGTGAGGAGATGTGGTACTTTGGAGTGGTGTGGGGCGGACTACAGTAATCATAGACTAAAAATATCTAGTAAAGGACTTTCGTTATGCAGCAAACTTGAGAGTGAGGTTGGAGTTGGATTGGTAAGGCTGAAGGAGGTAAGTTTGTTATTATTTTCCACCAAGGCGTGTAAAAGTACGGGAG
-67 TCGTTGGTGGTACTAAACATTGGTCTTGAATGTCTTAACCGTATATGCAGGTAGCACTAGATAAGTAGATTGTTTACTGTGGTCTACCTTAGTTCTACCTTAAGCGGTGCTGAACTTATCCTTTGATATTAGCGCGTCGAGGTTATGTTGCAACGTGGTAAGTCGTAGAGGGCGTTGTCCTGAGGTAAGAGTTTCGTATCATGGTTGTAAGTATATGTGGTATTTCGGAGTGGTGTGGGGCTGACTACCGTAAGCATAGACTAAAAATATCTAGTAAAGGACTGTCGGTATGCAGCAAACCAGGTAGTGAGGTTGAAGCTCGAACGGTAATGCTGATAGAGGTAAGTCTGGTATTATTTGCTACCGAGGCATGTAAAAGTGCTGGAG
-69 TCGTTGGTGGTACTAAAAAATGGTCCTGAATGCCTTAACCGTATATGCAGGTAGTACTAGATAAGTAGATTATTTACTGGGGTCTACCTTAGTCCTACCTTAAGCAGTACTGAAGTTGCGCTTTGAAACTAGCGGGTCTAGGTTAGCCTGCAACGTGGCAAGTAGTAGGGGTCGTTATCCTGATTTAAGCTTTTCGTATCATGGTTGTAAGAATATGTGGTATTTCGGAGTGGTGTGGAGCAGACCACTGTAGTCATAGACTAAAAATATCTAGGAAAGGACTGTCGGTATGCAGCAAACTAGCTAGTGAGGTTGAAGCTTGAATGGTAATGCTGACAGAGGTAAGTTTAATATTATTTGCAACCGGGGCATGTAAAAGTGCTAGAG
-8 TCGTTGGTGGTATTAAACATTGGTCTTTAATGACTTAACCGTATACGCAGGTCAGACTAGATAAATAGACTGTTTATGGTGGTCTACCTTATTCCTACTTTAAGCAGTACTTAACTTACGCTTTGATATTAGCGCGTCTAGGCTTGCTGGCACCGTTGTAGGTAGCGGGAGGCGTTTTGCCCAGTTAAGACTTTCGTATCATGGACGTAAGTATATGTGGTATTTTGGAGTGGTGTGACGTAGACGACAGTATTTGGAGACTAAAATGATCTAGTAAAGGACTTTCGGTATGCATCAAACTGGATAGGGAGGTTGAAGCTGGAATGGTAATGATGGTGGAGGTGAGTCTGGTACTATTTGCAACCAGGGCCTGTGAAAGTGTTGGAG
-94 TCGCTGGTGGGGTTAAACAATGGTCGTAAATGGCTTAACTGTATAAGTAGGTTAGACTAGCTAAGGAGATTGTTACCGGTGGTCTACCTTATTACTACTTTAAGAAGTACTGAACTTACGCTTTGATATTAGCGTGTTGAGGTTTTTTTGCATCGTTGGAAGTAGCAGGTGGCGTTCTCCTGAGCTAAGAGTTTCGTATCATGGTTGTGAGGAGATGTGGTATTTTGGAGTGGTGTGGTGCTGACTACTGTATTCGTAGACTAAAAATATCTAGTAAAGGACTTTCGTTATGCAGCAAACTTGATAGTTGGGTTGAAGCCTGAATGGTAATGCTGAATGAAGTAAGTCTAATATTATTTGCCGCCAGGGCATGTAAAAGTGTGGGAG
-91 TCGTTGGTGGGACTAAGCATTGGTCCTTAATGGCTTAACCGTGTACGTAGGTCAGACTAGCTAAGGATATTGGTAATGGTGGTCTACTTTATTTTTTTTTTAAGCAGTATTGATCTGGCGCTTCGATGCTAGCGCGGGGAGGGTTTTTTGCATCGTTGTAAGTAGTAGGGGGCGTTTTCCTGAACCGAGTGTGTTTTATCATGGTTGTGAGTACCGTTGGCAGTTGGGAGTGGTGTTGTGGTGAGCACTTTACCCATAGACTAAAAATATCCAGTGAAGGACCTTCGTTATGCAGCAAACTTGATATTAAGGTTGAAGTTCGACTGGTAATGCTGAGGGGAGTAAGTCTTATACTATTTACCGCCAGGGCATGTAAAAGTGCGGGAG
-26 TAGTTGGTTGAATTAAACAATGGTCTTAAATGGCTTAACCGTATACGTAGGTTAGTCTAGCTAAGGAGATTGTTAACGGTGGTCCACCTTATTTCTACTTTAAGGAGTACTGAACTTACGCTTTGATATTAGCGTGTTGAGGTTTTCTTGCATCTTTGGAAGTATTAGGGGGCGTTCTCTTGAGCTAAGAGTTTCGTATCATGGTTGTGAGTAGATGTGGTATTTTGGAGTGGTGTGGTGCTGATTACTGTACTCATAGGCTAAAAATATCAAGTAAAAGACTTTCGTTATGCAGCAAACTTGATAGTGAGGTTGAAGCTTGAATGGTAATGCTGAAGGAAGTAAGTCTAATATTATTTGCCACCATGGCATGTAAAAGTGTGGGAG
-25 TCGTTGGTTGAATTAAACAATGGTCTTAAATGGCTTAACCGTATACGCAGGTTAGTCTAGCTAAGGAGATTGTTAGCGGTGGTCCACCTTATTTCTACTTTAAGCAGTACTGAACTTACGCTTTGATATTAGCGTGTTGAAGTTTTCTTGCATCGTTGGAAGTATTAGGGGGCGTTTTCTTGAGCTAAGAGTTTCGTATCATGGTTGTTAGTAGATGTGGTATTTTGGAGTGGTGTGGTGCTGATGACTGTACTCATGGACTAAAAATATCTGGTAAAAGACTTTCGTTATGCAGCAAACTTGATAGTGAGGTTGAAGTTTGACTGGTAATGCTGAAGGAAGTAAGTCTAATGTTATTTGCCACCATGGCATGTAAAAGTGTGGGAG
-60 TCGTTGGTTGAATTAAACAATGGTCTTAAATGGCTTAACCGTATACGCAGGTTAGTCTAGCTAAGGAGATTGTTAGCGGTGGTCCACCTTATTTCTACTTTAAGCAGTACTGAACTTACGCTTTGATATTAGCGTGTTGAGGTTTTCTCGCATCGTTGGAAGTATTAGGGGGCGTTTTCTTGAGCTAAGAGTTTCGTATCATGGTTGTTAGTAGATGTGGTATTTTGGAGTGGTGTGGTGCTGATTACTGTACTCATGGACTAAAAATATCTGGTAAAAGACTTTCGTTATGCAGCAAACTTGATAGTGAGGTTGAAGTTTGACTGGTAATGCTGAAGGAAGTAAGTCTAATATTATTTGCCACCATGGCATGTAAAAGTGTGGGAG
-63 TCGTTGGTTGCATTGAACAATGGTCTGAAATGGCTTAACCGTATGCGTAGGTTAGTCTAGCTAAGGAGATTGTTACCGGTGGTCCACCTGATTTCTACTTTAAGCAGTACTGAACTTACGCTTTGATATTAGCGCGTTGAGGTTTTCTTGCATCGTTGGAAGTATTAGGAGGCGTTCTCTTGAGCTAACAGTTTTGTATCATGGTTGTGAGGAGATGGGGTATTTTGGAGTGGCGTGGTGCTGATTACTGTATTCATAGACTAAAAATATCTAGTAAAAGGCTTTCGTTATGCAGCAAACTTGATAGTGAGGTTGAAGTGTGAATGGTAATGCTGAAGGAAGTAAGTCTGCTATTATTTGCCACTATGGCATGTGAAAGTGTGGGAG
-48 TCGTTGGTTGAATTAAACAATGGTCTTAAATGGCTTAACTGTATACGTAGGTTAGTCTAGCTAAGGAGATTGTTAACGGTGGTCCACCTTATTGCTACTTTAAGCAGTACTGAGCTTACGCTTTGATATTAGCGCGTTGAGGTTTTCTTGCATCGTTGGAAGTATTAGGGGGCGTTCTCTAGAGCTAAGAGTTTTGTATCATGGTTGTGAGTAGAGGTGGTGCTTTGGAGTGGTATGGTGCTGATTTCTGTACTCATAGACTAAAAATATCTAGTAAAAGACTTTCGTTATGCAGCAAACTTGATAGTGAGGTTGAAGTTTGAATGGTAATGCTGAAGGAAGAAAGTATAATATTATTTGCTACAAGGGCATGTAAAAGTATGGGAG
-66 TCGTTGGTTGGATTAAACAATGGTCTTAAATGGCTTAACCGTATACGTAGATTAGTCTAGCTAAGGAGATTGTTAACGGTGGTCCTCCTTATTTCTACTTTAAGCAGTACTGAACTTACGCTTTGATATTAGCGCGTTGAGGTTTTCTTGCATCGTTGGAAGTAGTAGGGGGCGTTCTCCTGAGCTAAGAGTTTCGTATCATGGTTGTGAGTAGATGTGGTATTTTGGAGTGGTGTGGTGCTGATTACTGTACTCATAGACTAAAAATATCTAGTAAAAGACTTTCGTTATGCAGCAAACTTGATAGTGAGGTTGAAGTTTGAATGGTAATGCTGAAGGAAGTAAGTCTAATATTATTTGCCACCATGGCATGTAAAAGTGTGGGAG
-70 TCGTTGGTTGAATTAATCATTGGTCTTAAATGAATAAACCGTATTCGTAGGTTAGCTTAACTCAAGAGATCGTTGACGGTGGTCCACCTTATTACTACATTAAGCTGGACTGAGCTTAAGTTCTGATAGTAGCGTAGGAAGGCTTTCCGGCAAAATTGTAAGCATTAGCTGGTGACATCCTGAGTTAAGAGCTTTTTACTATGGTCACAAGCATGTGAGGTATTTTGTAACGGTATGGGGCTTATTGCTGTACTCAAGGACTAAAAATAGCTTGTAGGGGACCTTCGGGATTCAGCAAACGCGATAGGGATTCTGAAGGGGAGTTGGTAATGTTGTGTGAAGTATGTGTTTGATTATCTATTTCGATTGCATATAGAAGCCTGGGAG
-16 TCGTTGGTTGAATTAATCATTGGTCTTAAATGAATAAACCGTATTCGTAGGTTAGCTTAACTCAAGAGATCGTTGACGGTGGTCCACCTTATTGCTACATTAAGCGGGACTGAGCTTAAGTTCTGATAGTAGCGTAGGAAGGCTTTCCGGCAAAATTGTAAGCATTAGCTGGTGACATCCTGAGTTAAGAGCTTTTTACTATGGTCACAAGCAGGTGAGGTATTTTGTAACGGTGTGGGGCTTATTGCTGTACTCAAGGACTAAAAATAGCTTGTAGGGGACCTTCGGGATTCAGCAAACTCGATAGGGATTCTGAAGGGGAGTTGGTAATGTTGTGTGAAGTATGTGTTTGATTATCTATTTCGATTGCATATGGAAGCCCGGGAG
-7 TCGTTGGTTGGGTTAATCATTGGTCTTAAGTGGCTAAACTGTATTCGTAGGTTAGCCTAGCTCAAGAGATAGTTTACGGTGGTCCACCTTATTTCTGCTTTAAGCAGGACTGAACTTAAGTATTGATACTAGCGAGGTGAGGTCTTCGGGCAAATTTGGAAGCAGTAGCTGGCGAAATCCTGAGTTAAGAGCTTGTTATCATGGGTACAAGCAGGTGGGGTATTTTGTAACGGTGTGGGTCTTACTGCTGTATTCGGGGACTAAAAATAGCTTGTAGGGGACCTTCGGTATTCAGCGAACTCGATAGGGTTTTTGAAGGAGAATTGGTAATGCTGTGTGAAGTATGTGTTGTATTATGTATGACGATTGCATATTGAAGCTTGGGAG
-93 TCGTTGGTTGTGCTAATCAGTGGTCTTAAATGGCTAAATTGTATGCGTATGTTAGACTAGCTAAATAGATAGTTTACGGCGGTCCACTTTATTCCTACTTTAATCGGTACTGAACGTGAGCTTTGATATTAGCGAGGTGAGGTTATCGTGCAACATTGGATGCAGTAGCTGGCGTAGTCCTGAGTTAAGAGCTTCTTACTATGAGTGCAAGGAGGTGGGGTATTTTGTAGCGGTGTGGTGCTTACTGCGGTATTCAGCGACTAAAAATAACTAGTAAGGGGCTTTCGTTATTCAGCAAACTTGATAAGGATTTTGAAGCGGAATTGGTAATGCTGAGTGAAGTACGTGTAATAGTATTTATGACGAGGGTATATGGAAGCATGGGAG
-9 TCGTTGGTTGGTTTAAGCAGTGGTCTTAAATGGCTAAACTTTATGTGTAGGTTAGATTAGCTAAATAGATAGTTTACGGCGGTCCACCTAATTAGTACTGTAAGCAGTGCTGAACGTTAGCGTTAATATTAGCGCGGTTAGGTTTTCTGGCAACGTTGGAAGCAGTAGCCGGCGTATTCCTGTGGTTAGAGCTTCTTACGATGGGTGCCAGCATTTGAGGTATGTTGAAGCGGTGTGTTGCTTACCGCGTTAATCTGAGACTAAAAATAGCTAGTAAGGGACTTTCGTTATTCAGCAAACTTGAAGGGGATTTTGAAGCGGAACCGGTAATGCTGCGTGAAGTACGTGTAATAGTATTTATGACGAGGGCATTTAGAAGCATAGGGG
-35 TCGTTGGTTGGGTTAATCAGTGGTCTTGAATGGCTAAACTGTATGCGTAGGTTAGACTAGCTAAATAGATAGTTTACGGCGGTCCACCTTATTTCTACTTTAAGCAGTACTGAACGTGAGCTTTGATACTAGCGGGGTGAGGTTGTTGTGCAACGTTGGGAGCAGTAGCTGGCGTAATCCTGAGTTAAGAGCTTCTTACTATGGGTGCAAGCAGGTGGGGTATTTTGTAGCGGTGTGGTGCTTATTGCTGTATTAAGAGACTAAAAATAGCTAGTAAGGGGCTTTTGTTATTCAGCAAACTTGATAGGGATTTTGAAGCGGAATTGGTAATGCTGAGCGAAGTATGTTTAATAGTATTTATGACGAGGGCATATAGAAGCATGGGAG
-56 TTGTTGGTGGTATTAAGGAGTAGTCTAGATTGACCTAACTGTATATGCAGATGAAACTAGCTAAGTAGATGGTTTACGGTGTTCTACCTTATTTTTACTATAAGGGGTAGTAAGTGAGAGCGGTGAGATTAGCGAGGTGAGGTTGTCGTGCATCGTGGGATGCAGGGGCTAGTGTATTTCGGCGTTAAAGACTTTTTACTATGGATGTTAGGAGATGGGGTATTTCGTAGCGGTTTGGTGTCTATAACTGTATTTATAGACTAAAAATAGTCAGTAGGGTGCTTTCGTTTTTCGGCGAACTCGATAGGGATTTTGAAGTGAATTGGGTAATGATGTAGGAAGTTTGTGTACTAATATTTCAGGCTAAGGCATATATAAGCCTGAGAT
-24 TCGTTGGTTGTGTTAACTAATGGTTCATAGTGGCGGAACTGTATCCCTAAGTTAGACTAGCTAAGGAGATAGTTAGCTGATTTTCACTGTAGTACTGTCGTAAGCAGTATTGTAAGTACGCTGTGAGGCTAGCGGGGCAAGGATCCGGAGGAAATCTGTAAGCAATAGTAGTCGTTCTCCTCATTTAAGAACTTATAAATATGTGTACCATTAAGTATGGTCTTTAGGAGCGGTGTTACGTATACAACTGTATTCAATGATTAAAAATACCCAGAGAGTGTCTCTCGTAATTCAGCCAACTTGATTGTGATGCTGGAGTTAAATAGGTAATGTTGAAAGAAGTTTGTTTAGTACTATGCATTACGTAGACATTTGGAAATCTGGGAG
-45 GCGTTGGTTGAAGTAATTAATGGTTTAAAGTGGCGGAACTGTATACGTATGTTATACTAGCTAAGTAGAAAGTTTACAGTGTTCCACCTTAATTCTATTTTAAGCAGTACTGAATGTGCGCTTTGAGAGTAGCGTGGTAAGGTTCGATTGCAACCTGGGAAGCAGTAGGGGTTGTAGTTCTTAGTTAAGTTCCCCTTATTAGGAGTGCTATCAGGTGTGGTGTTTTGAAGCGGTGTGGTGCCGACCACAGTAATAGGAGATTAAAAATAACTAGTGAGGGGCATTCGTAATTCAGCCAACTTGAGTGGTATACTGGAGCGCAACCGGTAAGGCTGCACTAAGTATGTGTAATAATATGCGCCTCGTGGGCATATTGAAACTTGAGAG
-86 TCGTTGGTTGGAGTAATTAATGGTTTAAAGTGGCGGAACTGTATACGTAGATTATACTAGCTATGTAAATAGCTTACGGTGTTCCACCTTGGTTCTATTTTAAGCAGTACTGGATGTGCGCCTTGATATTAGCGCGGTGAGGTTCGATTGCAACCTGGGAAGCAGTAGAAGCCGTAGTGCTTAGTTAAATTCTCCGTATTAGGGGTGCCATCAAGTGTGGTGTTTCAGAGCGGTGTGGTGCCGACTACTGTAATAAGAGATTAAAAATAACCAGTGTGGGGCATTCGTAATTCAGCAAACTTGAGCGGTATACTCGAGCGCAATCGGTAAGGCTGCGCGAAGTATGTGTCCTAATATGCGCCACGTGGACATATCGAAACTTGGGAG
-40 TCGTTGGTTGGAGTAATTAATGGTTTAAAGTGACGGAACTGTATACGTAGGTTAAACTAGCTAAGGAGATAGATTACGGTGTTCCACCTGGGTTCTATGCTAAGCAGGACTGGATTTTCGCTTTGATAGTAGCGTGGTAAGGTCCGATTGCAACTTGGTAAGTAGGAGGCGCTGTATTGCTCAGTTAAATTCTCTTTATTAGGGGTGCCATCAAGGGTGGGGTTTCGGAGCGGTGTGGTGCTGACGACCGTAATAAGTGATTAAAGATATCTTGTGTGGGTCATTCGTAATTCAGCAAACTTGAGTGGTGTATTCGAGCGTCATTGGTAAGGCTGTTCGAATTATGTGTGCTAATATGCATCACATAGACATATTGAAACTTGGGAG
-11 TCGTTGGTTGAAGTCATTAATGGTTTAAAGTGGCGGAACTGTATATGTAGGTCACACTAGCTAAACAGATAGATCACGGTGTTCTACCTTGGTTCTATGTTAAGCAGTATAGGATTTGCGCTTTGATATTAGCGTGGCAATGTTTGGTTGCAACCTGGTAAGCAGGGGGTGCCGCATTGCTTAGTTAAATTCTCCTCATTAGGGGTGCCACTAATTGTGGTTTTTAGGAGCGGTGTGGTGCTGACGACCGTAATAAGAGATTAAAAATATATGGTGTGGGTCGTTCGTAATTCAGCAAGCTTGAGTGGTATATTTGAGTGGAGTTGGTAAAGCTGTTCAAAGTATGTGTGCTAGTATGCATCACGTAGACATATTGAAAGTTGGGAG
-17 TCGTTGGTGGTGGTAAAGACGGGTCGGAAATGTCTTAATTGCATTCGTAGGTTGGACTAGCTAAGCAGAAAGTTGATGGTGGGCTGCTGGCTTATTATTCTAAGCTGTACTGAACGTTCGCGTTTATAGAAGCGGTGCTAGGGTATGATGCGTTATGGTGAACAGCAGAATTCTCTATTCTGAGCTAAGGTCTTTGTACCATGTATGTAGGAAAGTGGGGTATATCGTAACGGTGAAGTAGAGACTACGATATGTAGGGACTAAAGGTTTTTAGTAGTTGGCGTTCGTAATTCAGCAAACTAAAGGGTAGTGTTATAGACGCAGTGGTTATGCTGAATGATCTAAGTCTGGTTTTCTTTGACAGCAAGGCATGCTGAAGTTTGGGAG
-98 TCGTTGGTGGAGGTAAAGACGAGTCGGAAATGTCTTAATTGCATTCGTAGGTTAGACTAGCTAAGCAGAAAGTTGATGGTGGGCTGCTGGCTTATTATTCTAAGCTGTACTGAACGTTCGCGTTTATAGAAGCGGTGCTAGGGTATGATGCGTTATGGTTAACAGCAGAATTCTCTATTCTGAGCTAAGGTCTTTTTACCATGTATGTAGGAAAGTGGGGTATATCGTAACGGTGAAGTAGAGACTACGATATGTAGGGACTAAAGGTTTTTAGTTGTTGGCGTTCGTAATTCAGCAAACTAAAGGGCAGTGTTATAGACGCAGTGGTTATGCTGAATGATCTAAGTTTGGTTGTCTTTGACAGCAAGGCATGCGGAAGTTTGGGAG
-84 TCGTTGGTGGAGATAAAGATGAGTCGGAAGTGACTGAATTGCATTCGTATGTTAAACTAGCTAAGTAGATAGTTGACGGTGGGCTGTTTGCTTACTGTTCTAAGTCGTACTGAACGTGCGCGTTTATAAAAGCGGGGTTAGGGTATGTTGCCTTATGGTGAGCAGCAGGTTTCTTTATTCCGAGCTAATTTCTTTGTACCATGTATGTAGGTATGTGGGGTATATCGGAACGGTGAAGTACAGACGACGATATGAAGGGACTAAAGGTTTTTAGTAGTTGGCTTTCGTAATTCAGCAAACGAAACGGTAGTGTTGCAGATTAATTGGTTATGTTGTGTGAGCTAATTTTCTTTTTCTTTGACAGCAAGGCATGCTGAAATTATGGAG
-19 TCGTTGGTGGAGATAAAGACGAGTCGGAAGTGGCTAAATTGCATTCGTAGGTTAAACTAGCTAAGTAGATAGTTGACGGTGGGCTGCTTGCTTACTGTTCTAAGTTGTACCGAACGTGCGCGTTTATATAAGCGGGGCTAGGGTGTGTTGCATTATGGTGAGCAGCAGATTTCTTTATTCTGAGCTAATGTCTTTGTACCATGTATGTAGGTATGTGAGGTGTATCGGAACGGTGAAGTACAGACGACGATAGGAAGGGACTAAAGGTTTTTAGTAGTTGGCTTTCGTAATTCAGCAAACTAAACGGTAGTGTTGCAGATTACTTGGTTATGCTGTATGAGCTAATTTTATTTTTCTTTGACAGCGAGGCATGCTGAAGTTTGGGAG
-54 TCGTTGGTGGAGATAAAGACGAGTCGGAAGTGGCTAAATTGCATTCGTAGGTGAAACTAGCTAAGTAGATAGTTGATGGTGGGCTGCTTGCTTACTGTTCTAAGTTGTACCGAACGTGCGCGTTTATATAAGCGGGGCTAGGGTGTGATGCCTTATGGTGAGCAGCAGATTTCCTTATTCTGAGCTAATGGCTTAGTACCATGTATGTAGTTATGTGTGGTGTATCGGAACGGTGAAGTACAGACGACGATAGGAAGGGACTAAAGGTTTTTAGTAGTTGGCTTTCGTAATTCAGCAAACTAAACGGTAGTGTTGCAGATTAATTGGTTAGGCTGTATGAGCTAACTTTATTTTTCTTTGACAGCGAGGCATGCTGAAGTTTGGGAG
-22 TCGTTGGTATAGCTAATGACGAGTCTGTAATGGCTAAATTGCATTCGTAGGTTAGACTAGCTAAAGAGATAGTTGGCGGTGGGCTGCCTGCTTACTATTTTAAGCTGGACTGAACGTGCGCGTTTATATAAGCGAGGCGAGGGTGTGGTGCATTATGGTAAGCAGCAGGTTTCTTTATTCTGAGCTAATGTCTTTGTATCATGTATGTGGGTATGTGAGGTGTATGGTATCGGTGAATGACAGACCACGATATGAAGGGGTTAAAGGTGTTTAGTAGTTGGCTCTCGTAATTCAGCCAACTAAATAGTAGTGTTGCAGATTAATTTGTTATGCTGAATGAGCTAATTGTAGTTTTCTTTGACAACATGGCATGCTGAAGTTTGGGAG
-14 TCGTTGGTATGGCTAATGACGAGTCTGTAATGGCTAAAATGCATTCGTAGGTTAGACTAGCTAAAGAGATAGTTGACGGTGGGCGGCCTGCTTACTATTTTAAGTTGGACTGAACGTGCGCGTTTATATAAGCGAGGCGAGGGTATGGTGCATTATGGTGAGCAGCGGGTTTCTTTATTCTGAGCTAATGTCTTGGTATCATGTATGTGGGTACGTGGGGTGTATGGGATCGGTGAATGACAGACTACGATATGAAGAGGCTAAAGGTGTTTAGTAGTTGGCTCTCGTAATTCAGCCAACTAAAGAGTGGTGTTGCAGAATAAGTTGTTATGCTGAATGAGCTAATTGTAGTTTTCTTTGACAGCAGGGCATGCTGAAGTTAGAGAG
-47 TCGTTGGTGGAGCTAAAGACGAGTCGTCAATGCCCAAATTGCATTCGTAGGTTAGACTAGCTGAGTAGATAGTTTATGGTGGGCTGCTTGCTTACTATTCTAAGCTGGACTGAACGTGCGCGTTTATACAAGCGGGGTTAGGGTGTGCTGCATTATGGTGAGCAGCAGGTTTCTTTATTCTGAGCTAATGTCTTTGTACAATGTATGTAGGTATGTGAGGGGTATGGGAACGGTGAATTAGAGACGACGATAGGAAGGGACTAAAGGTTTTTAGTAGTTGGCTTTCGTAATTCAGCAAACTAAATGGTTGTGTTGCAGATTAATTGGTTATGCTGTACGAGCTAATTTTAGTTTTCTTTGACAGTAAGGCATGCTGAAGTTTGGGAG
-50 TCGTTGGTGGAGTTAAAAACGAGTCGGCAATGCCCAAATTGCATGCGTAGGTTAGACTAGCTAAGTAGATAGTTGACGGTGGGCTGCTTGCTTACTATTCTAAGCTGGACTGAACGTGCGCGTTTATACAAGCGGGGTTACGGTGTGTTGCAGTATGGTGAGCAGCAGGGTTCTTTATTCTGAGCTAATGTCTTTGTACCATGTATGTAGGTATGTGAGGTTTATGGGAACGGTGAATTAGAGACGACGATAGGAAGGGACTAAAGGTTTTTAGTAGTTGGCTTTCGTAATTCAGCAAACTAAATGGTAGTTTTGCAGATTAATTGGTTATTCTGTATGAGCTAATTTTATTTTTCTTTGACAGCAAGGCATGCTGAAGTTTGGGAG
-77 TCGTTGGTGGAGTTTAAGACGAGTCGGTAATGTCTAAATTGTATTTGTAGTTTAGACTAGCTAAGTAGATAGTTGACGGGGGGCTGCTTGCTTACTATTTTAAGCTGGACTGGACGTGCGCGTTCATACAAGCGGGGCTAGGGTGTGTAGCACTATGGTGAGCAGCAGGTTTCTTTATTCTGTGCTAATGTCTCTGTAATATGTATGTAGGAATGTGAGGTATATGGGAACGGTGAATTAGAGACGACAATAGGAAGGGCTTAAAGGTTGTTAGTAGTAGGCTTTCGTAATTCAGCAAACTGAATGGTAGTGTTGCAGATTAACTGGTTATGCTGTAGGAGCTAATTTTACTTTTCTTGGACAGCAAGGCATGCTGAAATTTGGGAG
-33 TCGTTGGTTGTGTTCATCAGTGGTCTGAAATGTCTTAACTGTATGTGTACGTGAAATTAGGTAAGCAGATATTTGACGGTGGTCTACTTGATTTCTGCTTTACACGGTAATGGACGTACGCTTTGAGTCTAGTGGAGTGAGGTTGTCAGGCACCGTTGTAAGCATTTGGTGACGTGATTCTAAGTTAAGAACTTGTCACCACGAATGTAAGCAAGGGAGGTATTTTGGAGCGGTCTTATGATGACGACTGCACTATGCGACTAAATATAACTAGTAAGGGGCCTTCGTTATTCAGCCAACTTTTTAGGTATGTTGGAATTGAAGTGGTGATGCTGTAGGTAGTAAGTTTGGTATTATTTAGGACGAGTGCGTTTGGAAGCGTGGGAG
-6 TCGTTGGTGGATACAATCAATGGTCCTTAATGTCTTAACTGTGTATGTAGGTGAAATTAACTGTTAAGATATTTGATTGGGGTCCTCTTTGTTACTAGTATACCCGGTACTCTACGTGCGGTTTGACCTTAGCGAAGTTAAGTTTGCTCGCGTCTTTGTTAGCATTAGTTTGCTGACTCTTAGGTTAAGAACTTGGCGTTATGTATGGATGGAGCCAGGGTTATTAGAAGCGGAGTTGTACGGACTGCTGCAATCGGGGACTAATGGTATTTAGTGGGTGATTTTCGTTATTCAACCAACAGGCAATTGATGTTGTACCATACTAGGTAAAGTTGATAGTAGTGAATCTGTTATTATTAAGCACGAGTGCTTATTGAAACCTGGGGT
-0 TCGTTGGTTATAGTAAGCAATGGTCTGAAATGGTTGAACTGTATACGTAGGTTAGACTATCTAAGTAGATAGATAGCGGTGGTCCACTTTATTGTTATGGTAAGCGGTACTGAACGTACTCTTTGATAGCGGCGCAGTGAGGTTTTATTGCAACGTGGGCCGCAGTCTTGGTCGTTGTCCTTTGTTAAGATCATTTTATTCTGGGTGCAGATAAGTGGGGTGTCTAGGATCGGTGTGGGGACGACTTCTTCATTGAGAGGCTAATGATAGCTAGTAAAGGGCTGTCTTTATTCAGCAAACCCCGTGGGGATGTTGGAGTAAAACTGGTAATGTTGTGGGAAGTAAGTCTTCTAATATTTGACGCGAAGGCATTTTAAAGCTTGGGAG
-101 275
-0 CGTATTATATACAATGCGACCTTCCCGGCTAAGAGTGAGACGCATATTCTATAGTGTTACATGTCAACAGATAAAAAACGGTGCTACATAATTCCGGAATCCCGTATCTCGGTGCGGTGAGAACGTTTCTCAGAGTTTAACGGATCTAATATCCATCCAGAGCACTAGGGCGGTGATGGGTATAGTAAATATTGTTTTATAGATTTTTTTTTGTTCCTTACATTATTTCACTTTGGATAAATTCTCCCACGGGGTTCGGAGGCCCCGTTTGTATA
-41 CGTGTTATATAGAATGGGACCTTCTCGGCTAAGAGTCAGACGCATATTTTATAGTGTTATATGTCAACGGATAAAAGGCGGTGGTACATAGTTCCGGAATCCCGTATCTCGATGCGGTGGCAACGTTTCTCAGAGTTTAACGGATCTACTATCCATCCAGAGTACTAAGGCGGTGGTAGGTATAGTGATTATTGTTTTATAGATTTTTTTTTGTTCCTTACGTTATTCCACTCTGGCTAAATTCTGCCAAGGGACACGGAAGTCCCGTTTGGGGA
-10 CGTGTTATATAGAATACGACCTTCTCGGCTAAAAGCCAGACGCAGATTTTATAATGTTGTATGTCACCAAACGATATACAGTAGGAAATAGTTCCGGTATCCCGTATCTCGACGCGGGGAGAAAGTTTCTCAGAGTTTAAGCGATCTACTATCCATCTAGAGCGCTAGGGAGGTGGTAAGTATGGTGAATATTATTTTATAGAATTTTTTTTGTGCCTTAAGTTATTCCACTCTAGGTAAATTCTTCCAAGGGGTACGTGATTTCCGTTCGGATA
-97 CGTGTTATATAGAATACGACCTTCTCGGCTAAAAGCCAGACGCAGATTTTATAATGTTGTATGTCACCAAACGATAGACAGTGGTAAATAATTCCGGTATCCCGTATCTCGACGCGGGGAGAAAGTTTCTCAGAGTTTAAGCGATCTACTATCCATCTAGAGCGCTAGGGAGGTGGTAAGTATGGTGAATATTATTTTATAGAATTTTTTTTGTGCCTTACGTTATTCCACTCTAGGTAAATTCTCCCAAGGGATACGTGATTTCCGTTCGGATA
-12 CGTGTTATATAGAATGCGACCTTCTCGGCTACGAGTCAGACGCATATTTTATAGTGTTATATGTCAACAGATAAAACACGGTGGTACATAGTTCCGGGATCCCGTATCTCGATGCGGTGAGAATGTTTCCCAGAGTTTAACGGATCTACTATCCATCCAGAGCTCTAAGGCGGTGGTGGGTATAGTGAATATTGTTTTATAGACTTCTTTTTGTTCCTTACGTTATTCCACTTTTGATAAATTCTACCACGGGCCACGGAAGAACCGTTTGGATA
-36 CGTGTTATTTAGAATGCGACCTTCTCGGCTACGAGTCAGAGGCACATTTTATAGTGTTATACGTCAACGGATAAAACACGGTGGTACATAGTCCCGGGATCCCGTCTCTCGATGCGGTGAGAATGTTTCCCAGAGTTTAACGGATCTACTATCCATCCAGAGCTCTAAGGAGGTGGTGGGTATCGTGAATATTGCTTTATAGACTTCTTTTTGTTCCTTACTTTATTCCACTTTTGATAAATTCTACCACGGGCCACGGAAGAACCGTTTGGATA
-39 CGTGTTATATAGAATGCGACCTCCTCGGCAACAAGTCAGAGGCATATTTTATAGTGTTATATGTCAACAGATAAAACACGGTGGTACATAGTTCCGGGATCCCGTATCTCGATGCGGTGAGAACGTTTCCCAGAGTTTAACGGATCTACTATCCATCCAGAGCTCTAAGGCGGTGGTGGGTATAGTGAATATTGTTTGATAGACTTTTTTTTGTTCCTTACATTATTCCACTTTTGATAAATTCTACCACGTGCCACGGAAGAACCGTTTGGATA
-28 CGTGTTCTATAGAATGCGACCTTTTCGGCTAAAAGTCAGACGCATATTTTACATTGTTATATGTCAAAAAATAAAACACTGTGGTCCATATCTCCGGAATCCCGCATCTCGATGCAGGGGGAACCTTTCCCAGAGTTTAAAGGATCTACCACCCATCCAGAGAACTAAGGTGGTGATGGGTATAGTGAAGATTGTTTTATAGACTTTTTTTTGTTCCTTACATTATTCTACGATGGATAAATTATACCAAGGGCTAAGGGGGTCCCGTTTGGATA
-71 CGTTTTATATAGAATGCGACCTTCCCGGCTAAAAGTCAGACGCATACTTTATAGTGCTATATGTCAACAGATAAAACTCGGTGGTACATAGTTCCGGAATCCCGTATCTCGATGCGGTGAAAACCTTTCCCAGAGTTTAACGAATCTACTATCCATCCAGAGCACTAAGGAGCTGCTGGGTATAGTGAATATTGTTGTATAGACTTTTTTTTGTTCATTAAATTATTCAACTGTAGCTAAATTCTACCACGGGTTACGAAAGCCCCGTTTGGATA
-76 CGTGTTATATAGAATGCGACCTTCTCGGCTAAGAGTCAGACGCATATTTTATAGTGTTATATGTCAACAGATAAAACACGGTGGTACATAGTTCCGGAATCCCGTATCTCGATGCGGTGAGAACGTTTCTCAGAGTTTAACGGATCTACTATCCATCCAGAGCACTAAGGCGGTGATGGGTATAGTGAATATTGTTTTATAGACTTTTTTTTGTTCCTTACATTATTCCACTATGGGTAAATTCTACCACGGGCTACGGAAGCTCCGTTTGGATA
-52 CGTGTTATGTGGCATGCGATCTTCCCGGCTAAGAGTCAGACGCGTAATTTATAGTGCTATATGTCAACCGATAAAATACGGTAGTACATAATCCCGGTATCTCGTGGCTCGATGCGTTGATAACGTTTCACAGAGTTTAGCGAATCTACTAATCATCAAGAGCACTAAGGAGGTGGTGGGTATGGTGAATATTGTTTTATAGAATTTTTTTTGTTCCTTAAATTATTCCACTGTAGATAAATTATACCAAGGGTTACGGAAGCTCCGTTCGGATA
-55 CGTGTTCTATAGGATGCGATCTTGACGGCCAGGAGTCAGACGCATATTTTATAGGGCTATACGTCAACAGATCGAAAACGGTAACATGTAATTGCGGAATCCCGTATCTCGATGCGGTGACCCCGTTTTTCAGAGTTTAACGAATCTATTGTCCATCTAGAGCCCTAAGGCGGTGATGGGTATAGTAAATATTGTTGCATAGAATTTTTTTTGTTCCGTATATTATTTCACTCTAGATAAATTCTACCACGGGTTACGTAAGCCCCGTTTGGGGA
-68 CGTGTTCTGTAAGATGCGATCTTGACGGCCAGGAGTCAGACGTATATTTTATAGGGTTCTATGTCGACGGATCGAAAACTGTAATACGTAATTGCGGGATCCCGTATCTCGGTGCGGTGACCACTTTTTTCAGAGTTTAACGAATCTACTGTCCATCTAGATCCCTAAGGTGGTGATAGGTATAGTAAATATTGTTGCATAGAGTTTTCTTTGTTCCGTATATTATTTCACTTTAGGTAAATTCTGCCACGGTTTGCGTAAGCCCCGTTAGGGTA
-83 CGTGTTCTGTAGGATGCGATCTTGACGGCCAGGAGTCAGACGCATATTTTATGGGGTTATACGTCGACGGATCGAAGACTGTAATACGTAGTTGCGGAATCCCGTATCTCGGTGCGGTGACCACGTTTTTCAGAGTTTAACGAATCTACTGTCCATCTAGAGCCCTAAGGTGGTGATGGGTATAGTAAATATTGTTGCATAGAGTTTTCTTTGTTCCGTATATTATTTCACTTTAGGTAAATTCTGCCACGGTTTACGTAAGCCCCGTTTGGGTA
-38 CGTGTTCTATAAGATACGATCTTGACGGCCAGAAGTCAGACGCATATTTTATAGGGTTGTACGTCGACGGATCGAAGCCTGTAATACGTAATTGCGGAATCCCGTATCTCGGTGCGGTGACCACGTTTTTCAGAGTTTAACGAATCTACTGTCCATCTAGAGCCCTAGGGGGGTGATGGGTATAGTAAATATTGTTGCATAGAGTTTTCTTTGTTCCGTATATTATTTCACTCTAGGTAAATTCTACCACGGGTTACGTACGCCCCGTTTGGGTA
-30 CGTTTTCTGTAGGATGCGATCTTGACGGCCAGGAGTCAGACGCATATTTTATAGTGTTATACGTCGACGGATCGAAAACTGGAACACGTAATTGCGGAATCCCGTATCTCGGTGCGGTGACCACGTTTTACAGAGTTTAACGAATCTACTGTCCATCTAGAGCCCTACGGTGGTGATGGGTATAGTAACTATTTTTGCATAGAGTTTTCTTTGTTCCGTATGTTATTTCACTCTGGGTAAATTCTGCCACGGGTTACGTAAACCCCGTTTGGGTA
-89 CGTTTTCTGTAGGATGAGATCTTGACGGCCAGGAGTCAGAGGCATATTTTATAGGGTTGTACGTCGACGGATCGAAAACTGGCACACGTAATTGCGGAATCCCGTATCTCGGTGCGGTGACCACGTTTTTCAGAGTTTAACGAATCTACTGTCCATCTAGAGCCCTAAGGTGGTGATGGGTATAGTAAATATTGTTACATAGAGTTTTCTTTGTTCCGTGTATTATTTCACTTTAGGTAAATTCTGCCACGGGTTACGTAAGCCCCGTTTGGGTA
-20 CGTTTTCTGTAGGATGAGATCTTGACGGCCAGGAGTCAGAGGCATATTTTATAGGGTTGTACGTCGACGGATCGAAAACTGGCACACGTAATTGCGGAATCCCGTATCTCGGTGCGGTGACCACGTTTTTCAGAGTTTAACGAATCTACTGTCCATCTAGAGCCCTAAGGTGGTGATGGGTATAGTAAATATTGTTACATAGAGTTTTCTTTGTTCCGTGTATTATTTCACTTTAGGTAAATTCTGCCACGGGTTACGTAAGCCCCGTTTGGGTA
-74 CGTTTTATATAGGATGCGACCTTCGCGGCTAGAAGTCGGACGAATACTTTATAGCGTTATATGTCAATGGATAACACCCGGTTGTAAAGAGTTCCGGGATCCCGTATCTCGATCCGGTGAAAACGTTTCTCAGAGTTTAGCGAGTCCAATATGCATCTAGAGTACTAAGGCGGTGATAGGTATAGTGAATACTGTTTTATAGAGTTTTTTTTGTTCCTTACTTTATTCCACTCTGGCTAAATTCTGACACGGGTCGTGGAATCCCCGTTTGGATA
-32 CGTTTTATATAGAATGCGACCTTCTCGGCTAAAAGTCGGACGAATATTCTACAGTGTTATATGTCAACAGATAACAGCCGGTTGTACATAGGTCCGGGATCCCGTATCTCGATCCGGTGGGAAGGTTTCTCAGAGTTTAGTGGATCCAATATCCATCCAGAGTACTAGGGCGGTGATAGGTATAGTGAATATTGCTTTATAGACTTTTTTTTGTTCCTTACGTTATTCCACTATCGATAAATTCTGACACGGGCTGCGGAAGAGCCGTTTGGATA
-15 CGTTTTATCTAGAATGCGACCTTCCCGGCCAAAAGTCAGACGAGTATTCTACAGTGTTATATGTCGACAGATAACAGACGGTTGTACATAGACCCGGAATTCCGTATCTCAATCCGGTGAGAAGGTTTCCCAGAGTTTAGCGGATAAAATATCCATCCAGAGTGCTAGGGCGGCGATGGGTATAGTGAATATTGTTTTATAGACTTTTTTTTGTTCCCTACTTTATTACACTATTGATAAATTCTTACACGGGCCGCGGAAGATCCGTTTGGATA
-49 CGTTTTATCTAGAATGCGACCTTCCCGGCCAAAAGTCAGACGAGTATTCTACAGTGTTATATGTCGACAGATAACAGCCGGTTGTACATAGACCCGGAATTCCGTATCTCAATCCGGTGAGAAGGTTTCCCAGAGTTTAGCGGATCAAATATCCATCCAGAGTGCTAGGGCGGCGATGGGTATAGTGAATATTGTTTTATAGACTTTTTTTTGTTCCCTACTTTATTCCACTACTGATAAATTCTTACACGGGCTGCGGAAGATCCGTTTGGATA
-43 CGTTTTATATAGAATGCGACCTTCTCGGCTAAAAGTCAGACGAACATTCTATAGTGTTATACGTCAACAGATAACACCCGGTTGGACATAGTTCCGGGATCCCGTATCTCGATCCGGTGAGAAGGTTTCTCAGAGTTTAGCGGATCCAATATCCATCCAGAGCACTAAGGAGGTGATAGGTATAGTGAATATTGTTTTATAGACTTTTTTTTGTTCCTTACATTATTCCACTCTGGATAAATTCTTACACGGGCTACGGAAGTCCCGTTTGGATA
-69 CGTCTTATGTAGAATGAGACCTTCCCGGCTAGCAGTCGGACGCCTATTTTATAGTGTTATATGTCAACAGCTAAAAAACGGTAGTACCTAATTACGGAATCCCGCATCTCGCTGCGGTAAGAACGTTTTTCGGAGTTTAACGGATCTAATAGCCATCCAGAGTCCTAAGGTGGTGATGGGTATAGTAAATATTGTTTTATAAACTTTTTTTTGTTCCTTACATTATTTCACTTTGGATAAATTCTCCCACGAGTTACGGAGACACCGTTCGGATA
-67 CGTCTTATGTAGACTGAGGTCTTCCCGGCTAGCAGTCGGACGCCTATTTTATAGTGTTATATGTCAACAGCTAAAAAACGGTAGTACCTAATTACGGAATCCCGCATCTCACTGCGGTGAGAACGTTTTTCAGAGTTTAACGGATCTAATAGCCATCCAGAGTCCTAAGGTGGTGATGGGTATAGTAAATATTGTTTTATAAACTTTTTTTTGTTCTTTACATTATTTCACTTTGGATAAATTCTTCCACGAGGTACGTAGACACCGTTCGGATA
-8 CGTCTTATATAGAATGCGACCTTCTCGGCTAGCAGTCAGACGCCTATTCTATAGTGTTACACGTCAACAGATAAAAAACGGTAGTGCATAATTACGGAATCCCGCATCTCGCTGCGGTGAGAATTTTTTTCAGAGTTTAACGAATCTAATAGCCATCCAGAGTTCTAAGGCGGTGATGGGTATAGTAAATATTGTTTTATAAACTTTTTTTTGTTCGTTACATTATTCCACTCTGGGTAAATTCTTCCACGAGCTACGGAGGCACCGTTCGGATA
-51 CGTGTTATGTAGAATGCGACCTTCTCGGCTAACAGTCCGATGCATACTCTATAGTGTTATATGTCAACAGATAAAACACGGTGGTATATAATTCCGGAATCCCGTATCTCGATGCGGTGAAAACGTTTCCCAGAGTTTAGCGGATCTAACATCCATCCAGAGCTCTAAGGCGGTGATAGGTATAGTGAATATTGTTTTATAGACTTTTTTTTGTTCCTTACATTATTCCACTCTAGATAAATTCTGCCACGGGCTACGGAGGTGCCGTTTGGATA
-87 CGTATTATGTAGAATGCGACCTTCTCGGCTAACAGTCAGACGCATACTCTATAGTGTTATATGTCGTCCGATAGAACACGGTGGTACATAATTCCGGAATCTCGTATCTCGATGCGGTGAAAAAGTTTCTCAGAGTTTAACGGATCTAATATCCATCCAGAGCTCTAAGGAGGTGATGGGTATAGTGAATATTGTTGTATAGACTTTTTTTTGTTCCTTACATTATTCCAGTCTAGATGAATTCTTCCACGGGCTACGGAGGCACCGTTTGGATA
-79 CGTGTTATTTAGAATGCGACCTTCTCGGCTAACAGTCAGACGCGTACTCTATAGTGTTATATGTCAACAGATAAAACACGGTGGTACATAATTCCGGAATCCCGTATCTCGGTGCGGTGAAAATGTTTCCCGGAGTTTAACGGCTCTAATATCCATCCAGAGCTCTAAGGCGGTGATGGGTATAGTGAATATTGTTTCATAGACTTTTTTTTGTTCCTTACATTATTCCACTCTAGATGAATTCTGCCAGGGGCGTCGGAGGCACCGTTTGGATA
-1 CGTGTTATGTAGAATGCGACCTTCTCGGCTAACAGTCAGACGCATACTCTATAGTGTTATATGTCAACAGATAAAACACGGTGGTACATAATTCCGGAATCCCGTATCTCGATGCGGTGAAAACGTTTCTCAGAGTTTAACGGATCTAATATCCATCCAGAGCTCTAAGGCGGTGATGGGTATAGTGAATATTGTTTTATAGACTTTTTTTTGTTCCTTACATTATTCCACTCTGGATGAATTCTGCCACGGGCTAAGGAGGCACCGTTTGGATA
-29 CGTGTTGTGTAGAATGCGACCTTCTCGGCTAACAGTCAGACGCATACTCTATAGTGTTATATGTCAACAGATAAAACACGGTGGTAGATAATTCCGGAATCCCGTATCTCGCTGCGGTGAAAATGTTTCTCAGAGTTTAACGGATCTAGTATCCATCCAGAGCTCTAAGACGGTGATGGGTATCGTGAATATTGTTTTATAGACTTTTTTTTGTTCCCTACATTATTCCACTCTAGATAAATTCTGCCACGGGCTACGGAGGCACCGTTTGGATC
-27 CGTGTTGTGTAGAATGCGACCTTCTCGGCTAACAGTCAGACGCATACTCTATAGTGTTATATGTCAACAGATAAAACACGGTGGTAGATAATTCCGGGATCCCGTATCTCGTTGCGGTGAAAATGTTTCTCAGAGTTTAACGGATCTAGTATCCATCCAGAGCTCTAAGACGGTGATGGGTATCGTGAATATTGTTTTATAGACTTTTTTTTGTTCTCTACATTATTCCACTCTAGATAAATTCTGCCACGGGCTACGGAGGCACCGTTTGGATC
-3 CGTGTTGTGTAGAATGCGACCTTCTCGGCTAACAGTCAGACGCATACTCTATAGTGTTATATGTCAACAGATAAAACACGGTGGTAGATAATTCCGGGATCCCGTATCTCGCTGCGGTGAAAATGTTTCTCAGAGTTTAACGGATCTAGTATCCATCCAGAGCTCTAAGACGGTGATGGGTATCGTGAATATTGTTTTATAGACTTTTTTTTGTTCCCTACATTATTCCACTCTGGATAAATTCTGCCACGGGCTACGGAGGCACCGTTTGGATC
-75 CGTGTTGTGTAGGATGCGACCTTCCCGGCTAACAGTCTGACGCATACTTTATAGTGTTATATGTCAACAGATAAAACACGGTCGTAGATAATTCCGGAATCCCGTATCTCGCTGCGGTGACAATGTTTCTCAGAGTTTCACGGATCCAGTATCCATCCAGAGCTCTAAGGTGGTGATGGGTATCGTGAATATTGTTTTATAGACTTTTTTTTGTTCCCTACATTATTCTACTCTAGATAAATTCTCCCAAGGGCTACGGAGGCACCGTTTGGATC
-13 CGTGTTATGTAGCATGCGACCTTCTCGGCCAACAATAAGACGCATACTCTATAGTGTTATATGTCAACAGATAAAATCCGGTGGTACATAATTCCGGCATCCCGTATCTCGCTGCGGTGAAAATGTTTCTCAGAGTTTAACGGATCTAGTATCCATCCAGAGCTCTAAGGCGGCGATGGGTATAGTGAATATTGTTTTATAGACTTTTTTTTGTTCCTTACATTATTCCACTCTGGATAAATTCTGCCACGGGCTACGGAGGCACCGTTTGGATA
-18 CGTGTTATGTAGAATGCGACCTTCTCGGCTAACAATCAGACGCATACTCTATAGTGTTGTATGCCAACGGATGGAATACGGTGGCACATAATTCCGGAATCCCGTATCTCGGTGCAGTGAAAATGTTTCTCAGAATTTAACGGATCTAGTATCCATCCAGAGCTCTAAGGCGGTGATGCGTATAGTGAATATTGTTTTATAGAGTTTTTTTTGTTCCTTACATTATTCTACGCTAGATAAATTCTTCCACGGGCCACGGAGTCATCGTTTGGTTA
-59 CGTGTTATGTAGAATGCGACCTTCTCGGCTAACAATCAGACGCGTACTCTATAGTGTTATATGCCAACGGATGAAATACGGTGGCACATAATTCCGGAATCCCCTATCTCGATGCAGTGAAAATGTTTCTCAGAATTTAACGGATCTAGTATCCATCCAGAGCTCTAAGGCGGTGATGCGCATAGTGAATATTGTTTTATAGAGTTTTTTTTGTTCCTTACATTATTCCACGCCAGCTAAATTCTCCCACGGGCCACGGAGTCATCGTCTGGATA
-85 CGTGTTATGTAGAATGCGACCTTCTCGGCTAACAGTCAGACGCATACTCTATAGTGTTATATGTCAACAGATAAAACACGGTGGTACATAATTCCGGAATCCCGTATCTCGATGCGGTGAAAAAGTTTCCCAGAGTTTAACGGATCTAGTATCCATCCAGAGCTCTAAGGCGGTGATGGGTATAGTGAATATTGTTTTATAGAATTCTTTTTGTTCCTTACCTTATTCCACTCTGGATAAATTCTGCCACGGGTTACGGAGGCGCCGTTTGGATA
-62 CGCGTTATATAGAATGCGACCTTCTCGGCTAACAGTCAGACGCGTATTCTATAGTGTTATACGTCAGCAGATAAAACACGGTGATGAATAATTCCGGTATCCAGTATCTCGATGTGGTGAAAGTGTTTACCAGAGTTTAGCGGATTTACTATCCATCCAGAGCTCTAAGGCGGTGATGGGTATAGTAAATATTGCTTTATAGACTTTTTTTTGTTCCTTACGTTATTCCACTGTAGATAAATTCTGCCACGGGTTACGGAGTTACCGTTTGGGTA
-57 CGTGTTATGTAGAGTGCGACCTTCTCGGCTAACAATCAGACGCATACTCTATAGTGTTATACGTCAACAGATAAAACACGGTGGTACATAATTCCGGAATCCCGTATCTCGATGCGGTGAAAATGTTTCCCAGAGTTTAACGGATCTAGTATCCATCCAGAGCTCTAAGGAGGTGATGGATATAGTGAATATTGTTTTATAGACTTTTTTTTGTTCCTTACATTATTCTACTCTAGATAAATTCTGCCACGGGCTACGGAGGCGCCGTTTGGATA
-90 CGTGTTATGTAGAATGCGACCTTCTCGGCTAACAGTCAGACGCATACTCTATAGTGTTATATGTCAACAGATAAAACACGGTGGTACATAATTCCGGAATCCCGTATCTCGATGCGGTGAAAATGTTTCCCAGAGTTTAACGGGTCTAGTATCCATCCAGAGCTCTAAGGCGGTGATGGGTATAGTGAATATTGTTTTATAGACTTTTTTTTGTTCCTTACATTATTCCACTCTAGATAAATTCTGCCACGGGCTACGGAGGCGCCGTTTGGATA
-78 CGTGTTATGTAGAATGCGACCTTCTCGGCTAACAGTCAGACGCATACTCTATAGTGTTATATGTCCACTGATAAAACACGGTGGTACATAATTCCGGAATCCCGTGTCTCGATGCGGTGAAAATGTTTCCCAGAGTTTAACGGATCTAGTATCCATCCAGAGCCCTAAGGCGGCGATGGGTATAGTTAATATTGATTTATAGACTTTTTTTTGTTCCTTACATTATTCCACTTTAGACAAATTCTACCACGGGCTACGGAGGGGCCGTTTGGATA
-82 CGTGTTATGTAAAACGCGACCTTCTCGGCGAACACTCAGACGCATACTCTATAGTGTTATATGTCAACGGATAAAACACGGTGGTACATAATTCCGGGATCCCGTGTCTCGATGCGGTGAAAATGTTTCTCAGAGTTTAACGAATCTAGTATCCATCCAGAGCTCTAAGGCGGTGATGGGTATAGTGAATATTGTTTTATAGACTTTTTTTTGTTCCTTACGTTATTCCACTCTAGATGAATTCTGCCACGGGCTACGGAGGCGTCGTTTGGATA
-31 CGTGTTATGTAGACTCCGACCTTCTTGGCCAACAGTGAGACGCATACTATATAGTGTTATATGCCAAACGATGGAACGCGGTGGCATATAGTTTCGGAATCCCGTATCTCGATGCCGTGAAACCGTTTCTCAGAGTTTAACGCATCTAATATCCATCCAGAGTGCTAAGGCGGTGATGGGTATAGTGAATATTGTTTTATAGACTTTTTTTTGTTCGTTAGATTATTCCACTTCAGATAAATTCTGCCACGGGCTCCGGGGGTGCCGCTTGGGTA
-95 CGTGTTATGTAGAATGCGACCTTCTCGGCTAACAGTCAGACGAATACTCTATAGTGTTATATGTCAGAAGATGACACACGGTGGTCCATAGTTCCGGAATCCCGTGTCTCAATGCGGTGACAACGTTTCTCAGAGTTTAACGTATTTAATATCCATCCAGCGCTCTAAGGCGGTGATGGGTATAGTGAATATTGTTTTATAGACTTTTTTTTGTTCCTTACATTATTCCACTCTAGGTAAATTCTGCCATGGGATACGGAGGCACCGTTTGGATA
-4 CGTGTTATATAGAATGCGACCTTCTCGGCTAACAGTTGGATGCGTATTCTATAGTGTTGTATGTCAACAGATAAAACACGGTGGTACATAATTCCGGAATCCCGTATCTCGATGCGGTGAAAATGTTTCTCAGAGTTTAACGGATATAATATCCATCCAGAGCTCTAAGGAGGTGATAGGTATAGTGAATATTGTTTTATAGACTTTTTTTTGTTCCTTATATTATTCCACTCTGGATAAATTCCACCAAGGGGTACGGAGGCTCCGTTTGGATA
-61 CGTGTTATATAGAATGCGACCTTTTCGGCTAACAGTTGGACGCGTATTCTATAGTGTTGTATGTCAACAGATAAAACACGGTGGTACATAATTCCAGAATCCCGTATCTCGATGCGGTGAAAGTGTTTCTCAGAGTTTAACGGATCTAATATCCATCCAGAGCTCTAAGGAGGTGATGGGTATAGTGAATATTGTTTTATAGACTTTTTTTTGTTCCTTATATTATTCCACTCTGGATAAATTCACCCAAGGGGTACGGAGGCTCCGTTTGGATA
-72 CGTGTTATGTAGAATGCGACCTTCTCGGCTAACAGTTAGACGCGTATTCTATAGTGTTGTATGTCAACAGATAAAACACGGTAGTAAATAATTCCGGAATCCCGTATCTCGATGCGGTGAAAACGTTTCTCAGAGTTTACCGGATCTAATATCCATCCAGAGCTCTAAGGCGGTGATGGGTATAGTGAATATTGTTTTATAGACTTTTTTTTGTTCCTTATATTATTCCACTCTGGATAAATTCCGCCAAGGGGTACGGAGGCACCGTTTGGATA
-88 CGTGTTCTATAGCGTGCGACCTTCTCGGCTAAAAGTCAGACGCATACTCTATGGTGTTATATGTCAACAGATAAAACACGGTTGTACATAACCTCGGCATCCCGTCTCTCGATGCGGTGAGAACGTTTCTCAGAGTTTAACGGCTCTAATATCCATCCAGAGTGCTAGGGCGGTGATGGGTATAGTGAATATTGTTTCATACACTTTTTTTTGTTCCTTACGTTATTCCACTTTAGATAAATTCTACCACGGGTTACGGAGGCGCCGTGTGGATG
-53 CGTGTTATATAGCGTGCGACCTTCTCGGCTAAAAGTCAGACGCATACTCTATGGTGTTATATGTCAACAGATAAAACACGGTTGTACATAATCCCGGCATCCCGTCTCTCGATGCGGTGAGAACGTTTCTCAGAGTTTAACGGCTCTAATATCCATCCAGAGTGCTAGGGCGGTGATGGGTATAGTGAATATTGTTTCATACACTTTTTTTTGTTCCATACGTTATTCCACTTTAGATAAATTCTACCACGGGTTACGGAGGCGCCGTGGGGATG
-42 CGTATTATTTAGCATGTGACCTTCTCGGCTACAAATCAGAAGCATAATCTCTGGTGGTATATGTCAACAGATAAAACACGGTCGTACATGATCCCGGAATCCCGTCTCTCGGAGCAGTGAGAACGTTTCTCAGAGTTTAACGGCTCTAATGTCCATCCAGAGTGCTAAGGCGGCGATGGGTATAGTGAATATTGTTTCATATACTTTTTTTTGTTCCTTACATTATTCCACTCTGGATAAATTCTTCCACGAGCTACGGAGGGGTCGTTTGGATA
-46 CGTATTATTTAGCATGTGACCTTCTCGGCCACAAATCAGAAGCATAATCTCTGGTGGTATATGTCAACAGATAAAACACGGTTGTACATAATCCCGGGATCCCGTCTCTCGGAGCAGTGAGAACGTTTCTCAGAGTTTAACGGCTCTAATGTCCATCCAGAGTGCTAGGGCGGTGATGGGTATAGTGAATATTGTTTCATATACTTTTTTTTGTTCCTTACATTATTCCACTCTGGATAAATTCTCCCACGAGCCGCGGAGGCGTCGTTTGGATA
-37 CGTGTTGTATGGCATACGACCTTCTCGGTTAAAAGTCGGCCGCATACTATATGGTGTTATATGTCAACAGATACAACACGGTTGTACATAATCCCGGAATCCCGTCTCTCGACGCGGTGAGAACGTTTCGCTGAGTTCAGAGCATCGAATGTCCATCCAGAGTACTACGGCGGTGATGGGTATAGTGAATATTGTTTCATATACTTTTTTTTGTTCCTTACCTTATTCCATTATGGATAAATTCTACCACGGGTTGCGGAGGGGCCGTTTGGATA
-64 CGCGTTCTATAGCATGCGACCTTCTCGGCTAAAAGTCAGACGCATACTCTATGGTGTTATATGTCAACAAATGAAACACGGTCGTACATAATTCCGGGATCCCGTCTCTCGATGCGGTGAGAACGTTTCTCAGAGTTTAACGGATCTAATGTCCATCCAGAGTGCTAAGGCGGTGATGGGTATAGTGAATATTGTTTTATATACTTTTTTTTGTTCCTTACATTATTCCATTCTGGGTAAATTCTGCCACGGGTTACGGAGGCGCCGTTTGGATA
-100 CGCGTTCTATAGCATGCGACCTTCTCGGCTAAAAGTCAGACGCATACTCTATGGTGTTATATGTCAACAAATGAAACACGGTCGTACATAGTTCCGGGATCCCGTCTCTCGATGCGGTGAGAACGTTTCTCAGAGTTTAACGGATCTAATGTCCATCCAGAGTGCTAAGGCGGTGATGGGTATAGTGAATATTGTTTTATATACTTTTTTTTGTTCCTTACATTATTCCATTCTGGGTAAATTCTGCCACGGGTTACGGAGGCGCCGTTTGGATA
-81 CGCGTTCTATAGCATGCGACCTTCTCGGCTAAAAGTCAGACGCATACTCTATGGTGTTATATGTCAACAAATGAAACACAGTCGTACATAATTCCGGGATCCCGTCTCTCGATGCGGTGAGAACGTTTCTCAGAGTTTAACGGATCTAATGTCCATCCAGAGTGCTAAGGCGGTGATGGGTATAGTGAATATTGTTTTATATACTTTTTTTTGTTCCTTACCTTATTCCATTCTGGGTAAATTCTGCCACGGGTTACGGAGGCGCCGTTTGGATA
-2 CGTGTTGTCTAGCAAGTGACCTTCTCGGCTAAAAATCAGACGCATACTCTATGATGTTATATGTCAACTAATGAAACACGGTTGTGCATAATTCCGGAATCCCGTCTCTCGACGCGGTGAGAACGTTTCTCAGAGTTTAACGGATCTAATGCCCATCCAGAGTGCTACGGCGGTGATGGGTATAGTGAATATTGTTGTATATACTTTTTTTTGTTCCCTACGCTATTACATTCTAGGTAAATTTTGCCACGGGTTACGGAGGCTCCGTTTGGATA
-92 CGTGTTGTATAGCAAGCGACCTTCTCGGCTAAAAATCAGACGCATACTCTATGATGTTATATGTCAACAAATGAAACACGGTTGTGCATAGTTGCGGAATCCCGTCTCTCGACGCGGTGAGAACGTTTCTCAGAGTTTAACGGATCTAATGTCCATCCAGAGTGCTACGGCGGTGATGGGTATAGTGAATATTGTTTTATATACTTTTTTTTGTTCCCTACGCTATTACATTCTCGATAAATTTTGCCACGGGTCACGAAGGCTCCGTTTGGATA
-21 CGTGTTATATAGCATGCGACCTTCTCGGCTAAAAGTCAGCCGCATACTCTATGATGTTATATGTCAACACATGAAACACGGTTGTACACAATTCCGGAATCCCGTCTCTCGAAGCGGTGAGAACGTTTTTCAGAGTTTAACGGATCTAATGTCCATCCAGAGTGCTACGGCGGTGATGGGTATAGTGAATATTGTTTTATATACTTTTTTTTGTTCCCTACATTATTCCATTCTGGATAAATTCTGCCACGGGTCACGGAGGTGCCGTTTGGATA
-58 CGTGTTATATAGCATGCGACCTTCTCGGCTAAAAGTCAGACGCATACTCTATGGTGTTATATGTCAACAGATAAAACACGGTTGTACATAATCCCGGCATCCCGTCTCTCGATGCGGTGATAACGTTTCTCAGAGTTTAACGGATCTAATGTCCATCCAGAGTGCTACGGCGGTGATGGGTATAGTGAATATTGTTTTATATACTTTTTTTTGTTCCTTACATTATTCTATTCTGGATAAATTCTACCACGGGTTACGGAGGCGCCGTTTGGATA
-34 CGTGTTATCTAGCCCGCGACCTTCCCGGCTAAAAGTCAGACGCATATTCTATGGTGTTGTATGTCAACAGATAAAACACAGTTACACGTAATCCCGGAATCTCGTCTCTCGATGCGGTGAGAACGTTTCCCAGAGTTTAACGAATCTAATATCCATCCAGAGTGCTAGGGCGGTGATCGGTATAGTGAATATTGTTTTATAGACTTTTTTTTGTTCCTTATATTATTACATTTTGGGTAAATTCTACCACGGGTCACGGAGGCCCCGTTTGGATA
-7 AATGTTATATAGAATGCGACCTTCTCGGCTAAGAGTCAGACGCATAATCTATAGTGTTATATGTCAAAAGATAGAACGCGGTGATACATAATTCCGGAATCCCTTAGCTCGATGCGGTGAGACCGTTTCACAGAGTGTAACGGATCTAATATCCATCGAGAGCACTAAGGCGGTGATAGGTATAGTGAATATTGTTTTATAGACTTTTTTTTGTTCCTTACGTTATTCTACTCTGGATAAATTCTACCATTGGTTACGGAAGCCCTGTTTGTATA
-70 AATGTTATATAGAATGCGACCTTCTCGGCTAAGAGTCAGACGCATAATCTATAGTGTTATATGTCAAAAGATAGAACACGGTGGCACATAAGTCCGGAATCCCGTAGCTCGATGCGGTGAGATCGTTTCACGGAGTGTAACGGATCTAATATCCATCGAGAGCACTAAGTCGGTGTTGGGTATAGTGAATATTGTTTTATAGACTTTTTTTTGTTCCTTACGTTATTCTACTCTGGATAAATTCTGCCATGGGTTATGGGAGCCCCGTTTGTATA
-16 AATGTTATATAGAATGCGACCTTCTCGGCTAAGAGTCAGACGCATAATCTATAGTGTTATATGTCAAAGGATAGAACACGGTGGCACATAAGTCCGGAATCCCGTAGCTCGATGCGGTGAGATCGTTTCACGGAGTGTAACGGATCTAATATCCATCGAGAGCACTAAGTCGGTGTTGGGTATAGTGAATATTGTTTTATAGACTTTTTTTTGTTCCTTACGTTATTCTACTCTGGATAAATTCTGCCATGGGTTATGGAAGCCCCGTTTGTATA
-93 AATGTTATATAGAATTCGACCTTCTCGGCTAAGAGTCAGAAGCATAATCTATAGTGTTATCTGTCAAGAGATAGAACACGGTAGTACATAGTTCCGGGATCCCGTAGCTCGATGCGGTGAGACCGTTTCACAGAGTGTAACGGATCTAATATCCATCGAGAGCACTAAGGTGGTGATAGGTATAGTGAATATTATTTTATAGACTTTTTTTTGTTCCTTACGTTATTCTACTCTGGGTAAATTCTACCATGGGCTACGGAAGCCCCGTCTGTATA
-35 AATGTTATATAGAATTCGACCTTCTCGGCTAAGAGTCAGAAGCATAATCTATAGTGTTATCTGTCAAAAGATAGAACACGGTAGTACATAGTTCCGGGATCCCGTAGCTCGATGCGGTGAGACCGTTTCACAGAGTGTAACGGATCTAATATCCATCGAGAGCACTAAGGTGGTGATAGGTATAGTGAATATTATTTTATAGACTTTTTTTTGTTCCTTACGTTATTCTACTCTGGGTAAATTCTACCATGGGCTACGGAAGCCCCGTCTGTATA
-9 AATGTTATATAGAATGCGACCTTCTCGGCTAGGAGTCAGATGCATAATCTATAGTGTTATAGGTCCCAAGAAAAAACGCAGTCGTAAATATTTCCGGCATCCCGTAGCTCGATGCGGTGGGGCAATTTCACAGAGTGTAACGGATTTAATAGCCATCGAGAGCACTAAGGCGGTGATAGGTATAGTGAATATTGTTTTATAGACTTTTTTTTTTTCCATATGTTATTCCACTCTGGGCAAATTCTGCCATGGGCTACGGAAGATCCGTTTGTATA
-56 CGATTTTTATAAAAGACGACCTTCTCGGCTAAGAGTCAGATGCACAGTCTATGGTGTTATATGCCAACAGATAGAAGTCAGTAGCAAATAATTCCGGAGTCCCGCGTCTCGATGCGGTGGGACTATTTCTCAGAGTTTAACGGCTCTAATATCCATCGAGAGCGCTAAGGTGGTGATGAGCATAGTGAATATTGTTTTATAAACTTTTTTTTGTTCCGTAGGTTATTTTACTTTAGACAAATTCTACCACGGGCAACGGAAGCCCCGTTGGCCTA
-94 CGTGTTATATAGAATACGACCTTCTCGGCTAAGACTCAGACGCATATTCTATAGTGTTATATGTCGACAGATAGAACACGGTGATACATAATTCCGGAATCCCGGATCTCGATGCGGTGAGACCGTTTCACAGAGTTTAACGGATCTAATATCCATCGAGAGCACTACGGCGGCGATGGGTATAGTGAATATTGTTTTATAGACTTTTTTTTGTTCCTTACGTTATTCCACTCTGGATAAATTCTACCACGGGCTACGGAAGCCCCGTTTGTTTA
-91 CGTATTATATAAAATGCGACCTTCTCGGCTAAGAGTCAGACGCACATTCTATAGTGTTACATGTCAACAGATAGAACACAGTGGGACATAATTACGGAATCCCGGACCTCGATGCGGTGAGACGGTTTATCAGAGTTTAACGGATATAATATCCATCGAGAGCACTAAGGCGGCGATCGGTATAGTGAATATTGTTTTATAGACTTTTTTCTGTTCCTTACGTTATTCAACTCTGGCTAAATTCTACCACGGGCCGCGGAAGCTCCGTTTGTTTA
-63 CGTGTTATCTAGAATGCGACCTTCTCGGCTAGTAGTCAGACGCATATTCTATAGTGTTATATGTCGACGGATGGAACACGGTGGTACATACTTCCGGGATCCCGAGTCTCGATACGGTGAGACGGTTTCCCAGAGTTTAGAGGATCTAATATCCATCGAGAGCACTAAGGCGGCGATGGGTATAGTGAATATTGTTTTATAGACTTTTTTTTGTTCCTTACATTATTATATTCTGGATAAATTTTACCACGAGTTATGGAGGTCCCGTTTGTTTA
-26 CGTGTTATATAGAATGCGACCTTCTCGGCTAGGAGTCAGACGCATATTCTATAGTGTTATATGTCTACAGATAGAACACGGTGGTACATAATTCCGGAATCCCGGGTCTCGATACGGTGAGACCGTTTCTCAGAGTTTAGCGAATCTAATACCCATCGAGAGCACTAAGGCGGCGATGGGTATAGTGAATATTGTTTTATAGACTTTTTTTTGTTCCTTACCTTATTACATTTTAGATAAATTTTACCACGAGTTATGAAGGTTCCGTTTGTTTA
-60 CGTGTTATATAGAATGCGACCTTCTCGGCTAGGAGTCAGACGCATATTCTATAGTGTTATATGTCTACAGATAGAACACGGTGGTACATAATTCCGGAATCCCGGGTCTCGATACGGTGAGACCGTTTCCCAGAGTTTAACGGATCTAATACCCATCGAGAGCACTAAGGCGGCGATGGGTATAGTGAATATTGTTTTATAGACTTTTTTTTGTTCCTTACATTATTATATTTTAGATAAATTTTACCACGAGTTATGGAGGTTCCGTTTGTTTA
-25 CGTGTTATATAGAACGCGACCTTCTCGGCTAGGAGTCAGACGCATATTCTATAGTGTTACATGTCTACAGATAGAACACGGTGGTACACAATTCCGGAATCCCGGGTCTCGATACGGTGAGACCGTTTCCCAGAGTTTAGCGGATCTAATACCCATCAAGAGCACTAAGGCGGCGATGGGTATAGTGAATATTGTTTTATAGACTTTTTTTTGTTCCTTACATTATTATATTTTAGATAAATTTTACCACGAGTTATGGAGGTTCCGTCTGTTTA
-48 CGTGTTATATAGAATGCGACCTTCTCGGCTAGAAGTCAGACGCATATTCTATAGTGTTATATGTCTACAGATAGAACACGGTGGTACATAATTCCGGAATCCCGGGTCTCGATACGGTGAAACCGTTTCACAGAGTTTAACGGATCTAATACCCATCGAGAGCACTAAGGCGGCGATGGGTATAGTGAATATTGTTTTATAGACTTTTCTTTGTTCCTTACATTATTATATTTTAGACAAATTTTACCACGAGTTGTGGAGGTCCCGTTTGTTTA
-66 CGTGTTATATAGAACGCGACCTTCTCGGCTAGGAGTCAGACGCATATTCTATAGTGTTATATGTCGACAGATAGAACACGGTGGTACATAATTCCGGAATCCCGGGTCTCGATACGGTGAGACCGTTTCCCAGAGTTTAGCGAATCTAATACCCATCGAGAGCACTAAGGCGGCGATGGGTATAGTGAATATTGTTTTATAGACTTTTTTTTGTTCCTTACATTATTATATTTTAGATAAATTTTACCACGAGTTATGGAGGTTCCGTTTGTTTA
-5 CGTGTTATGTAGAATGTGACCTTCTCGGCTAAGAGTCCGACGCATAATCTATAGTGTTATACGTCAACGGATTAAAGACGGTAGTACGTAATTCCTGTATCCCGTGTCTCGATACGGTGAGACGATCTTACAGAGTTTAGCGGATCTAATCTCCATCGAGAGCACTAAGGCGGTGATGGGTATAGTGAATACTGATTTATAGATTTTTTTTTGTTCCTTACATTATTCCACTTTAGTTAAATTCTTCCATGGGTTACGGAAGGCCCGTTTGTGTA
-65 CGTGTTATGTAGAATGCGACCTTCTCGGCTAAGAGTCAGACGCATGATCTATATTGTTATACGTCAACGGATAAAAAACGGTGGTACGTAATTCCTGGATCCCGTGTCTCGATACGGTGGGACTGTCTTACAGAGTTTAGCGGATCTAATCTCCATCGAGAGCACTAAGGCGGTGATGGGTATAGTGAATACTGTTTTATAGATTTTTTTTTGTTCCTTACGTTATTCCACTTTAGTTAAATTCTTCCATGGGCGCCGGAAGCCCCGTTTGTGTA
-99 CATGTTATATAGAATGTTACCTTCTCGGCTAAGAGTCAGACGCATAATCTATAGTGTTATACGTCAACTGATAAAAGACGGTGGCGTGTAATTCCTGTATCCCGTGTCTCGATGCGGTGAGACCGTCTTACAGAGTTTAGCGGATCCAATCTCCATCGAGCGCACTAAGGCGGTGATGGGTATAGTGAATATTGTTTTATAGATTTTTTTTTGTTCCTTACGTTATTCCACTTTAGCCAAATTCTTCCATGGGCTACGGAAGCTCCGTTTGTGTA
-80 CGTGTTATGTAGAATGCGACCTTCCCGGGTAAGAGTCAGGTGCACAATCTATAGTGTTATACGTCAACGAATACAAGGCGGTGGTAAGTGATTCCGGTATCCCGTGTCTCGAGGCGGTGAGACTGTCTTGCAGAGTTTAGTGGATCTAATACCCATCGAGAGCACTAGGGCGGTGATGGGTATAGTGAATACTGTTTTATAGACTTTTTTTTGTTCCCTACCTTATTCCACTCTAGTCAAATTCTACCAGGGGACGCGGGAGCACCGTTTGTATA
-23 CGTGTTTTCTAAAGTGTGACCTTATCGGGTAAGAGTTAGATGCACAATCTATAGTGTTCTACGTCAGCGGATAATAGCCGGTCACATGTAATTCCGGGACCCCGTATCTCGATGCAGTGAGACAGTCTGTCAGATTTTAACGGATCTAACATCCATCAAGAGCACTAAGGAGGTGATGGGTATAGTGAGTACTGTTTTATAGAATTTTTTTTGTTCTTTCCGTTATTTCAATCGAGACAAATTCTAACAGGGGGTAAGTAAGCACCGTTAGTACA
-73 CGTGTTATCTAGAATGCGACCTTCTCGGCTAAGAGTCAGACGCATATTCTATAGTGTTATATGTCAACAGATAAAACACGGTGGTACATAATTCCGGCATCCCGTGTCTCGATGAGGTGAAACCGTTTCCCAGAGTTTAGCGGATCTAATATCCATCGAGAGCACTAAGTCGGTGATGGGTATAGTGAATATTGTTTTATAGACTTTTTTTTGTTCATTACGTTATTCGACTTTGGATAAATTCTGCCACGGGTTACGGAAGCTCCGTTTGTATA
-96 CGTGTTATCTAGAATGCGACCTTCTCGGCTAAGAGTCAGACGCATATTCTATAGTGTTATATGTCAACAGATAAAACACGGTGGTACATAATTCCGGCATCCCGTGTCTCGATGAGGTGAAACCGTTTTCCAGAGTTTAACGGATCTAATATCCATCGAGAGCCCTAAGTCGGTGATGGGTATAGTGAATATTGTTCTATAGACTTTTTTTTGTTCATTACGTTATTCGACTTTGGATAAATTCTGCCACGGGTTACGGAAGCTCCGTTGGTATA
-44 CGTGTTATCTAGAATTCGACCTTCTCGGCTAAGAGTCAGACGCATATTCTATAGTGTTATATGTCAACAGATAAAACACGGTAGTACATGATTCCGGCATCCCGTGTCTCGATGCGGTGAGACCGTTTCCCAGAGTTTAGCGGATTTAATATCCATCGAGAGCACTAAGTCGGCGATAGGTATAGTGAATATTGTTTTATAGACTTTTTTTTGTTCATTACGTTATTAGATTTTGGACAAATTCTGCCATGGGTTACGGCAGTCCCGTCTGTATA
-86 CGTGTTATATAGAATGCGACCTTCTCGGCTAAGAGTCAGACGCATACTCTAAAGTGTTATATGTCAACAGATAAAACACGGTGGTACGTAATTCCGGCATCCCGTGTCTCGATGCGGTGAGACCGTTTCCCAGAGTTTAGCGGATATAATATCCATCGAGAGCACTATGGCGGTGATGGGTATAGTGAATATTGTTTTATAAACTTTTTTTTGTTCCGTATGTTATTCCACTATGGATAAATTCTGCCACGGGCTATGGAAGCCCCGTTTGGATA
-40 CGTGTTATATAGAATGCGACCTTCTCGGCTAAGAGTCAGACGCATACTCTAAAGTGTTATATGTCAACAGATAAAACACGGCGGTACGTAATTCCGGCATCCCGTGTCTCGATGCGGTGAGACCGTTTCCCAGAGTTTAGCGGATCTAATATCCATCGAGAGCACTATGGCGGTGATTGGTATAGTGAATATTGTTTTATAAACTTTTTTTTGTTCCGTATGTTATTCCACTATGGATAAATTCTACCACGGGCTATGGAAGCCCCGTTTGGATA
-45 CGTGTTATATAGAATGCGACCTTCTCGGCTAAGAGTCAGACGCATACTCTATAGTGTTATATGTCAACAGATAAAACACGGTGGTATGTAATTCCGGCATCCCGTATCTCGATGCGGTGAGACCGTTTCCCAGAGTTTAGCGGATCTAATATCCATCGAGAGCACTAAGGCGGTGATGGGTATAGTGAATATTGTTTTATAGACTTTTTTTTGTTCCGTATGTTATTCCACTATGGATAAATTCTGCCACGGGCTATGGAAGCCCCGTTTGGATA
-11 CGTGTTATATAGAATGCGACCTTCGCGGCTAAGAGTCAGACGCATACTCTATAGTGTTATATGTCAACAGATAAAATACGGTGGTAAGTACTTCCGGCATCCCGTCTCTCGATGCGGTGAGACCATTTCCCAGAGTTTAGCGGATCTAACATTCATCGAGAGCACTAAGGCGGTGATGGGTATAGTGAAGATTGTTTTATAGACTTTTTTTTGTTCCTTATGTTACTCCATTATGGATAAATTCTGCCATGGGCTATGAAAGTCCCGTTTGGATA
-24 CGTGTTCTATAAGACACGACCTTATCGGCTAAGAGTCAGAAGCATAGTCTATAGTGTTATAGGTCAACAGATCGAACACGGTGGTATATAATTCCGGGATCCCGAGTCTCGATGCGGTGAGACCGTTTGTCAGAGTTTAGCGGATATAATATCCATCGAGAGCACTAAGGTGGTGATGGGTATAGTGAATATTGTTTTATAGACTTTTTTTTGTTCCTTACGCAATTCCATTATGGATAAATTCCGCCAAGGGATATGGAAGCCCCGTTTGTATC
-19 CGTTTTATCTAGGACGCGGCCTTGTCGGCTAAGACTCTGACGGATAATCTATATTGTTGTATGTCGACCGTTACTACGCGGTATTGCATAACTCCGGAATCCCGTATCTCTATGCGGTGGTACAGTTTGTCAGAGTTTACCGGATCCAACACCCATCAAGAGCACTAAGGTGGTGATGGGTATAGTGAATATTGTTTGATAAAACTTTTTTTGTTCCTTACATTATTCCATTTTGGATAAATTCCACCACGGGCTACGCAAGCACCGTTCGTATA
-54 CGTTTTATATAGGACGCGGCCTTGTCGGCTAAGACTCTGACGGATAATCTATATTGTTGTATGTCGACCGTTACTACGCGGTATTACATAACTCCGGGATCCCGTATCTCTATGCGGTGGTACAGTTTGACAGAGTTTACCGGATCCAACACCCATCAAGAGCACTAAGGTGGTGATTGGGATAGTGAATATTGTTTGATAAAACTTTTTTTGTTCCTTACATTATTCCATTATGGATAAATTCCACCACGGGCTACGCAAGCACCGTGCGTATA
-14 CGTTTTATATAGGACGCGGCCTTGTCGGCTAAGACTCCGACGGATAGTCTATATTGTTGTATGTCGACCGATACTACACGGTGTTACATAATTCCGGAATCCCGTATCTCGATGCGGTGGTACAGTTTGCCAGAGTTTACCGGATCCAACACCCATCGAGAGCACTAAGGCGGCGATGAGTATAGTGAATATTGTTTGATAAAACTTTTTTTGTTCCTTACATTATTACATTTTGGATAAATTCCGCCACGGGCTACGCAAGCACCGTTCGTATA
-22 CGTTTTATATAGGACGCGGCCTTGTCGGCTAAAACTCCGACGGATAGTCTATATTGTTATATGTCGACCGATACTACACGGTGTTACATAATTCCGGGATCCCGTATCTCGATGCGGTGGTACAGTTCGCCAGAGTTTATCGCATCCAACACCCATCGAGAGCACTAAGGTGGCGATGGGTATAGTGAATATTGTTTGATAAAACTTTTTTTGTTCCTTACATTATTACATTGTGGATAAATTCCGCCACGGGCTACGCAAGCGCCGTTCGTATA
-98 CGGTTTATGTAGGGCGCGACCTTGTCGGCTAAGAATCCGACGGATAGTCTATCTTGTTGCATGTCTACAAACCCTACACAGTATTATATTGTTCCGGGATCTTGTATCTCGACATGGTGGTACTGTTATTAAGAGTTTACCGGATTTAACCCCCATCGAGAGCGCTATGGTGGTGATGGGTATAGTGTATACTGTTTGATAAAATTTTTTTTGTTCCTTATGTTCTTCTACTTTGGATAAATTATGCCACGTGCTACGCGCGGACCGTTCGTAAA
-17 CGTTTTATGTAGGACGCGACCTTGTCGGCTAAGAGTCCGACGGATAGTCTATCTTGTTGCATGTCTACAAACCCTACACGGTATTATATTATTCCGGAATCTTGTATCTCGCTGTGGTGGTACAGTTAGTAAGAGTTTACCGGATTCAACCCCCATCGAGAGCGCTAAGGTGGTGATGGGTATAGTGCATACTGTTTGATAAAATTTTTTTTGTTCCTTACTTTCTTCTACTTTGGATAAATTATGCCACGTGCTACGCGCGGACCGTTCGTAAA
-47 CGTCTTATATAGGACGTGGCCTTGTCGGCTAAGAGTCCGACGGATAATCTATCTTGTTGCATGTCGATAGACATTACACGGTATTATATAACTCCGGAATCCCGTTTCTCGATGCGGTGGTACAGTTTCCAAGAATTTACCGGATCCAACACCCATCCAGAGCACTAAGGTGGTGATGGGTATAGTGAATATTGTTTGATATAATTTTTTTTGTTCTTTACATTCTTCTACTCTGGATAAATTATACCACGTGCTACGCACGTGCCGTTCGTAGA
-77 CGTCTTATATAGGACGTGGCCTTGTCGGCTAAGAGTCCGACGGATAATCTATCTTGTTGCACGTCGATAGACATTACACGGTATTAGATAACTCCGGAATCCCGTATCTCGACGCGGTGGTACAGTTTCCAAGAATTTACCGGATCCAACACCCATCCAGAGTACTACGGTGGTGATGGGTATAGTGAATATTGTTTGATATAATTTTTTTTGTTCCTTACATTCTTCTACTCTGGATAAATTATACCACGTGCTACGCACGTACCGTTCGTATA
-50 CGTCTTATATAGGACGTGGCCTTGTCGGCCAAGAGTCCGACGGATAATCTATCTTGTTGCATGTCAATAGACATTAAACGGTATCATATAACTCCGGAATCCCGTATCTCGATGCGGTGGTACTGTTTCCAAGAATTTACCGGATCCAACACCCATCCAGAGCACTAAGGTGGTGATGGGTATAGTGAATATTGTTTGATATAATTTTTTTTGTTCTTTACCTTCTTCTACACTGGATAAATTATACCACGTGTCACGCACGTACCGTTCGTATG
-84 CGTTTTATATAGGACGCGACCTTGTCGGCTAAGAGTCCGACGGATAATCTATCTCGTTGCAGGTCGACAGACACTACACGGTGTTATATAATTCCGGAATCCCGTATCTCGATGCGGTGGTACAGTTTGCAAGAGTTTACCGGATCCAACACCCATCGAGAGCACTAAGGTGGTGATGGGTATAGTGAATATTGTTTGATAAAATTTTTTTTGTTCCTTACATTCTTCTACTCTGGATAAATTATACCACGTGCTACGCACATACCGTTCGTATA
-33 CGTTTTATATAACACGCGACCTTGTCGGCGAGGAGTCAGACGGATAGTCTATATGGTTGTACGTCAACCAATATGACGCAGTGTTAAATAAGTGCGGAATCCCGTATCTCGATGCGGTGGTACAGTATGACAGAGTTTACCGAATCCAACGCCCATCGAGAGCGCTAAGGCGGGGATGGGTATAGTGGATATTGCTTGATAAAATTTTCTTTGTTCCTTATATTATTCAACTCTGGGTAAATTATACCACTGGCTAGGCAAGCACCGTTAGTATT
-6 CGTTTTATATAATACGTGACCTTATCGGCTAAGAGTCCGACGGAGAGTCTATATAGTTGTACGTCGACCAATACTACGCGGTGTTAAATAATTGCGGAATCCCGTATCTCGATGCGGTGGTACAGTATGACAGAGTTTACCGAATCAAACGCCCATCGAGAGCTCTAAGGTGGGGCTCGGTATATTGAATATTGCTTGATAAAATTGTTTTTGTTCCTTATACTATTCACCTCTAGATAAATTGTATCACGGGTTAGGCAAGTACCGTTCGTAGA
\ No newline at end of file
diff --git a/addons/ASTER/example/genetree.nw b/addons/ASTER/example/genetree.nw
deleted file mode 100644
index 10212433b206cd0a175a7e8f4886d4c714b113ef..0000000000000000000000000000000000000000
--- a/addons/ASTER/example/genetree.nw
+++ /dev/null
@@ -1,2000 +0,0 @@
-(((GALGA:0.08377431052715295090,(MELGA:0.05682381219312587078,ANAPL:0.11233397823555341111)32:0.00315264564389563856)39:0.00447001267881514709,(((((((((BUCRH:0.09699489701531013863,LEPDI:0.10378260144416162625)25:0.00337851467950173482,(PICPU:0.21188360424631011436,MERNU:0.16610255719967759180)31:0.02103378229645283884)20:0.00424884471406725226,COLST:0.13136049942818700531)16:0.00843464119654929387,(HALLE:0.00411589692418326807,HALAL:0.00169948070591385749)100:0.04712553451594352766)6:0.00142401164787427504,(CATAU:0.03482335336988792718,(APAVI:0.09212007290233019396,(CARCR:0.07299035887725666139,(FALPE:0.09657714159312831559,((MELUN:0.10784997866147441603,NESNO:0.05438813902110055387)98:0.05919734948875422786,(ACACH:0.09617237328479849578,(MANVI:0.07280461321169473532,((TAEGU:0.03731611029427812920,GEOFO:0.05497403327619487107)99:0.03172834558564776447,CORBR:0.03992228369212302841)100:0.08622226821940570662)81:0.02044939989779536935)95:0.02994982236598515979)35:0.00585486473018064987)3:0.00000173612040141334)8:0.00176414979134006879)16:0.00231729070613975654)17:0.00226395398635066171)6:0.00247095302739345742,PHALE:0.08355446350118930776)1:0.00000173612040141334,TYTAL:0.11454185671553666903)9:0.00562478058041427590,(TAUER:0.10099892502055370092,((((PTEGU:0.06450514281979118081,MESUN:0.11566218946276414503)45:0.00993344810774232818,PHACA:0.07234797364524446495)32:0.01527466297098501423,(CHAVO:0.05971513186291901171,(COLLI:0.11357267443127072593,((CALAN:0.21533378567805819270,CHAPE:0.11712861342543735843)41:0.02798063691638290676,(CAPCA:0.06868190928866538258,EURHE:0.11894841150635926397)11:0.00568510495544791248)9:0.00352698292961834510)2:0.00000173612040141334)9:0.00221959693001766694)1:0.00000173612040141334,(PHORU:0.02491888356564115475,PODCR:0.08198663553190162212)99:0.04487344380084509060)1:0.00000173612040141334)27:0.00426637129317324840)14:0.00260821787665433931,(OPHHO:0.12000019210933972336,((BALRE:0.10645264695674952482,(((APTFO:0.02196594904495621434,PYGAD:0.00638528110103973607)100:0.03927959777153028353,FULGL:0.03299086001208650226)46:0.00209119305629561041,(NIPNI:0.06015628274367356559,(EGRGA:0.07215590147205359906,PELCR:0.09935473495717438153)27:0.00000173612040141334)37:0.00383658379703257510)56:0.00945542062417656891)7:0.00000173612040141334,((CUCCA:0.12269297286522812263,GAVST:0.07538429357754908300)35:0.00429167738114970103,CHLUN:0.07790597351508105062)9:0.00110379482627409402)36:0.00443461382114509681)51:0.01244682451028001312)32:0.00487679928322202680)83:0.03666308846324025511,(TINMA:0.18032540406898542318,STRCA:0.23279120409371903411)83:0.03666308846324025511);
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-(((((((((CARCR:0.06975310805339085540,((COLST:0.22255849929743790061,(PYGAD:0.02433192597654084202,APTFO:0.01302138930402256707)100:0.08835816480905565873)14:0.01571021139881982609,(PICPU:0.24437922484842627968,(MERNU:0.16005357165393951924,(PODCR:0.14505295110688476434,PHORU:0.05934021742845713154)96:0.04688575025284105052)7:0.00000187127284785769)4:0.00859888569802814452)2:0.00200310938951327091)3:0.01325592668507532407,(((EURHE:0.13215067373070146783,CHAVO:0.06705231105698324090)17:0.00667717880773204160,BALRE:0.07624583181389736619)2:0.00619125782585515632,((((NIPNI:0.06794869522045218768,(PHACA:0.07054614178781357103,EGRGA:0.07969693088600830755)37:0.00904571972260407621)13:0.00063213361701361566,FULGL:0.01988410868688736746)21:0.00730278373493388391,(OPHHO:0.06379413083185729583,PELCR:0.05453023955473357970)9:0.00537857150253363142)1:0.00000187127284785769,(((FALPE:0.11832979793747282204,(((MANVI:0.07491911386850609589,(CORBR:0.04934075244425518980,(GEOFO:0.05293206078754545546,TAEGU:0.01964159237292189761)100:0.04261994487510415569)100:0.05426604947355279096)94:0.03888512968684823545,ACACH:0.14400155558171556791)90:0.05000627743517639667,(NESNO:0.09632751962698735126,MELUN:0.08098028716406627248)71:0.01911650658205207853)38:0.00684714830788562233)14:0.00998016690139889862,(APAVI:0.13190874826320522772,CATAU:0.03535963758559814568)4:0.00000187127284785769)5:0.00190261982872871730,((LEPDI:0.12513409633103556029,(TYTAL:0.07414850517599481938,BUCRH:0.09882717697600050533)14:0.00576382998553779530)8:0.00281375192260985675,(HALLE:0.00000187127284785769,HALAL:0.00217822646651324135)100:0.04151498979626242619)3:0.00000187127284785769)12:0.00611643069607521132)0:0.00268364414000810212)0:0.00206254230572372986)2:0.00474596565400830193,((PHALE:0.06127266703198976094,GAVST:0.07343567996378118357)12:0.00237298306108575663,(CAPCA:0.12739879736073866923,(CALAN:0.09384200169011830406,CHAPE:0.14094568758344394599)39:0.02314044067442452834)8:0.00439557709189327718)3:0.00084350282765071661)11:0.00226603218493323958,(CUCCA:0.15593403973352357172,(TAUER:0.07798160117745060738,COLLI:0.08420007993911945987)30:0.00671672318512199495)3:0.00000187127284785769)4:0.00000187127284785769,MESUN:0.14161604491360030300)12:0.00283370727175323535,PTEGU:0.07811882874428718870)21:0.00000187127284785769,CHLUN:0.10473601041818063340)81:0.02764202169914346460,(MELGA:0.05358702683453315380,(GALGA:0.04863027277599724779,ANAPL:0.19241095880172159882)70:0.01844741697453448903)100:0.03864345550993327633)95:0.02383039347580883163,(TINMA:0.17952583503469710102,STRCA:0.12514545452026040739)95:0.02383039347580883163);
-(((MELGA:0.04959229029703634412,(GALGA:0.03174260255703936773,ANAPL:0.14416141822949279927)59:0.00550353615047034176)89:0.03462238921278201070,(((CALAN:0.29683088035924320991,CHAPE:0.08030216065924049296)79:0.04214108174746588470,CAPCA:0.07257344440938286179)67:0.02552724323723223193,(((APAVI:0.15588809037844431060,COLLI:0.09868796724674143428)20:0.01456385246702468668,CATAU:0.02886394735156675578)7:0.00414556689664214752,((((FALPE:0.13625613169593456253,OPHHO:0.07688866639941922820)14:0.00650127037426368858,(CHAVO:0.09643404687072031078,CUCCA:0.17087664197106808284)23:0.01578485721446327636)3:0.00653457503552458754,((((LEPDI:0.05564487784752110422,(NESNO:0.05247311353625820629,MELUN:0.06025939521410896005)90:0.02761765049972886299)7:0.00015520554536317132,((PTEGU:0.10219715882428914711,(TAUER:0.08592498899024302028,MESUN:0.10196976894936050917)39:0.01027752055268582425)19:0.00503729747852995052,(CARCR:0.08421506939704100081,(PHALE:0.05828959367101026190,BALRE:0.05587977234600921550)22:0.00951209911322510072)5:0.00246007122366599489)1:0.00229108237203975822)0:0.00233555945961559782,(((((CORBR:0.02289359382933487536,(TAEGU:0.05067341310517409908,GEOFO:0.05704189913235079012)100:0.12404751504565893205)100:0.05662116891065339247,MANVI:0.08596340431279414496)76:0.00254466214970605793,ACACH:0.09771046272106992392)100:0.15689622069841988039,CHLUN:0.04520314685112519076)36:0.01405387181830953548,((TYTAL:0.08511391202800901168,(PICPU:0.16346288308266385125,(PHORU:0.02580061489646891595,PODCR:0.09067705699629605154)64:0.01022330786464150862)26:0.01017931955685501440)3:0.00017943010399600255,((MERNU:0.10620389182708694920,BUCRH:0.11507332766245800815)46:0.03125255493440329269,(COLST:0.17942998747828667327,EURHE:0.09574963829137594917)26:0.01836950631570822071)1:0.00286952890016821133)0:0.00264628400431102381)0:0.00000197426031738596)0:0.00000197426031738596,(GAVST:0.07799265460728829757,((FULGL:0.03716783882722864835,PHACA:0.06914390508582364536)34:0.00203705127316078415,(((EGRGA:0.06486198500699646985,PELCR:0.07258863740791986208)61:0.00921502612756888370,NIPNI:0.05757176183399830699)68:0.00995349833410940840,(PYGAD:0.01790148013622956669,APTFO:0.01495966182096620210)100:0.07067966032310975255)19:0.00085373186774210337)51:0.00463879387049843505)27:0.00419247729765915254)0:0.00000197426031738596)0:0.00177387786939058414,(HALLE:0.00000197426031738596,HALAL:0.00204684120205165425)100:0.05261273217078683839)0:0.00000197426031738596)21:0.01342342178063642491)53:0.02038160195119189874)100:0.07688093102341211904,(STRCA:0.26744515207023983328,TINMA:0.15291658183916212455)100:0.07688093102341211904);
diff --git a/addons/ASTER/example/genetrees.tre_1.fas b/addons/ASTER/example/genetrees.tre_1.fas
deleted file mode 100644
index b0067f09ec9876b5f82f8a81edf2a028a5540877..0000000000000000000000000000000000000000
--- a/addons/ASTER/example/genetrees.tre_1.fas
+++ /dev/null
@@ -1,53 +0,0 @@
->0
-GTTGCATGTAGATCCTCAAAGTCTATAACGAGGTATATGATAGGCGTCAAACTCATTTAAGCTGCTCATACGTCTTTCAAGATCTTAGTGCAATTCTTCAGAATGTTGATGATCTGGGATTGCAAAAATCGAACTCTTAATTGAATTTATCATGGTTAACCAGTCAGCGTCCCATCCTGGATAGATCTTCGCGTCACGCACTCCGTCACATGGAATATCCACTAATGTAAATAACTGATCTTCATTTTACCTAGGCTATACGACTGTACATTTAAAGTGAGCAGTACTTAAATTCCTATGGTAAACACAAATCTGCACTCGTATACGGCCTGCCTAGAGACCAGTGGAGTTTTTGAACAGTGCACACGAATGCCGCTAGCCAAATTCTATTGATAATCAGGGACGTACTCCGCCAGATACCGCAAGCTATTATAGCCTCACTAGAGATTTCGGAGTATTTCACCTTTAACCAAACATACTGCCTGTGGTCGCGTACATGT
->20
-CAAAGTCTATTCATAAAATAGCGAGTAGTGGAATTCCATGCTACTCTTTATGCGTTACACTAGGGGATGCTCTTGGATTGACCTATTTGGCCTAAAATTAAGAGCGGCACCCAACACCATTGTTTTTCCTGAGAATCCCGGGATGATCTGATTGAAGCCTTTTAAATGATTTAATCGAAGTAAAACACGAAGACTTATAGATATCACACGATGACATTATCACTTCCCCCATTATACTATATTTATGCGAATCAAATTGATTTTTGCTCGCATAAGGATCCTACTTTATAAGTACACAAGACGAAGAGTCAGAACTTCGTCAATTTTGCGTTTATTATTGAACATACATAGCATCGAAAACTTGAATTAATCTGAACTACCGTTTTGATTCAAAAAAACCTTATGGAGACTTCTATAATAGATTGTTCTTAATAACATGTTGTTAGTACGTTAAACTATATCCCAGTAAAAAAAAAAACTCCGCAAACATAGGGAAATGT
->21
-CAAAGTCTATTCATAGAATAGCGATTAGTGGAATTCCATGCTACGCTTTATGCTTTAGACTAGGGGATGCTCTAGGGTTGACCTATTTGGCCTAAAATTAAGAGTGGCACCCAACACCGTTGATTTTCCTGAGAACCCCGGGATGATCTGAGTGAAGCCTTTTAAATGATTTAATCGAAGTAACACACAAAGACTTATACTTATCACACGCTGACATTATCACTTCTCCCATTATACGATATTTATGAGAATTAAATTGATTTTTGATCGTATAAGGATCCTACTTTATAAGTACACAAAACAAAGAGTCAGAACTTCGTCAATTTTGCGTTTATTATTGGAGATTCCTAGCATGGAAAACTTCAATTAATCTGAACTACTGTTTTGATCCAAAAAAACCTTACGTACACTTCTATAATAGATTGTTCTTAATAACAGGTTGTTAGTACGTTAAACTATATTCTAGAAAAAAAAAAACCTCCGCAAACATATTGAAATGT
->19
-CAAAGTCTATTCATAAAATAGCGAGTAGTGGAATTCCATGCTACTCTTTATGCGTTACACTAGGGGATGCTCTTGGATTGACCTATTTGGCCTAAAATTAAGAGCGGCACCCAACACCATTGCTTTTCCTGAGAATCCCGGGATAATCTGATTGAAGCCTTTTAAATGATTTAGTCGAAGTAACACACGAAGACTTATAGATATCACATGATGACATTATCACTTCCCCCATTATACTATATTTATGCGAATCAAATTGATTTTTGCTCGCATAAGGATCCTACTTTATAAGTACACAGGACGAAGAGTCAGAACTTCGTCAATTTTGCGTTTATTATTGAACATACATAGCAGCGAAAATTTGAATTAATCTGAACTACCGTTTTGATTCAAAAAAACCTTATGGAGACTTCTATAATAGATTGTTCTTAATAACATGTTGTTAGTACGTTAAACTATATCCCAGTAAAAAAAACAACTCGGCAAACATAGGGAAAGGT
->23
-AATAAGTATGCTAAGACCTCAATGGTCTTAACTAGTCCTATATAACTCATATGTCTGGGGCTGAAAAGTCATGTCTCATGAATAACAATTATGAACTTTTATTAGATTTTGCTTCAGGCTTTTTGATTATACACATGCGATCTTAACTTAGGTATACTACTTAATAGTAAAGGGTGGGCATCAGTGGCCACTCTGGAATTATCCGTGACTTAGGGACTCCTAAGGATGAATCGTGGTTCGAGCTTATGACAAGAACTGCCTAGAATCTGCGCCAGACTCTCCCAGTACCGGTCCATATCCTTTGTTTGAAACAGATGACGCTATATACAAATGTGCTCAAGAGGAGTCTAATACCTTTCGAGCGATTTAGTTGCAAGACCCAATAAGGGAAACCTTGAATGAAACAGTTTAATATAAGCGGAACCCTTATTATGGACGGCTACTGAGATAAGACTAAATTGTTGGCGATGAGTTCGGGCTAAGGCAGTCGTTTTGAACTG
->25
-AACAACTTTCTCAATGACTCAATCTGGTAGCTAAAACCTAAGTAATTCAAAGAACTCGAGCTGCCCCGTTTAGGATCTCGGCGAACAACAATTTACTACTAGTAGCTCTTACATCAATCTCGTCTTTAATCTACTATCCATACTATGGTCAGTAGAAAGCATACTTTAATATAAAGTGGATTTTCGGATAAGTATAACGTATTTTCAAAACATGCTCCTCGTAGTTTTACTCAAAATCAAAACTTGCTGTAAGATTGTCATGGTCTGTACAGGAGGTTCATCTAAGAGTACTCCATTTTATGAGTTCTAGACTTTTGAAACGGTGACGAGTAGGGCCAGACCCGGGCCTGGGAATACCGTACATACTGATATTCAACTAGCCAGGTACATAAGGTTAGTCCAGACGTTTAAAACAAGACAGATTATATATCATAAGGTGTCATCTACGCTGGATAAGCTACTTGTCCGTGAAAAATGGGCTCTTTAGAGGTCATGGCACT
->22
-AAAATTCTTGTGAATGACACGATATAGTAGATTAATCCTAAATAGTTCGAACCCTTCGATCTTCCACGCTAAGGACCTAGCCTCATTGAAAGATACTAGTACTATCTCTAGTGTCACACTCTTTTTTAGCCTAGTATTAACGGAGCGGGCAGAAGGAACGATACTTTTACCTTGTGTGATTTATAGGCCAAATATTACGTATTATGACGACGTGCTGACCGGAGCCTCATCTACAGCCAGGACTAATCATAAGGCTGTGCTGGCTTTTACGAGAGGTTGCACTGAGGGTATTCCTCTCTATGTATTTTAAGTTTTCGAAGCGGCGACGTCGAGGACCATGTCTAGTCTTGCCAATACTGCGCACGTTAATATTTGGCTGATTCCTTACATAAGGTTGGATCGGACTTATTAATACGAAAAAGTCATCAATTATACCTTATCACCTATCTCGGATATATTACGAGTCTATGAAGAATACTGTATATAGATGTTATGCTTTT
->24
-TCGATATTGCCATATCATTAAGCATTCAGGATGATAGTGGTAACAAAAAGAAGCCAAGGGGATAAATAAGAACCGGCTCAAGTGCCTGGCCAAGTCCCTAACTGACCTCATCGCTTATGTGAACCCTAGGGATTAAACACCTCCGAGCTTACGTTCTGGCAAGATGCGCTAAATGATCTCTCAGCTATGCTACCCCTCAACAAAGTGGGTTCCAAACTAGGAGCTTCCGGATTGCCCCTCGTTAGATGAGTTATGCCGCGCCTGCAAAAACCAAGTTGATTATGTTTTTGCTCGCTTACCGACGGATTTCATGTACAGCCTAACAGCCTGCGCCAAAAGACATTCGGCGGCTTATTACTGAATGGAAGTGTACTTTTTAAGGCGAGCGGGATAACCGTCAGGAACGCACCACACACTCCACCGATTGTGTAAGTATAATCTATACGTTTTAATGGAGTTTGATTGTTTGAAGGGTAAAATATGGTTCTCTCGCCGTCATT
->2
-ATTAACTTACTCTGACACTTATAAATGATGCGATTCGATGGCGTCCTTTACTGGATTTAGGACATGTAGCTCTTGTTGTACCTAGCACAATGTAATATTAGAGGACGAACCCTTCGTCATCACTCTTAAACACCATCGTGGTGCGACGATACTGACTATCGTTTTTACGCTAGATCACATGGAGATTAACTATTGTGCAGTCACCAGATCGTGCGCTATTCATTTTCCGCGTCCTGCTAACGTTAGCGTATTTCGAATCACTTTTACATATTACAGGACCGCTGGGAGTAATTACACATAACGAACCGTCAGCATTTCGTATCTCGTTTGCTGTATATAATACGTATGGGGCCTTGTGACACCAAATGATCCCCAGACATTGCTTTAGTAATAGAATGTAGTATGATGGTCTCTTCAATATCTGGGTCTTGATAATACCCCCAATTGCAGTTAAGGTGGACCCTATGAACAAAGAAAGTGGGAGGTATGTCAGCAGATGT
->12
-CAAGGGGTCCGTTTTAATTGCGAGCCTTTGAAAGCGCAGAAGGGGTACGATTCCGTCTTTAACTCGCTCGTTAGCGGAGTATTGAGTAGGATAAAGAGGGAAAACACTATAGCCGTTGGCTATCTTCGATATGTAACCCCTCTTAGCTGAGCTAAATGAGATTTCCTCCGAGAGTACGAGTTGTAAGCGCTCGTTTACCCCACGGCAGTACTACTACAGACTCGTTTCCCGCGGGCCAAACTGATCAACATTATAGTTCAATTTCAGCAAACATAGGCATGTTTGCTTACTCAACACCATCGTTATCAGTATACCGTACTAAACCAGTTATATAAACCACTTAATCCCCAGGATTTTGGCAAGAACAATGGAGTAGCTTTTGTAAGGCCCACAACGAATGAGCGGTTTCTCTACACATATTGTAAATCCTTACTCTTCAATTAAGTGCATATGTAATTAGCTTCGAATTTAAATGCTATGTTAACTAAGTAGCTCCGTAT
->7
-GCTACCTCAGGGGTGAATTATTTAACGTTGATCGGTGGGCATGGTAATAGCTGCTGGCATTTTGAAAACTACCTATCTCCGATAATCCTTGGAATAGACAACAGCACCAGAATCGTGTCTCGCCCTTACTAAAAAACCTGTTACTCCTACGTTCGAGAGTCTTCATAACCGAGACGAACCCTAGTGAGGTCACCTGACTATAACGGCATATTTACATGTTGGCTGCATTTATGATTGAGACATTTAAGAGCGGCACGGGACATGTGGCGTACCTAAAATCCTATGTTGCAGGTCCAGAGTGTAAGACGCCCAATACGACTCGATTTCTTTGCTAGAACCGTACAGATATATGCCCTATGCACTGGTCCAGATTATATTCGCTTTATGAGTGAACAGTGTGTATGATCCGCCCTTGCAACAACACGGCTATATCAAAATGAGAGCGTGGGCGTAATATACAGTCGACTTCAAGGTAGCGCACATAACAGCTCATTGGGAAA
->13
-AGTAGCTTACCTGATTAATATTGAATCTTTATGGTGCAGCGAACTACTCGCTCCTTTCTTTTGAGAAGGTCCGTCTCTCCGGCAGCCCCATGAAACGTCAAAAGCACCAAAGTCATTGGTCGTTCTTGTTGAGAAATCTCTTACATCTATGTTGAAGAGTGTTCATTATCTCGATAAAGTCCACAGATACTACCTGATTGTAGAGGCATGTTTACATGCGCCCTTTGCGTATGGTGGAAATCTCAAAGAACGACACTCAATTGGCGCAGATATTAACAACCCATGTCGCTAGTTCGCATTGTAAGGCGTACGCACCGACTTAACCTCTTTGTCAGGACCGTACGTTCACAGGGCCCATACATTGAATCGGAATAAACTCGTATTATGATTGAAGACCATGCACGATCCACCTTTACAACATCTCGGCTATAGCAAAATAGCAGAGTAGGCGCAAGGTAGATTCGATTTCAAAATGACACACGTAATACCTGAGCGGGAAG
->1
-AGTAGCTTACCTGATGAATATTGAATGTTTATGGTGCAGCAAACTAATCGCTCCTTTCTCTTGAGAAGGTCCGTCTCTCCGGCAGCCCCATGAAACGTCAAAAGCACCACAGTCATTGGTCGTTCTTGTTGAGAAATCTGTTACATCTATGTTGAAGAGTGTTCATTACCTCGATAAAGTCCATAGATACTACCTGATTGTAGCGGCATGTTTACATGCGCCTTTTGGGCATGGTGGAAATCTCAAAGAACGACACTCAATTCGCGCAGATATTAACAACCCATGTCGCTAGTCCGCATTGTAAGGCGTACGAACCGACTTAACCTCTTTGTCAGGACCCTACGTTCACAGGGCCCATACATTGAAGCGGAATAAACTCGTATTATGATTGAAGAGCATGTACGATCCACCTTTACAACATCCCGGCTATAGCAAAATAGCAGAGTAGGCGCAAGGTAGATTCGATTTCAAAATAACACACGGAATACCTGAGCGGGAAG
->4
-AGTAGATTACCAGGTGAATATTTCATTTTTATGGTGTATCTGACTATACGATCCGTTCTCTTGGTAAGGTCCGTACCTCTAGCAGCCCTATAAAGCATCGAGAACATCAGGGCTATTGGCCGTTCTGGTAGAGAAATGTGTTACATCTATTGTGAACAGTGTTCATCGCCTCCATAGAGTCAATAGATGTTACGTAAGTAAAGTAACACGATGACTTGTCCCCTTGGCACATGCTGGAAATTTCAAACAACGAGACTCGATTCGCGCAGATACTAACAACCCATGTTGCCAGCCCGCATTTTAAGGCGTACGAACCGACTTAACCTCTTCACGAGAACTCCACTTTCCTGGGGCCCACACATTGAAGCGGAATAAACTCGTATTGTGCTTGAATAGTACATACGCTCCAACTTTACAGTATCACGGCGATGGCAGAATATCAGAGTATGCGCAAGGTAGATTCGATTTCAAAATAGCTCACGGGATACCCTACCGGGCAA
->3
-AAGAATTTACCTGGATAAAAATTTATGCCCATTAAAGGACTTACCAAGGGCCTTGCGTTCTTGAAGAGATTAGGATCCATAGTACAGCCTTGAAAACTCATACATGCAGCAGCCATCGACTGGCTACACCGAAATAACGGTTGCAGTTAGATTATAAATTCTTCTTGAGCCTAAGCATGACTGTAGAAGGGACTGTATCGCCATAGAATAATTATACGTACCTGCTGCGAATACTGGAGAATCCAAGAAACTCTACTTAATCTGCGTCCTCACTAACAATTGAAAGCGGTAGCTGACCCTGGTAATACTAGAAATCCTGGTATAATCCTGGCTAAGAGCCTACTGTCGCATGAAACATGGGTTGGGAGTGCATCAACATATACATGGCGTGATGACTTAGTAATCTTGACTAATATAGTATCACTCACAACGTCTAAGAGAATGATATGTCTCAGTTAGATATAGTCTGAAAACGATACACGGCGCAGTTAGCCGAGCAG
->16
-AATACCTTAGTTGAGAAGTAGTGAGTAGTCAGATTGCAGCAGGTAAGTCACGGATTTCCTATGTGAAGATCTGTCAATGTCCAATCCCAATAACCAGTCAGACTTGCAATATCTCTTGCTCTATATTGTTAAGGAACTCTTCACAACGCTGTTCAAGGTTAGTTATTACTGCGCTGGGATAAGCAGATAGTAATTAATAAATATGCGATTGCTACCTACGCTTAGAGCGCGTCACTTGTCGCCCAGGGGATTGTACTCAATGGGGTTAAATAGTTGCTACCTATATCGGTATTGCGCTATAACCGCAGTAGTGATCGGGGAAGTCATTACAATACCGTTCTAAAGTGGAGGGAGGTGTACCTGCGGACGGTTTGATGTCCGATAATCATGTGAAAGCTTTTACTAACTATCGTGGCTACGCGCTGCTTATAATAAAACGGTGGATCAGGTGAGGTATAGCTCTAAGCTGAAAATTACATGCTGGACAGCAGAACGTTAAC
->6
-TGTAGCTTAGTTGAGAAGTATTAGGTGGTCATGTTGCAGCACGCGAGGCACTGATTTCCTATGGGAAGAGCTGTTAATGTCCCAACCCGAGATGCAGTTAAATTTGTTAGACTCCCTGCTACATATTGTCGAGAAACTGTTCACAACGTTGTCGAGGGTCGTTTATTACTATGATAGCATAAACAGATAGTAGTGAATAAGTACGTGAGTGCTCATTACGCTCGTCACACATCAGGCGCTGCCCAGCAGAGTGTACTCCATGGGGGTAGATAGTTGTTACGAATCTTGCTATTCCGATATAGCTGTCGTAGCGATTGAGAAAACCACGACAGTACTATTCGAAAGTGGGGGAATGCGTATCTGAGGATGACCGGATGTTCGATTATGATGTGAAAGCCTTTACTACCTAACGTGTCCACGTTCTGCTTATAATAACAGGAGAGATGAGGCGAAATGTAGCTACAATTTGAAAATTACATTCTGCACCGCTGAACATCAAT
->10
-TGTAGCTTAGTTGAGAAGTATTAGGTGGTCATGTTGCAGCACGCGAGGCACTGATTTCCTATGGGAAGATCTGTTAATGTCCCAACCCGAGATGCAGTCAAATTTGTTAGACTCCCTGCTACATATTGTCGAGAAACTGTTCACAACGTTGTCGAGGGTCGTTTATTACTATGATAGCATAAATAGATAGTAGTGAATAAGTACGTGAGTGCTCATTACGCTCGTCACACATCAGGCGCTGCCCAGCAGAGTGTACTCCATGGGGGTAAATAGTTGTTACGAATATTGCTATTCCGCTATAGCTGTCGTAGCGATTGAGAAAACCACGACACTACTATTCGAAAGTGGGGGAATGCGTATCTGAGGATGACCGGATGTTCGATTATGATTTGAAAGCCTTTACTAGCTAACGTGTCCACGTTCTGCTTATAATAACAGGGGGGATGAGGCGAAGTGTAGCTACAATTTGAAAATTACATGCTGCACCGCTGAACATCAAT
->8
-ATTAGCTTAGCTGAGAAGTCCTGAGTGGTCAGATTGTAGTAGGCGAGTTACTAATGTGCAATAGGAAGTTCTGTAAAGTTTCCAGCTCAATAAACAGTCAAACTTGTCATGGTTTTGGCTCCATATTCTTTAAAGGATCTTTACAATGCTGCTGAATGTCGTTTATTACTACTGTAGAGTAAATAGATATTAATTAATAGTTACGGGATTGCTACCTACTGTCATCATATTTTACTCGCTGCGTAGCGGATTGTACCCAACGTGGTGAAATATTTAATACCCAGATCGCTATTTGGCTATGTCCGGGGTAACGCACAAAGAAGCCGCTATGCTAGTGTTGCAAGCTGGTGGGACACTCATCCTAGGATGACTTGATGTCCGATTAGCATGTGGAAAGCTTTACTTACTAACGTAGCTCCATGCTTCTTACGATAAAATGGTGGGTTCGGTGCAACGTATCTCCACTCAGGGAATTACATACTGAACACCTAAACGTTGAT
->11
-AGTCGCTTACCTAGGGGATAGAGACGGATTAAATCGCAGCAGAGTAGGCACTCACCCCGCTCGCCAGGGTCCGTCACTCCGACAGTGCCATACAAACTGAAAATCCGTATTTTCATTGGACATTCTTGGCGAGGAACACGACGCACATACGTTTGGGCTTGACAAGGACCTCGATAACATCGATGTGGATAACTTAATGAAATGAACAAATTTAAATGAGATCTTTACTCCTGACGTAAATGTCAGCTAATTATATCTCAGCGGAGTACATATTATCCACCTATTTCATTATTACATATTCCGTCTAACGCGCAACGAATAATACACCTTGTCAATCTCTTACGTTTACAGGACCGGTATATGAAAAGAGTACAAACTGCTGTTATGTTAAAGGTGCAGCTACGAGCTGATCTCCCGATATATGGTCCATTGTAGCGTGAAAGGGTAGCCGTAAGATAGATTTGTTTGAGAAAAAAGATACGTAATAACTAAAAAGGAAT
->5
-TCGCACGTACGTGAGGGCTGAGATCACGGAAAATCGTGCTAGGTCAGGTTCGTACCCCGCCGAGCGGTGATGTTCAACCCTATTATTACTTGGATTGCTAAACTGTTGCCGTTGTATGGACATGATCTCTGAGGGAAGAACTATATATGCGCTAAGGATAGTTAGAGACACCCAGGATCCGTATGTGAGCTACATTATATAATGAACAAGTTAAATTTCGTTTTCTACCAAAGCTAAGCAGTTCAGTCGATTACACGACATGTAACCGCATATAAGTATGGTATTGCTATGTTTGTAATTGCTTTCAACTGGTGGGAACCGAGGCAGGTACCAAGAACCGTGCATTAAGTGGGTACGTGCGTCTTTAATACCTCAACCTTTGCGTTATTCGGGATAATTGCAAATCCTTATCAGGTATAATAAGTGCGGATGTAGGATAAGAGGTTAATCGAAAGATAAACCCGGAATCGAGAAAAGATTGTTAATAATTAATCAGAAGC
->14
-TGTAACGTATCCGACAAGCAGAGTCAAATTTATTCACGGTATTACAATAAATCACCACGCCCGGTAGTGTCCGCCACTCCGCCAATGAGACGTACTGTCGAAAGCTATTGCTTTGATTCACGCTCTTTTTGAGGAATACGATATGTAGACATTAACGCTAGATAGGGACCTCGAGAACCTCTATGTGGAGAACTTCATACAACGAAAAAATTGATTTGTCCCCTTTAATAGAGATGTAAATTCCGGCTAATTACGCGTCAGGACAGTGTATCCCAGCAACCTCATCCCCCGATTTGGTTTGTTAACTATATGCGCGAACTAAGACACTGTCTTAATACCTTAAGCTAACGGGACTGGTTTACGAGAAAGGTGTAAACCGTGACTGTGGTGAGGATTGTTCTAAAAGCCGATCATTCGCGATATGGCTTGCTGTATGTTAACAGAGGAGTCGAAACATAAGGTTAAAATTAAAAAAAGATGCATAGCAATTAATAAGGAGC
->15
-TTTCACGGACCAAATAAGTAGAGATAGACTAGATCACGTCAGGGTGAGAATTCATTCTATCTGGCAGTGATCATCACTTGGACAATTACTGGTAGTATTCGAATCTGTACTCTCGATTGGCACTTACCTCGATAAATACTGCACATATACATTGCAGTTGGATAATGTCCTTTAGAGCCTCGACCTGGATCAATTATTAAGATGAAGTAACTCAATTTTGCCCCGTTCGAAGGATGTAAGTGTCATTTAATTGAACGTAATCATATTGCATTCCAATTCTCTCCCCTCGTATTTCAGTTTCTAGATAATTAACGGCGAGGAGGGCTCATCACCAATACCTTAGTTCTGCAGGGATGCTTTGCCTAAAGTACTTGACTCTTGACTCTGTAAGGAATGTTTTTAAAAGATGATCATTCGCAGTGGAAGCTAAGTCATGATCTTAGGTTAGCCGGGGTACAGGACCAAAATGTAAGAAAGACGCCTAAAACTTTATGAGGGGC
->9
-TTTCACGTACCAAATGAGTAGAGGTAGACTAGACCACGTCAGAGTGAGAATTCATTCTATCTTGCAGTGATCATCACTTGGACAATTGCTAGTAGTATTCGAATCTATACTCTCGATTGGGACTTACCTCGTGAAATACTGCACCTATACATTGCAGTTGGATAATGACCTATAGAGCCTCGACCTGGATCAATTATTAAGATGAAGTAGCTCAATTTTGCGCCGTGCGAGGGATCTAAGTTTCATTTAATTGAACGTAATCATATTGCATTCCAACTCTCTCCCCTCGTATTTCAGTTTCTAGTTGATTAACGGCGAGGAGGGCGCAGCACCAATACCTTAGTTCTGCAGGGATGCTTTGCCTAAAAGACTTGACTCTTGACTCTGTAAGGCATGTTTTTAAAAGATGATCATTCGCAGTGAGAGCTAATTCATGAACTGAGGTTAGCCGGAGTCCAGGACCGAAATGTAAGAAAGACGCCTAAAACTTTATGAGGGGC
->17
-ATTAGCCTATTGGAATAGTAGTGAATGGCTAGATTCCATGATATCTTTGAGTTGTTTTTCTGAAGAATTCTCGTCGTTGGTCTGGTTTCGCATAACTTTAGAGGCGGCAATCTCAACCTCTGTGTATGGAGGGAATTCTGCGACGCCAATGGTGAAGATTTTTTAAACGGTCAGTAACATTGACACACACGACCCAATAGAGACCGGGTCGTGGCCTGGTCATTTTCCACACCCTGCTGGATTTATGATATCAAAATTGATTTTCTGCTATGTCAGGCTCCCACATCGTATTTACGCATTATGAATAGCCCGAACGGCGGAAATCACTCGCTCAGCATCGGACGTATATGGCACTGAAGCATTAAATAAGTCCAAAGCGTTTCTTTCATAGAGGATCACCTACTAGTCATGCCTACAATACACTGGCCCCAATAATGTACCGGAACGCAGGTAAGATATATACGATTCAGAAACAACGTACCGAGAGCGCGAGCAAATGT
->18
-AGTATTCTTCTTGGGTAACATTGATCAGTTCAATTCCATGATATTTTTAAGTTTTTTTTCAGAAGAAGGTTGGTGGCTTGTCGACTTTGGCGCAATTTTAACAGCGGCGCCTCCTATTATTATGAATGCATAGAATTTTGGGACGCTTAGATTAAAGGCTTTTTAAACGATCAAATATATGAATGCACGCAACCCAACGGACAGCGGGTTAAGGCATGTTCTCGTTCTACATCCCGCTGAACTTCGGATAGCAAACTTGGTGTCGACGGATTTCAGGCGCCCGTGCAGTATTTACGCATTAAGTATAGCCCGAACGGCCGAAATCTATCGCTCACCACCAAACCTATATGGTGTGGAGGCATTCACTAAGTCTAAATCACATCCTTCGTTGAGGTGCACGTACTTGTTACGTCTGAAATACATTGGTCCTAATAATGTGCTTGAACGCTGGCAAGATGTGTTTGGTGTAAAAGAGAAGTAGAGAGAGTGCGAGGAAATGT
-
diff --git a/addons/ASTER/example/genetrees.tre_2.fas b/addons/ASTER/example/genetrees.tre_2.fas
deleted file mode 100644
index ce51184c943edf9e3c0b4aa6b525e1c323c39f42..0000000000000000000000000000000000000000
--- a/addons/ASTER/example/genetrees.tre_2.fas
+++ /dev/null
@@ -1,53 +0,0 @@
->13
-TGCGTATTGAAACTTAGATGCATAAACTGTTTATACGCGTGTAGACGATCGGGCGGGGTGAGGGATCGTGGTGATGGCTAACCGGCTGATACGTGGTACCCAGATAATATCGGAGGCAGCAATTTAAGATGATAGTAACTTTTGTTCTAACGCCAGAGTTGATCCTGAACATCCGGTCACGCTGCGAAGTGACCTTGAAATAGCACGAGCGAGAAAGGGAGCGGTCGGATACTGGGCTATGTCGCTTGAGTTTTATGATATTCGTTTGTGCTGCACGAAAGGTGGCTATGAGTTCCCTGAATCTTGATCGGCTGGTCTCGTATAGCATGGACAACGTCGTGTGCGATAAGTCTTTTCGTTTAAACAGATCGCGATGCTTTCTGGAATACTCCATCCTTGGTGGTGTCTTACGATTGAATTATAGAGGAAATCGACTTGAACTCCGCGGAACGGGACCACTCTCCCCTATAACTCAATTGATGGATTATGCACCCCATTCT
->17
-TACGGAATTGAACGTAGATGCACGCACCGGTTACACGGGTGTAGAGGATCGGGCGGGGTGAGTGATCCTGGTGATTGCCGAGCGACTGGTACTGGGTACCCAGATAGGGTCGGAGTGATCAATTTAAGATAATAGTGACTTTTGTTCTAGTGCCAAGGTTGATCCTGAACGTCTATTCACGCAGAGGAGTGACCTTGAAATAGCACGGGTTAGAAAAGCATCGGTCGGCTTATAGACTATGCCGCTTTTGTTTTATGACATTCGTTTGTGCTGGATAAAAGATGGCCATGAGGTCCTTGAAGCTTAATCGTCTGGGCTCGTATAACATGGACAACATTTTGAGCGATTACTATTTTCGTTTAAACAGACCGCAATATTTTTGGAAATGCTCCATCGTTGATGGTGTCTTACACTTGAAGCTTAAAGGAATACGGCTTAGACTCTGCGGAGAGGGACCAGTCCGCCCTATATCTCAACTTAGAGATAATGGACCCTACGCT
->8
-GACCAAGTTACGTGAGACTATGTGGGCCGTCAATCCTTACCTAGTCGGTGAGGGGACCAGACGCCGTGTTCAATAATTGAACGAGGTATTACATTGTGAGTAGATGATATTGTAATCGCCGCTATAAACTGGGAGCGACTTTTCCCCTATCACCAGAATTGGTATCGGGCTACTCTGCACGCTTTGAAGTAGCTGCAAAGCGTCACGGCCTAAATATGTAGGTATGGTGTACTCAAGCAGGGAACAGTGACTTTACAGTACTCTCATTTGCTTATTGCAAAAAGACATTGGACTCCCTGGTGGTCAACTCTTGGTGAACAGGAGCCGCGGGCAACTGTCAATACAATAGGTTCGTGTCGTTAATCTGACCACGACGTTCTTTGGAATTCTTCACGCCTTCCTTATTTTCGCAAGTTACCTGTCGTGTGAACTGAGGATGTCCCCTCAGGACCAAAGTGGCACCTCTAATAAGCCGAGAGAGATATGATATACCCTTTTCC
->16
-TTCTTGGTAGGTTCTGGGAGTCTGCACATTTTACGATCGAGTGGACGGTGCCGGTACCTAGTACCTCTTTCGTTGGACCGGGAAGCTACAGTAAAAAGCAAAGTTAGCAACGTATTCTTCATGTTCAATGAGTAGTTATTTCTTTGCTGATACCTGAGTTTAGTACGGTGTGGTCTCCAAGCTGAGATATGACTAGAAACCAGCGTAATGGAATGGGTGAGGTTCCGTGTACTTATGTATGAGAGGTTAGGTCGAGAAGTGTGGCCGGTGTTACGCTAAGGTAGGAGGTGAACTGCGCAGATTTCCCTTACAGTGCCACGAAGAAAGAGAAGAGATCATAATATTATTAACGCGTCCGTGCAATCGAACCATGAGACCTCTTCGAATTTCTCGTCCCGGGCATCTCTTAGAATTGGAAATGTCTGTGAAATCCACTTAGTCATCCTTGAAGAAAGGCGTCTCCACTAATAACGCCAGGGACGGACGATATTCCCCGTACC
->7
-TGCGTACTGAATTTTGGATACATATCCGGTTTGGTCTTGTGTTGACGGCCGGATGGTCTAATGCCTCGTGACATGGACTAACAATTCACAGCGTAGCGCGCAGGTATGACTGTAGGCGTCGTGTTGAACCAGAAGGGACTTCTTCTCTAGCACCAGAGTTGGCTATATGCGCGCCGTCATGCGTCCAGGTCACTAGGAAATAGGGCGGGTGGGAAAGTGAGGTGTCGGGGACGCAAGTATGAGACATGATCTCTACCATACTAGCTGGTGCTACGCGAGAGGAGGCAGTGGAGTGCTCAGAGATTGGTTTTCGGGCCACACAGGTCGCGGAGGACGTTTAATGTAATTAATTCGGCCCTGTAAACGAACCGTGAGATTTCGTGAAATTCTTCGCCCCGGCCGACTCTTCGCATTGTAACTGGTAGTGTAATTGACTGGGTCTGCACAGAATAAAGGCGTCACCTCTGATAACGCCAGGGACGGATTATTTGCCCTATTCC
->10
-TGCCAACTGAATTTTGGAAACATGTACGGTTTGGTCTTATGTTGTCGGTCGTAGGACCTAATGCCTCGTACCATGGACTAACAAGTCACAGCGTAGCGCGCAAGCAGAAGAGTAAGCATCGTGTTGAACCAGAAGGGACTTTCTCTCTGGCACCAAAGTTAGCTATGTACTTGCCTTCATACGTCGAGGTCACTAGGAAATAGAGCGGTTGAGAGAGTGGGATGTCGGGGACTCAAGTATGAGACGGGATCTCTATCATACTAGCTGGTGCTACGCGAAAGGAGGCTATGGTCTACTCAGAGTATTATTTTAAGGTCACACAAGTCGCGGATGACGTGTCATGTAATTGATCCGTTCGTATTACCGCCCCGTGAAATTTCATGGAATTCTTCGCTCCGGCCAACTCTTCGCATTGTAACCGGCAGCGAAATTGACTGGGTCTGCACAGAATGAAGGCGTCCCCTCGAATAACGCCAGGGACGTATCATGTTCCCGGTTCC
->6
-TGCCTACTGAATGTTGGATACATATACGGTGTATTCCGGTCTTGGTGGACGCAGGAACTGATGCTCCATGCCGTAGACTTGCAAAGCGCATTTAAGCGCGCAGAGAGGGGTGGAGGCGGCGTGTTGAACCGGAAGGGATTTCTTCTCTAGCAATAGAGTTGACCACGGGCGTACATTTATGCTTACAAAGCACGTGAGAATATTGCGGGTTAGAGAGTGAGCAGTTGGCCACTCAAGTAGAAGACGCGAGCCTTACTATACTAGCTGGTTCTGCGCGAAAGGAGGCGGTGGACTCCCAGGATTTTTATTCTAGGGCCACACGGGTCACCGTCAAAGTCTAATGGAATTGGATCGCCCATATAAATTAACCGTGAAATTGTAGGGAAGTCTCCGCCCCGTTCAACTCTACGCATTTTAACTCGCAGTGAAATTAAGTGGATCCCCACAGAATAATGGCGCCCTCTGCACTAACGCCGGAGAGCGATGATGTGCCCTGTTCC
->1
-TGTCTACTGAATTTTGAATACATGTACTGTGTATTCTTGTCTTGACGATCGTGGGACCTGATGCATCGTGTCATAGACTTACAAGTCACAACGTATCGCGCAGGGAGTGGTGGAGGCGTCATGTTGAACCGGAAGAGACTTCTTCGCTGGCACCAGGGTTTGCCTTGGGCGTCCCTTGATGCTTCCAAGTCACTTGGGAATAGTGTGGGCGAGGGATTGAGCTACTAGATACTCAAGTATGAAACATGAATTTTACTATACTAGACTGTGTTACCCGAAAGGAGGCGGCGGAGTCCCTGGAGTTTGATTGTAGGGCCACACAAATCTCGGACAACGTTTTAGTGAATTAATCCGTCCGTGTAAACAAATCGTGAGATTTTGTGGAATTCTTCGTCCCGGCCTACTCTTCGCAATTTAAATGTCAGAGAAATTGAGTGGGTCCCCACAAGATAAAGGCGTCCCCTCCAATAACGCCAGAGAGACATGATGTACCCTGTTTC
->18
-TTCTCACGTAATGTTTGATACATAAATTGTCCTGTCTTGTGCACTTAGAGGAGTGACATAATATATCTGGCTACATTCATAGTGCGTCCATGGTGGTAGCCGGGGAAAAGGGGATAATTCAATTAAGAGTGGGGATGATTTCTCTTATGACAACAGCATGTGCTTCGGGAGTGGTCTCGAGCTATGAAACAATACCAAAATAGCAATGGTGAGAGAAAGCTGGGTCGGATACGTGGACAAACTACAGTGGATACGCAATATTAGCCAATGCTACGCAAGTAGTAGCTGGTGATCCCCGAGGGCTTAGAGGTCGGGTCATGTAAATTGTAGACAACGCTTAATGTAATTAATCCGTCTGTTTGGATAAAAATTGGGACCATGTTGGATTCTTCAGGCTAGCCTGTACTCCGCTAGTAAACTGGTGGGCATAATGACTAGGTGCCAGCAGAATAGAGTGGTGCTGCCCAATGACGGTACTAAAAGATAATGCACCTCCTTGG
->3
-TTCCCACGTAATGTTTAATACATAAATTGGCCGGTTTTAGGTACTCAGTCGAATGACATTATATGTCAGGCGACAGTCATACTTCTTACATGGTGGTATGCGGGAAATAGGGGATATTTCAAATAAGGTTGGGAGTGGTTTGGCGTTTTACACCAACATTGTCTTTAACCGTCGTTTCGATCTACGAAACATTATCATAACAACGTGTCTAAGAGATAGGGCGCTCATATAGGCGGGTATACTACAGTGAAATTGCAATATGAGGTAGCACTACGCGAGGAGTAACAGTTGAGTCCCGTGGGCGTGGATGTAGGGCTACGTAAATTGTAGATAACGTTTAATGTTATTGGTCGGTGTGATTGAATAAACATTGGGATCATGTTGCATGCTTCGAACTAGGATCTACTCCGTAAGTATACAGTTAGAAATAATCATTAGGTGCCAACAGAATAGGGTGGTCTTCCCCAACGACGCTACTGAAAAACAATGTACCCTTTTTG
->4
-TTCTCACGTAATGTTTAATACATAAGTTAACCGGTCTTTGGTACTCAGTCGAATGACATTATATATCAAGCGGCAGTCATACTTCTTACATAGTGGTGGGCGGGAAATAGGGGATATTGCAACTAAAGTTGGAATTGGTTTGGCTTTTTACACCAGCATTGTCTTTAACCATCGTTTCGATCTACGAAACATTATCATAGCAACGTATTTAAGAGATAGGGCGATCGAAAACGCGGGTATACTACAGCAAAATCGCAATATGAGGCAGTACTATGCGAGGGGTAACTGTTGAGTCCCGCGCGCGTGTATGTAGGGCTACGTAAATCGTAGATGACGTTTAGTGTAATTAATCCGTCTGATTGTATAAACATTGGGATAATGTTAGATGCTTCGGACTAGCATTTGCTCCGTAAGTATACTGTTAGAAAGGATGACAAGGTGCCGGCAAAATAGAGTGGTCTTCGTCAACGACGCTACTGAAAGACAATGCACCCTTTTTG
->2
-TACATACCGAGCTTTGAATACCTGGACTGTTGATTCTTGTCTACAAGGGTGGGTGACATGATACACCGGGCTACAGACATACTCCCCACTTATTAGCAATCGGGTAGGAGCTGAAGCATTATCTAGGATCGTAGGAAACTTCTTTTCTGGCGCCATCGTTAGCCTTGGGCGTCCGGGAGCGTCACGAAATGATGTCACAACAGCATGGTTGAGAAACAGGGCGGATGGGTACTCAGTTGTGGGGCACGGAGTTTGCGATATTAGGTAGTGCTACACAAAAATAGACTGTTGGCTCCTAAAAGTTTTATGGTAGGACGCCATAAACTTTAGACAATGTTTAATGGAGTTAATCCGTCTGTTTAAGTGAAACTTTAGACTATGCTGAATGTCTGATGCTGCCTTGTACCCCGTAATCCCACTTTTGGAGACGTGGGGTATGATCCCATAGAATAGAGTTGTCCTTTCCAAGGAAGCCACTGATTAATGATGCACCCTTTTCC
->14
-TACCTACCGAATTTTAATTTCGTGGACTAGTCATGTTTGTCTATAGAGTGGGGGGACATGATACACCGGGCTTCAGACATAGTCCCCACTTACTAGCTTTCTGGAGAAAGTTGATGCATAACGTGGGATGTTAGGAAACTTCGTCGCTATCACCAGCGTTCGTCTCGTATGTCTCTTCGTACTACGATGGCATGTCACGAAAGGGTGGTTGAGAAATAGGGCGCGTGCGTACCCAGTGGTTGGATATGGGGATTACGGTACTAGCGAATGCTACACGAAAATAAGCTGTGCGGTTCCGATAGTTTTGTAGTAGGACGCCATAAATTTTGGATGACGTAGAATGCAATTAAGCCGTCTCTTTAAGCTAACCTTTAGACTATGCTGAATGTTTCATTCCGTCTTGTACCACGTAGTTCCTCTGTTGGAGAGATTGAGTACGATCCCACGGAATAGAATTGCCCCCTCCAGAGAGGCCACTCATTAATGTCGCCCCCTCCTCC
->5
-TACCTACCGATTTTTAATTTCATGTACTGTTTAGTCTCTTCCACAGGGTAGAGGGACATGATACACCGGTCTACTAACAAACTTTCCGCTTACTAGCATACTGAAGAAAGGCAATACATCATGTAGGATGTTAGAGTGCCTCGTCGGAGGCACCAGCGGTCTTCTTTAACCTCCCTTTATACTACGATGGAATTTCACAATGGTATTACCGAGTAATATGGCGCTTACGTACCCAATTGCCGGGTGATGTCATTGTAATACTAGCGAATGCGACAGGAACATAAGCAGGGGGGACCCAAGAGTCTTATAGTAGGACACCATATATTTTGGATGGCATTGAATTCAATTTCGTCTTCTCTTTAAGCACACCTCTAGACTATGCTGAATGCTTCATTCGGTCTTGTACGACGTAGTTCCACCGATGGGGAGATTGAGTACGATCCCACAGAATAGGACTGCCCTCACCAGAAAGGCCACTCTTTAATGTTGCCCCCCTTTGC
->11
-TACCTACCGGTTTTTAAAATCATGGACTGTTTAATCTTGGCTACAGGGTGGGGGGATATGATACACCGGGGTACAAACATACTCCCCACTTACTAGCATTCAGGAGAAAGTCGAGGCATAATTTAGGATGGTAGAGAACTTTGCCGTTTGCACCAAGGCTCGTTTCAGATATCCCTTCGTACTTCGATGGTATGTCACAAGAGGATGGTCGGGTAATAGGGCGCGTGCGTACCCAGTTGCCGGATGTGTGTATTACGATACTAGCGTATGCTACACATAAATAACCAGTGGGGTCCCAATAGTTTTACGGTAGGACTCCATGAATTTTGGATGACATTGAATGCAATTAGGCCGTCTCTTTAAGCAAACCTTTAGACTATGCTGAATGTTTCGTTCGGCCTTGTACCACGCAGTTCCACTGTCGGAGAGATTGAGTACGATCCCACAGAATAGGATTACCCTTTTCAGTGAGGCCACTCATTAATGTTGCCCTCCTTTCC
->15
-TGTCGAGCGAGTCGTAAATAGATCGACTGCTTGTTCTTGCCTACAGGTGCGCGGGACGTTAAGTATTGGGACACATACAGATCACTCCTTTACTAACAATTGGGGAATAACGGAAGCATCACCTGTTTTCATAAACGGGCTCGGTTCTCGAACCGGTGTGAGCCATGTTAGTCCCTCCGCACTACGTGTTGAGTTTGTAACGGCGCGTGTTAGAAATAGGACGGAACGGAACGGAGTGGGATAATGTACAAATTACAGTAGCATCCAGGGCTACATAAATATAAACTATTAGCGTTCAGAAGTTTTGGAGTAGGGCATCGTAAAATTGTATCAACCATTGAAGATTTTGGTCCGTCTGTGTAAATAGACCCGTAGGCGAGTTTGAATACCTCTTCCTTGCCCTTGCTCTGTATTGTTACGCTAGAACAGGTCGGGCACGATCCCACGGAATTAGGATGTTCTGTAGAAGAAGGCAGCTCGTCGATGATACGCCCATTTCT
->9
-TGTCTAGCGAGTCTTATTTGCATTGACTGCTTGTACGGGTCTACAAATTCGTAGTACATCGAGTATTGTGCCACAGGCAGAAGACCCACTTATTAAGAACCGGAGAATAATGGAAGCTTCGCCTGGATCTGGAAAAGAGGAGATTTCTCCAACTAGTGTTAGCCTCGTTCACGCCCTCTCTCTACGAAGAGATTTCATGTTAGCGCAATTTAGAAGTATGACGGGTCGGGACTGATTTTTATAAAAGACGACTTACATTACCGAGTGGGACTACATGAATATAGACTATATGCTTTCTTTAGTTTGAGAGTTTGTCGCCGTAAAATTTAGACAGCGGTTAACGAATTTAGTTCGGCGGTTGAAAGAGACCCTTAGACGATGTTGACTGCATGGGTCTGGCCCAGGCAGCGTAATCCTACCGATGAAGAGTTCGGGCACAATCCAACGGATTTAAGCTGTCCTGTTCAATATGGCGGTTGATCGATAACGCACCGGTTTCC
->12
-CACCTGCCGGATACTGCATACATCGTCTGGTTGGTCGCTTCCACACGATCGAGGGACACGAAACGGCGACCGACATACATACTCCCTACTTAGTGGTATGCGGGGAAGAGCATATATACCATCTATGACTATTAGGAACTTGTTTTGTTATATCATGGTTGTTCTTTTACATCCTTTCGCATTTCGAATTCACGGCTAAATAATGTGGGGAAGAAAAAGGGCCGTCGGGTAGTCAGTTTTGGGGCATGAAATTCGCAATATTAGCGAGTGCTACGCGGAATTGAACTGTGGACGCTCAGTAGCTCGAAAATATCGATTTACGATTCTGATATATCGTTTAGTGTAGGTAGTCTATCCCTATAAATAGATCATGAGACTATCCTTAAAGCCTCAGATAGTTCTTTACTCCGCGTTTCAACTATATGGATATTTTGGGAAGATCTCACGGAGTATAGTCGTCCTCCCACATTAGGCCCCAGACTGGGGGTGCACGTTTACGT
->20
-CTTCCACAACACTTTAGCTTCGGGGATTGTATCTTCCTGCTTAAACGGAATTTGAACAAGATACCCTGGGATGCCCAATGGCTTTCGTACAACTAGCGTTTAAGGAAGTGCGGAAATATCATTTATTTTCGGGAGCAATTTCAGGTTCGGAGAGTAATCTAGGAATCGAATTGTTGCGATGATAGGGAGTCACGTCACTATAATAAAGACGGTGAATAACGCAATCAGTTACGGAAGGGTGCGCCAAGAGGCTTAAGTCGGTACAGGGAGGGGGAGAAAAGAACATCTCTGAATCATTATGCTAATATTGTTGGCTTACATGAGATGTCTTTAATTGTCTAGATTTACAATTCTGCCCTTCGGATTGATATGGACACTTCGAAGAAATACGGACCCGTCTGGACCCTACGCAATTCGACTTTCGTCAAAGCAGAATGTGACTCAGCTAAAAAGAGCCTTCCTATACAATGATGCCAAAAAGCAGTGCTCCACGTCAAACA
->21
-CATCCACGTTACTGTAGCTTAGGGGGTTGTATCTTCCTGCTTAAACGAAATTTGAACAAGATGCCCTGCTATGCCCAATTCCTTGCGTACATGTAGCGTTTAATTAAAAGCGGAAATACCCTTTTTTTTCGGAAGCAATTTCAGGTCCAGAGAGCAGTCTAGGAATCGAATTGTTGCGTTAATAGGGGGTCACCCCACTATAATAAAGACGTTGTATAACGCAATCAGTTACGGAAGGGTGTGCCAAGAGGCTTGTTTCGGTACAGGGAGGGGGAGAACAGATCATCTCTGAATCTTTATGCTAATATGATTGGCTTACATGAGATTTCTGTAATTGTCTATATATACGATTCTGCCCTTCGAATTAATAAGGACACGCCGAACACAGATGAACCCGTTCGGGCCCTACACAATTCGGCGTTCCTCAAAGCAGAATGTGACTCAGCTGAAAAGACCCCTCCTATACGATGACGCCAAAGAGTAGTGCTCCACGTCAAACA
->19
-CGTTCACAACACTTTTGCGTCGGAGATTGTATCTGCCTGCTCAAACGGAATTGAAACAAGATATCCTGGTATGCCCAATTGCTTGCGTACAAGTAACGTCTAATGAAGGGCGGAAATCTCATTTTGTTTCTATAGCTATTTCAGGTTCGAAGAGGAATCTAGAAATCGAATTTTTACGATGATAGAGGGTCACATCACTATAATAAAGACGGTGAATAACGCGATCAGTTACGGAAGGGTGCGCAAAGAGGCTCATGTCGGTGTAGGGAAGGAGAGAACAGAACATCTCTGAATCTTTATGCTATTATGATTGACTTACATGAGATGTCTTTAAATGTCTAGATGTACAATTCTGCCTTTCGAATTAATCAAGACACTCTGAAGAAATATGTACCCGTCCGGACCCTATACTATTCGACTTTCCTCAAAACAGAATGCGACCCGGCTGAAAAGAGCCTTCCTACACAATGACGCCAGAAAGCAGTGCCCCGCGTCAAACA
->24
-CGCCCACATCGCTTCAGCCTCCCGGTCAAGGCGCTTTGATTAAAAGAGCAAGTGGAAGGGGGAGCCCGAACTGGTCGAGAGCCCGCGAGCAACCTGGGTTTAAGAAAAGGTAGTGTTATCGCTTCCCCGCGGAAGCAGGTTTACTCTCCGCGGACATTCTGCTAATCGGGTCACAACTAAGATGCTAAACCACGTCACTGGCGTTCTTATGAAGCACAATACGGCCAGCCTCACTGGATTATCCGCAAATGTACAAGTAAATTCCGTAAGTTTCTGGAATTATTACCCTCTGACAGTACGGCTGATTTAATTGGCTTGCACGAGATGTTATCAAGGTGCTAGAACTTCACTTGAACTTTTTGAATGACCGGGTGCACTGGAAGGAATTTCATACGCGACCGAAATCTAGTCCGGGCAAATTTCTTAAGAAATCGAAGTACGCCTGTAAAACAAATGGTAGGCATATACTATTAGTAGATGACGAAGATCCCGACTTAAAA
->22
-CGCCCACATCGCTTCAGCCTCCCGGTCAAAGCGCTTTGTTTAAAAGAGCAAGGGGACGGGGGAGCCCAAAGTGGTCGAGAACCTGCGAGCAACCTGGGTTTAAGGAAAGGTAGTGTTATCGCTTCCTCTCGGGAGCAGGTTTACTCTCCGCGGACATTCTACTAATCAGGTCGCAATTAAGATGCTAAACCACGTCACTGGCGTGCTTATGAAGCACAATAATGCCAGCCTCATTGGACTATCTGCAAATGTACAAGTAAAGTCCGGAAGTTTCTGAAATGATTACCCTCTGACAGTACCGCTGATTCAATTGGCTTGCACGAGATGATATCGAGGTGCTAGAACTTCACTTTGAGTTTTTGAATGACCGGGTGCATTGGGAGGAATTTCATGCGCGGCCGAAATTTAGTCCGGGCAAACTTCTTAAGAAAACGAAGTACGCCTGTAAAACAAATGGTACGCATATACTATTAATAGATCACGAAAATCTGGACCCAAAA
->23
-TACCAACAACAGTCTAGCCGCCGGGATTATACTTGCGTGCTCCAATGGTAAGAGGACGGGATGCCCCAGGTGACCCAAAAGCTGGTGAACAAGCAGGTTTTAATGGAGTGCAGAAATATCACGTTTCATCGGAAGCATTGTTAGGTTCGGACGGTTATCTAAAGATCGCCCTTCAGCTAGGGAACTAATCCACGTCACGAAGGCCAGATTATTTAATAGCGTGTTCGTGTTCACTTGTGCACGGGTAGGGTTTCGAGCAGATTCGGTTAGATGGAGAAGGGGACAACGCTAGTGCGTATGACCCGATTAAGGGGCTTACATGAGATATCGTCAATGGGCTGAATATATGATTCGGCCTTTTGGATGGTCCAGGACAGCTGGATAAGATACGTACCAGTCCGGGACCAACGCGATTCAATTTTCGCCAAGATACGACGTAGCCCAGCTTAATAGATTATCCTTGTGCAACGATGCTAAAACTCAAGGCGCCAGAGGAAACA
->25
-TGCTGACAATTGTCTAGCCGCCGAGAGTACACTATTGGGCGCAAATGGCAGGTGTACGACATTCCCCAGAGGGCCCGAAGGCTGATAAACAACCAGTGTTTAATGAAGGGCAGAAACATCACTTTTCACCAGTGGCTTCATTAGGGGCGTAAGGCAATTTAATGATCGATTTCCGGCGAGGTTACTGAGCCACGTCACGGAAACAAGAGTGTTTAATATCGCGGCCAGCACCACCGGTTTACTTGTAGGGCTCGGAGTGGATTCGGATGTATGAAGAAGAGGGCAACGCTAGCGCATATGCCCCTATTAAGAGACCTACACGAGACGTCGTCGATTTTTCTTATGTAGGGTTTCGCCTATTGTATGGTCGGGTATAGATAGAGGAGGTACCTACCCTTCCGGGATCAACTCCATTCAATTTCCGTCAAGGGACCATTTAGCCCAGCAGTATAAATTATCTGTTCGCAATGATGCTAAAGCTCAGGTATCTAAAATTAACA
->0
-GTTAACTGAGGCTATGGAGCAAAGGGCTATTTTTAAGCTTCACTTGATTCTCGTGAGTACCGAGGTCCAATTATCTTGACTTACGAAGGACGAAGTTTTTTACGAAAACTAAGGTATACCCTGAGACGGGGATTGAATACCTAGTTCTTTTGTTAGGGGAGAGAGCGCCTTACCCTTCGTGCAACACAACTTTCGCTTTGCTTGATAAACTTCACACATGAAGGCCAAGGAGAGGTTCCGATTACTCCAATCATAATTAGATAAGGTATCCAAGATTCCACTAGGCACGGACCATTCATTGTTGAGACTATGCCTTGCCGTCCCATAGTGGGGTTCAATGGAACTATGGGACCCGTTTTTTTCGTGTACGAGTGACGTTTGGGAACCCATTCATCATATTTTAGCGCAGATTAGTCGATGGCCGCCTTGGGGGTTAATATCCTGCTCAAAGTCATATAGTAGCACATCGATGTGAAAAACGACGGACTTGGTGCTATGTT
-
diff --git a/addons/ASTER/example/genetrees.tre_3.fas b/addons/ASTER/example/genetrees.tre_3.fas
deleted file mode 100644
index 50b96d97440160cd6740dcc7cb2e11c7c8d15d57..0000000000000000000000000000000000000000
--- a/addons/ASTER/example/genetrees.tre_3.fas
+++ /dev/null
@@ -1,53 +0,0 @@
->0
-TGTAGCACAACGTATTGCCTGCCGATCGTTTTGTGACTCTTTGGTGGTACGTGTCTTCTCTCTGTCCATCACCATCATCGCCTGCTCTCTTCTCCAACGAACCGCGTCAGCGAACGCTCTAATGCAATTTCGGGACTTTATATGCCTTTTAACCAGTTAGGTTTTCTAGCGGCCCCCCCCGCTATCTCCATTCCATAACTGCTCTAGAACGGATATCATTGGTCTGAAACGCGACACTCATTCTTGATTCCACCGTTCTTACGTAAGCTGTCACACGCCCCACCTTTGCATCGCGTCACACCTGCGAAGGAAATGGATATTAGTCGGAGGTCCCGTCTACCATCAGCTTAATGCTTACTTCTGTGCCAACCATCAGAGCAAGAACCACGACAAGTCTATCAAACTACCCTCCCTACACCCGTGTACTACTCTCATATTCGTGTTCTATTCCAAACATAATGATTAACTTTCCGGCCTTGAAATGTCACCGGCTAAGACGT
->19
-TATCATGTCACTTAGTAAGCGACCACGGTGCGGACATTGAATTTTGCAGATCGTCTCGTATGGCCTTATCAACGCTGTTATTTGAACAACACGACCGTAGGTAACTGTATAGCTTGAAGCTTTGCAATCTAGAAATATGAGTCACCGTTATACTACTAGAATTTACACTCCCCTATGCTTGCTAACTCACTTGTAGGACCGACGTACGGCAGTCTCTTCTCCGCGATCAGAGGACACATGAGACTCTGCTCTTTCGCATAGCGCCATCTCGAAATGAGACAGCCTCCTCCACACTCCCAATTCGTGACTGCACCGGTTCCAAGTAACGAGTTTACATCTGAAAGGGTCCATACTTGTCTGGGTACGATAGCCTATAAGGACCCAGCTCGCTACACGCTTTACAATTCCGTCTATGCTCTATGGCGCATGATCGTAATTCTCACCGTGCTCAGAAACACAGCGAGATCTCCTTGAATCCAGGAACCTACTTCACAAGACAT
->21
-TATCATGTAACGTAGTTAGTGCCCACGGTGCGGACATTGAATTTTGCAGATCGTCTCGTATAGTCTTATCAACGCTGTTATTTGAGCCACACGACCGTAGGTAACTGTATAGTTTGAACCTTTGCAATCTAGAAATATGAGTCCTCGTTTTACTAATTGAATTTACAATCGCCTATGCTGGCTTCTTCACTTGTAGGACCGACGTATGGCAGTCTCTCTTCCGCGATGAGAGGACACATGAGACTCTGCTCTTTCATCTAGCACCATCTCAGAATGGGACCGCCTCCTCTAGGCTCCCAATTCGCGACTGAACCAGTTCCAAGTGACGAGTTTACATCTAAAAGGGTCCATACTTGTCTGGGTACGATAGCCTATAAGGACCCAGCTCACTACACGCTTTACAATTCCGTCTATGCCCTATGGCGCATGATTGTAATTCTCACCGTGCTCAGAAACACAACGGGATCTCCTTGAATCTAGGAACCTACTTCACAAGACAT
->22
-TACCCGACAACCGAAATGGTAACCAACCTTCGGTTGCTCCAGCTTTCTAATTGCCACCAGTCGCTTACTCATTGCTACGATTTACGCCGACCATGAGTACATATTTATGTGACCTATGCCCCAGCAATCTAGTCAAATTAATGCCTACTAAATTATTTGTGTCCGCTATCATCCATGACTTCTTCACGTCACGTGTCTGCAGCGTAAGGAAGTCCCCCCTGGAATTAGGAGGGACTCTTCAGGCTGCGTCTGTTATCTTCAGGCTCATCTGACGTTATACGGACTACAACGGTCCAGGGGCTCGGGACCTTTGTTTTAACCGATCACTGTTGTGAATTTAACGGTCTCAATCCTTTTTAAGATACAAATGTCCATATAAAATCAGCGCCATACAAGCCCTCCACTTCCGTCTTTGCCCACCGATATATGCTTTGGACTTTCGCCACGCTCAAAAGTCCCCCTTGCTCTGTTTGGGTATATGATTTTTTTATCCACGTTGA
->23
-TATCCGACAACCGAAGTAGTAATCAACCTTCGCTTGCTCCAGCTTTTTAATTACCACCAGTCGCTTACTCGTTGCTACGATTTACGCCGACCACGAGTACGTATTTATGTTACCTATACCCCAGAAATCTAGTAAAATAAGTGCCTACTAAATTATTTGTGTCCGCTATCATCCATGACCTCTTCACGTCACGTATCTGCAGCGTAAGGAAGTCCCCCCTGGAATTAGGAGAGACTCTTCAGGCTGTGTCTGTTACCTTCAGGCTCAGCTGACGTTGTACGGACTCCAACGGTTACGGGGCTCGGGACGTTTGCTTTAACCGATCACTGTTGTGAATTTAAGGGTCTCCATCCTTTATAAGATACAAATGTCCATACAAAATCAGCGCCATACAAGCCCTCCACTTCCGTCTGTGTCCCCCGATATATGCTTTGGACTTTAGCCACGCTCAAAAGTCCCCCGTGCTCTGTTTGGGTATATAATTTTTTTATCCACGTTGA
->24
-TATCCCAAAACAAAACTGCTGATCGACGTACGCACGTTACATCATGTTAATCGTCCCCTATCGCTTCCTCAGTGCTATGATTCGCGACAACAGTCCGTACATAATCACATAGCTTAAACGTTAACAATCCAGCAGAATTGGTGCTTGTTGAATTATTTGTATCCGCTACCCTCCATGACTGCTACGCTTCATGCACCATTAACCCAAGGCATCCCCTCCCGCACCAGGGGAGGACTTTTGCGACATTGTCTGTCATCCTAAGGCAATTTCGGCGTGTTACAAAATCTTACGGTCTCGAGCTTTGGGACACCAACAGCACCAGCTCACGGGTATGAATTTATAAGTGTTCATCCTCTTCAAGATGTAAATAACTATAGTAATACAGCTCAATACATGCGCTGCAATTCCGTATACGCCCCCCGCTACACGATTGAAACTTTATCCCCGATCAAAACTCTCCTGTAATTTCTTTGGGCCAATGACTTTACTATACAAGCCCG
->25
-TGACCCCCAACCTGATTAGTGGCCTAAACTCGGACGTTGCATATCGCTGTTCGTCCCCTACCGATTTATCAGCGCTACGACCTGCATCGCGCGACCATAAGTACCTATATCGCTCACAATTTAGCAATCCCGCAACGTAGGTGATGGTTAAACTATTTGCATCTCCCACCGTCTATGGTTGCTTAAATTCATGTTTTCTCTACGTGCGGTCATCATCACTGCACTATGGGGGGACTCGTGAGACTCAGCCCGTTGTCCTAAGACTATGTCTGTGTCTCACAGAATCCTACAGCCTCGAAATTTGCGACGCTTAGAGTTTCAACTCAAGTGTATGGGTTTAGAACGACCCACCCTTTTCTAGATACAAACGAATGTAGAAATTTAGTCCAATTCACGATTTACGAATCCGGCTATGCCCCCTGGTACGCGATTGAGACTTTCGTCGTGTTCGAAAATATTTCGAAATGGCTTAACGTCTTGGACACCATTCCTTAAGATAC
->20
-TATCACATAACATAGTTAGTGACCAAAGTACGGACATTGGACTCTACTGATCCTCCCCTATCGCTTTCTCCACGCTATTACTCACGCCACACGACCGTGGGTAACTGTGTAGCTTGGACCTTTGCAATCTAGAAATATAAGTGATCATTTAACTCATTGAATCTACAACCGCCTATGCCTGCTCCCCTACATGTAGGATCGACGTACGACAGTCCCTCTTCCGCGATGAGGGGACTCATGAAACTATGCTCGTTATCCTAGGACCATTTCAGCATGTGCAAGCCCCGTACAGGCTGAAAAATCGCGACGCATCTAATTACAACTTACGAGTTTGGGTTTAGAAGAGCCCATTCTTTTCTAGATACGATAATCTATAAGAATCCAGCCCAATACACGCTTTACAATTCCGTCTATGACCCATGGTACATGATTGAGATTATCACAGTGCTCAAAAACGCAACGAAATCTCCTTGGATCTAGGAATTTACTCTACAAGCCAT
->2
-TCTCTCACCCTGCCCATCGTCGCCACCGACCTGGAGATGCACCGTGTCTAACATCTATTATAACTTGATTTTTATCACCGCCTGAGTCTCGAGACTCTAACTAGCCGCATGTATTAGTGTTCTGTGAACTACGGACATGCAAGACTGTTCGAACAGTCATCCTATCAATCAATCGGGCTCGTTTTCCCCCCATCAGGACCATTTTACATCAGTCTCTTCTACATGTCAGAAGAACAAACATGTCTGTACTCATCTTGCCCAGGACACTTTACATGTAAACGGGTCCTACCAGATAACGGAACTATGGACTGGGCTATATCCACTGGCGAGTTTGCATATCGATTGCCCTGTTTTTATCTCCAATTGCTAGTATATAAGGAACCACCTCAACCCTAACCTTCAACCTCCTTCCATACCTGATCATGAACCTTTAGCTTATTCCACGTCAGAATCGAACGAAGTTGTATACCATGGCCTACAAGACTCCGGATAGACGGCAC
->15
-AATCTCACACTGCGCCTCGTGTATCCCGACCCGAAAATGTATGCTATCGTAGATCTTTTTCAACTTGATGTGCCTCATCCCTTGAGTCCCGTGAATCTACTCTACCGCATATCGTGATGTTCTGAGAACTAGGAATGCGCCAGAGCGTTCATATAATCCTCCTTTCGATCAAACGGGCACGTTCGTCCCCTATCAGGACAATTTCACATCGAACTATTTCACAATTCAGAAGAAACGGTGCGTTTGTGCTATTCGTACTCGGACCACGCTACATGCAAACAGCTTTTAGCAAATAACAGCATTGTAGACTGTAACCTGCCCAATGGAGAGTTTGCGTTTCGGTTCCCCTGCTCTAATCTTTATTCGTTAGTATATAAAGAGTTGCCTTGACCCAAGTCTTCGGCACGAGCCGATACCTGCTCGTGCACCTTTAGTCCATTCCACGTCAACATAGACCCAAACTATTCACCCCGACGTATAAAACTCGTGACGGACAGCAT
->9
-CACCTCAGCAGGCACATTGTGGACCCCGATCTGAAAATATATCCAGCCGACGATCTTTTCTAACTTGACGTTGCATATCATTTGAGTCTCGTGACCCTACCTTGCCGCATACCTCAATGTTTCTTGAGCCATCGAAACGCCGGACTGTTCAAACACTCGTCCTTTCGGTCACACGGGAACGTTTTCCCCTTATCAAGACCATTTTGCGTCAGCCACTTTTACATGTCAGATGAGCAATCATGTCCATGCTAGGCCCGCAGGGATCGCGCTACATGTCTACAGCTCCTGCCCCATACCTGTACAGTGCACTGTACCATGTCCTATGGCGATTTTGCATGTAGAACCCTCTGCTTTTATCACTGTTCACCAGTACATAAGGAGTCACCTAGAACCAAAATTCAGCCCTGACTCCGCACCTGAGTGTGCATCTTCAGCGCGTTCTACGTCCGAATAAAATCAAACTGTGTACCCTAACGTACAAAGCTCCTGGTGGACAGCAA
->12
-CACCCCAACCGGCACAATGTGGACTCCGATCTGAAAATGTAGCCCGGCGGAGACCTTTTTTAACTTGACGTTACATATCATTTGAGTCTCGTGACTCCACCTTGCCGCATATCTTAATATTTCGCGAATCAGCGAACCCCCAGATTGTTCGAACATACATCCTCACAAGCACACAGGCGTGTTTTACCCGTATTAGGACCATTTAACATCAGCCCCTCTTACATGTCAGAAGAGCTACCGTGTCCATGCTCGGCCCACAAGGATCACGCTGCATGCCCACAGCTTCTACCCTATACCGGTACTGTACAGTGTACCATGGCCAATGGCGATTTTGCATTTAGAACCCTCTGCCCTCAGCACTGTTCGCAAGTATATAAAGAGTCACCTCAAACCAAACCTCAGCCCTGAGTACATACCTGATCGTGAACCTTAAGCGCATTCTACGTCCACATAGAACCATACTGTGTACCCTGACGTACAAAACTCCTAATGGACAGCAC
->5
-CAACTCACCCTGTAAGTAGTGGACCCCGACCTGAAATTGCATATTGCCGAAGATCTCTTGTAACTTGATTGACCCTATCACTTGAGTCTCGCTACTCTGACTTGTCCCCTACCTTAATGTTCTGAGAACTTCGAACATGCAAGACCCTTCGAACAGTCATGCTCACGATAAAAGGGGCTCGTTTAGCCCCTATCAGGACCACCTAACATCAGCCTCTTTCACGTGTCAAATGAGAAAACATGCCTGTGCTAATTATACCGGTAACACGCCACACGACAAAAGCTCCTACCAAATAACGGGACCGTAGACCGCACTACGTTCAATGGCGAGGTTGCATTTCGATCCCTCTGCTCTTAGCCCCATTTGCTAGTATCAAAGGAACCACCTCAACCCACACTCTAGACCCTTGGTTATACCTGAGGTTGCGCCTCTAGCTCATTCTACGTCAACATAGACCCAAACTGTATATCCTGGCGCAGGGAACTCCTTTTAGATGGCAT
->14
-CAAGTCAGCCTGTACGTCAGGGGCCCCGACCTGAAATTACCTATTCCCGCAGATCCTTTATAACTTGATTTATCTAATTACTCGAATCTCGTGACTCTAATTTGTCGCGTGTCTTAATGTCCTGTGAACTGTGGACTTGCAAGACCATTCACAGAGCCATGCTCACAAAAAAAAGGGCTAATCTCCTCCCTATTAGAACCACTTAACATCAGTCTTTTTCACATGTAAAATGAAAAAGCATGCTTGTGCTAACTTTACCCGGAACACGCCACATGTAAATAGCCTCTACCACATGACGGGCCTGTAGACTGCATTACTTTCAATGGCGAGGCTGCATTTTGGTCCATCTGCTCTTAACTCCATCCGCCAGCATCTAAAGAACCACCTTAGTCCGCACTTTAGATCTGTGTTTATACCTGATGGCGCATCTTTAGCCTATTATACCTCAGCATAGACCCGGACTGTATACCCTCACGCATGGAACTCCTGATGGACAGCAT
->11
-CAACTCACCCTGTACGTCGTGGACCCCGACCTGAAATTGCATATTGCCGAAGATCCTTTATAACTTGATTTTCCCTATCACTTGCGTCCTGTGACTCTAATTTGCCGTATGTCTTAATGTTCTGTGAACTACGGACATGCAAGACCATTCGCACAATCATGCTCACAATAAAAAGGGCTCATTTCCCCCCTATCAGGATCACTTAACATCAGACTCTTTCACATGTCAAATGAAAAAACATGCCTGTGCTAATTATACCCGGAACACGCCACATGTAAACAGCCTCTACCAAATGACGGGACTGTAGACTGCACTACGTTCAATGGCGGGGTTGCATTCCGATCCCTCTGCCCTTAACTCCATTTGCTAGCATCTAAAGAACTACCTCAACCCCCACTCTAGACTTGTATTTACACCTGATGGTGCACATTTAGCTCATTACACGTCAACATAGACCCAAATTGTATACCCCGCCGTACGAAACTCCTGATAGACAGCAT
->6
-AATCTCCTCATGCATCCCGTTGCCTCTATCAGGTAAACGCACTTCTCGAAACCTATGCTATCCTTCTATTTCCCCCATCCCTTGGACCTCGCGTCTCCAACTTACTAAAAAACCTAATGTTATATAGACGACGGACACGAGGGAACCTTAGACAAGTGATGCCCCAGATCGGACGGCGCCGGATTCTACCTTCTCGAACCAATTCGCATAATACACTTGTGAATGGCAGAAGAAAAAATATGTATAAACTCATCGTACTAGGACCCTGCTACATACAAACAGTGTCTCCCAGGTAACGGATCCGCGAATGGTCCTATATGTAATAGCAAATTTACATTTGGACCCGACTCATCTTTTCCCCATTAACTCTTATGTAAAGGATTACCGCAACACGCACGTTTGAACTTCGTCCAAACCCTATCGTACACCTTTAGCTTTATTCATGCCAGCTTAGCGACAATGTATGCTACTTGATGTACAATACTTCTTCCATACTGACT
->13
-AATCTCATCGTGCGTGCCGTGGTCTCTGTCAGGTAAACGTACTTTCCGAAACCTATCTTATTCTTCTATTTTCCTTATCACTTGGACCTCGCGTCTCCAACTTATCGAAAGAATTAGTGTTATATAGACGACGGACACGAGGGAACCTTAGACACGTGATCCCCTCAATCGGACGGCGCCGTATTCTACCTTCTCGAACCAATTCGCACAATTCACTTGTAAATGGCAGAAGAAAAAATATGTATGAACTCATCACACTAGGACCCTGCTACATACAGACAGGCTCTCCCAAGTAACGGATCCGAGAAAGGTCCTATATTTAATAGCGAATTTACATTTGGACCCGACTACTCTTTTCCCCATTAACTATTATGTAAAGAATTACCGCAACACGCACGTTAGAACTTCGTTCACACGCTATTGTGCACCTTTAGCTTTATCCACGCCAGCCTAACAGCAATGTATGCTACTTGATGTAAAATACTTCTTCCATACAGACT
->16
-AATCTCGTCGTGCGTGCCGCGGACTCTTTCGGGCAAACTTACTTTTCAACGACTAGCTTACACTACTATCTTTCTAGTAACTTGAACCTTGCGTTTCAAACTTATCGAAGGCCCTAATCCTATATTGGCGACGGGCACGCGGGAACCTTAGAAACGTGACCCCCTCAATCGGACTACGCAATAACACACCCTTTTGAGCCCATTCGTACAATTCCCTTGGAAATGACAGCAGGCAAGATATGCACGGACTTATCGCACTAGGACCCTGCTACCTACAAACAGGCTCTTCCAAGTAATGGAACCGAGACAGGTCCCACACTTAATAGCGGATTTACATTTAGCCCCGACTACTCTTTCATCAATGAAATACTAAGTAAAAAACCACCGCAACACAAACGTTAGACTTTCATTGATACCCTATATTGCAACTTGCGCTTTATCCGCGATAGCCTATCAACAATGATTGCTCCTTGGTGTAGAATATCCGTTCTATACAGGTT
->1
-AGTCCCATCGTGAATGCCGTGGTCTCTGTCAGGTAAACGTACTTTCCGAAACCTCTCTTATCCTTCTATTTTCCTTATCACTTGGACCTCGCGTCTTCAACTTATCGAAAGACTTAGTGTTATATAAACGACCGGCACGAGGGAACCTCAGACACGTGATCTCCTCAATCGGACAGCGCCTTATTCTACCTTCTCGAACCAATTCGCACAATTCTCTTTCAAATGGCAGAAGAAAAAATCTGTATGAACTCATCACACTAGGACCCTGCTACATACAGACAGGCTCTCCCCAGTAACGGATCCAAGAAAGGTCCTATATTTAAAAGCGAATTTACATTTGGACCCGACTACTCATTTCCCCATTAACTATTATGTAAAGAATTACCGCAACACGTACGTCAGAACTTCGTTCACACGCTATCGTGCACCTTTAGCTTTATCCACGCCAGCCTAGCAACAATGTCTGCTACTTGGTGTAAACTACTTCTTCCATGTAGCCT
->7
-AATCCCATCGTGCATGCCATGTTCTCTGTCAGATAAACATGCTTTCCGAAACCTCTCTTATACGTCTAATTTCCTTATCACTAGGACCTCACGTCTCCAGCTTATCGAAAATCTTAGTGTTATATAGACAACGGGCATGAGGGGAACTCAGACACGTAATCTCCTCAATCGGACAGCGCCGTATTCCACCTTCTCGAACCGATTCGTGCTATTCTCTTTCAAATGGCAGGAGAAAAAATATCAATGAACTCATCACACTGGGCCCCTGCTACGAAAAGACAGGCTCCTCCCAGTAGCAGATACGAGAAAGGTCGTATATTTAATAGCGAATTTACATTTGAAACCGACTACTCTTTTCCCCATTCAATATCTTGTAAAGAACTACTGCAACACGCACATTAGAACCTCGTTAACACGCTATTCTGCACCTTTAGCTCTCTCCACGCCAACCTAGCAGCAATGTATGATACTTTATGTAGAAAACTTCTTCCCTAGAGCAT
->17
-GATCTCATCACGCATGCCATGGTAATCGTCCGATAAACGTATTTTCCCAAAACTCTTCTATACTCCTATTTTCCTAACCTCTTGAACCTAGCGTCTGGCAGTTACCGTACTGATCAGTGTCACATAGTCGATGGCTCCGGAAGAATATTCAATAAGTCATACTCTCGTTCGGACAGCACCGTATCCTGACATCTAGGATCAGTTTGCACAATTATCCCTTAAATAGCAGAGGAAAAAAAATGTATGTTATCATCAAACTAGAATCATGCTACATACAGATAGATTCCCACAAGTAATTGGTCCGTAAAAATTCATATATGTAATAACGGTTTTAAATTTGGACCCAACTACTCTTTTACCCGTCAAAAACTGTATAAAGAATTATCTCGACGCGCGCGTTGGACCTTCGTTAATACACTATGGTATGCATCTGGCTTTATTCACAGCCGCATAGCAACACTGTGTGTTCTTTGATGTGCAATACTTCTTATGTACAGCCT
->10
-GGTCCCAACGTACATGCCGTGGTTATTATCCGATAAACGTCCTTTTCCAAATCTTTTTTATATTTCCACTTTCCTAACCGCTTGGGCCTATCGTCCGGAACTTACCACAGGGATTAGTGTTGTATAATAGACGGGCGCGAAAGAATATTCGACAAGTCATCCTCTCATTCAAACAAGGCCATATTCTACTTTCTAGGACAAACCTGCACCCTTCTTTCTTAAACGGCAGAAGAAAAAATATGTATGTGCTTATAAAACTAGGATCCCGCCACATATAGATAGATTCCCTCAAACGACCGATCAGTGAAAAATACTACATTTAAAAACATTTTTACATTTGGACCCGACTACTCATTTACCCATCAAAAACTATGTAAAGACTTACCTCAGCACGCACCCTGGACCTTCGTTGCTACGTTTTGGTGCACCTTTAGTTTTATGCGCAGCCGCATAGCAACAATGGGCGTTCCTTGATGTAAGATACTTCTTATATACAGCCC
->8
-GGTCCCAACGTACATGCCGTGGTTATTATCCGATAAACGTACTTTTCCAAATCTTTTTTATATTTCTACTTTCCTAACCGCTTGAGCCTATCGTCCGAAACTTACCACAGGGATTAGTGTTGTATAATAGACGGGCGCGAAAGAATATTCGACAAGTCATCCTCTCATTCAAACAAGGCCATATTCTACTTTCTAGGACAAACCTGCACCCTTCTTTCTTAAACGGCAGAAGAAAAAATATGTATGTGCTTATCAAACTAGGATCCCGCCACATATAGATAGATTCCCTCAAACGACCGATCAGTGAAAAATACTACATTTAAAAACGTTTTTACATTTGGACCCGACTACTCATTTACCCATCAAAAACTATGTAAAGACTTACCTCAGCACGCACCCTGGACCTTCGTTGCTACGTTTTGGTGCACCTTTAGTTTTATGCGCAGCCGCATAGCAACGATGGGCGTTCCTTGATGTAAGATACTTCTTATATACAGCCC
->4
-GGTCTCATCATACATGGCGGGGTTATCGTCGGACAAACGTGATTTCCTAAATCTTTTTTACTCTTCTATTTTCCTAACCGCTTGAACCCAGTGTCTCAAACTTACTGCAGGGATTAGTGTTGTACAATCGTCGACCGTGAAAGAATATTAGACAAGTCATCAATTCATTCAAACAAGGCCGTAATCTACCTTCTAGGATAAACTTGAACAATTCTCTCTTAAATGGCGGAAGCAAAAATGCGTATGTGCTTATCAAACTAGGATCACACTACATGTAGATAGGTCCCCCCAAACGACCGATCAGTGAATTATACTAATTTTAAAGGCGTTTTTCGATTTAGACCCGCCTATTCTTTTACCCATCAAAAACTATATGAAGAACTACCTCAACACGAACATTAGACCTTCGCTCATACGCTATGGAGCACCTTTAGCTTTATGCGGAGCCGCACAGCAACAACGGGCGTTCCTTGATGTAAATTGCTAGTTATATACAACCT
->3
-GGCCTCATCATACATCGCGTGATTATTGTCAGATCAATGTACTTTCCCAAATCTTTTTCATACTTCTATTTTCCTAACTGATTGATCCTAGCGTCACAAAATCAGCGCAGGAATCAGTATTATACAGTCGGCAACCACAAAAGAACATTCGATAAGTCATCGTTTCATTAGAACAAGGCCGTATTCTACATTCTGGGACCAACTTGCACCATCCTCACTTCAATGACAGAAGCAAAAATATATATGCGCTTATCAAACTAGGATTATGCCACATGAAGATAGATTATCCCAAGCGACGAATCGGTGTAAGATACTACATTTAAATATACTTCTCCATTTGAACCCGACTGGTCTTGTACCCATCAAAAACTATATAAAGAATTACTCAACCATACACATTGGACCTTCACCCATACGCTATTGTGCACCTTTAGTTTTATGCGCCGCCGAATAGCAACAGCGGGCGTTCCTTCATGTAAAATACTTCTCATATACGGACT
->18
-AGTCTCATTACACATGCCGTAATTATCGTACGATAAACGTCATGTTCCAAATATTTTTTATACTTCTATTTTCTTGGCTACTTGGGCTTAGCGTTTGAAACTTACCGCAGGGATTAGGGTTGTATAATTAACGGGCGCGAAAAAACCTTCGACTAGTCATCCTCTCATCCAAACAAGGCTGTATTCTACCTTCTAGGACCGACTTGCACCCTTCTCTGTTAGATGGCGGAAGAAAAAATACCTGTGTGCTTATCAAACTAGGATCACGATACCTATAAATAGATTCCCCCAAGCGGCTGATACGTGAAAAATGATACATTTAAAGTTATTTGTACATTTAAACCCGACTAGTCTTTTACCCATCAAGAAATGTATAAATAATCACCCCAACACGCATATTGGAATTTCGTTCAAACGCTATGGTGTACCTTGAGCTTTTTGCGCAGCCCCATAGCCACAATGGGCGTTCCTCGATGTAAAATACCTATTATATACCGCCT
-
diff --git a/addons/ASTER/example/list.txt b/addons/ASTER/example/list.txt
deleted file mode 100644
index 3007720f4968a95a145839756655b434c53b0d5d..0000000000000000000000000000000000000000
--- a/addons/ASTER/example/list.txt
+++ /dev/null
@@ -1,3 +0,0 @@
-example/genetrees.tre_1.fas
-example/genetrees.tre_2.fas
-example/genetrees.tre_3.fas
\ No newline at end of file
diff --git a/addons/ASTER/example/multitree.nw b/addons/ASTER/example/multitree.nw
deleted file mode 100644
index 899625f2fc08369ca5eb6beb0280b6c635c2bab1..0000000000000000000000000000000000000000
--- a/addons/ASTER/example/multitree.nw
+++ /dev/null
@@ -1,1000 +0,0 @@
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-((((((11:0.61081205,12:0.32815495):0.02873497,((((10:0.07589218,6:0.06837113):0.09422972,((16:0.65632630,((6:0.06703572,(10:0.00070468,6:0.00703374):0.00908314):0.03865458,((7:0.16490303,17:0.09147289):0.00691033,8:0.09665562):0.00116994):0.00600799):0.02451162,8:0.30672790):0.01147785):0.05102136,16:0.46108646):0.02353537,3:0.50721301):0.03071263):0.54478299,((9:0.38584926,((2:0.06772710,5:0.21553725):0.12847300,((((15:0.07620313,9:0.05160035):0.31056835,(9:0.06928593,15:0.12002451):0.16349135):0.01789802,12:0.25210615):0.12265841,(((5:0.09161199,14:0.07036207):0.43062678,11:0.09912184):0.00355434,2:0.11819604):0.03562150):0.07537273):0.07225011):0.92902898,(((18:0.23450031,4:0.34227178):0.02850064,1:0.06208902):0.27942084,((((9:0.00939541,15:0.03101346):0.36816803,((((10:0.13397140,(8:0.01407219,6:0.07417150):0.16616413):0.02451506,13:0.07932794):0.11688469,(((9:0.04568325,15:0.05856230):0.40738760,(4:0.25435939,3:0.19432766):0.05314555):0.00703054,(16:0.45873152,1:0.11859954):0.06087862):0.00201555):0.00040914,18:0.44805414):0.01783875):0.00441883,(12:0.48073586,(7:0.06858112,(17:0.04216738,7:0.13051692):0.04771373):0.24370766):0.05114647):0.08932944,(((15:0.37628638,12:0.36092853):0.50649323,(14:0.07618299,7:0.08179246):0.03024943):0.02053092,(13:0.07774940,17:0.21627376):0.11221281):0.05608179):0.32405384):0.02068553):0.01468513):0.32678536,(((15:0.46861131,(14:0.22164606,11:0.16222155):0.04616454):0.29836846,((3:0.02094260,4:0.04679906):0.11623967,(18:0.44134635,(10:0.07458047,8:0.02339095):0.09866151):0.00829540):0.42066590):0.28348356,((((7:0.19287898,6:0.19801760):0.20850922,((13:0.02314166,(17:0.29802942,16:0.45725312):0.00663847):0.04658395,(8:0.01855633,(10:0.00387207,6:0.01673088):0.01706257):0.23545111):0.12031864):0.08843786,((5:0.09051517,2:0.06507341):0.10334442,1:0.12002947):0.06206233):0.01297211,(12:0.24865372,9:0.85060337):0.35145852):0.39365007):0.42673353):0.71279853,25:1.94363666):0.36554561,((16:0.41676119,(((15:0.56727497,((4:0.43309001,(17:0.31700378,13:0.05648581):0.08487135):0.01776861,(7:0.30484185,(8:0.22868875,(6:0.26138364,10:0.14383693):0.04624562):0.00413529):0.07365102):0.05821735):0.31350968,(2:0.32683949,(18:0.23557178,1:0.04999848):0.08913627):0.14232173):0.30988468,(((5:0.19449278,(11:0.02125861,14:0.13561472):0.05680573):0.11666806,((9:0.26786787,(15:0.17117527,(9:0.01448669,15:0.10610565):0.09588359):0.13934067):0.03493035,12:0.42326782):0.11284094):0.30529067,3:0.37796768):0.23352236):0.16745649):1.61637464,((22:0.16420731,(24:0.03303459,23:0.12306428):0.40517858):1.01088206,(((19:0.07088487,(21:0.07388371,20:0.03049461):0.00001835):0.01066533,((20:0.01737337,20:0.01507492):0.00376377,(21:0.16160772,19:0.04629955):0.00945802):0.00501672):2.10245471,((20:0.02881119,(21:0.12775396,19:0.32461812):0.00439168):0.04307877,((21:0.10617400,19:0.21653749):0.00917583,20:0.02255926):0.04345654):0.73890995):0.12027919):0.22398366):0.08412737);
-((((22:0.01479387,((24:0.01455986,23:0.01474465):0.00273229,24:0.00509023):0.00435270):0.11538197,(19:0.03767640,(21:0.01186957,20:0.00515513):0.00080732):0.00584570):0.02118494,((22:0.02541679,(23:0.02405374,24:0.01239076):0.00039043):0.07858212,(25:0.04581031,(23:0.01624310,22:0.00847199):0.01967256):0.01597356):0.05741829):0.06949745,((((12:0.05506207,(5:0.00815944,2:0.00697181):0.01264153):0.01116474,((18:0.01912032,4:0.00654110):0.02200890,12:0.06043255):0.00046781):0.01706609,(((13:0.00241719,13:0.00293085):0.02033806,3:0.02971483):0.00214020,((14:0.03477921,11:0.02439174):0.02495898,((1:0.00019039,1:0.00014506):0.00437237,16:0.11440284):0.01671084):0.00110561):0.02319864):0.02601635,((15:0.04620437,9:0.02614218):0.09536492,((10:0.08505510,((8:0.02068731,7:0.02487416):0.01394634,13:0.00331854):0.01218349):0.01272547,6:0.09933879):0.02037231):0.00368877):0.35375737);
diff --git a/addons/ASTER/feast.cpp b/addons/ASTER/feast.cpp
deleted file mode 100644
index eb46de03a3bd5d38881261a27da1f0d586115b9b..0000000000000000000000000000000000000000
--- a/addons/ASTER/feast.cpp
+++ /dev/null
@@ -1,207 +0,0 @@
-#include<iostream>
-#include<fstream>
-#include<unordered_map>
-#include<cstdio>
-#include<cstdlib>
-#include<cstring>
-
-//#define LARGE_DATA
-#ifdef LARGE_DATA
-typedef long double score_t;
-typedef long long count_t;
-#else
-typedef double score_t;
-typedef int count_t;
-#endif
-
-#include "sequence.hpp"
-#include "algorithms.hpp"
-
-using namespace std;
-
-TripartitionInitializer tripInit;
-
-int npos = 0;
-vector<string> names;
-unordered_map<string, int> name2id;
-
-string formatName(const string name){
- string res;
- for (char c: name){
- if (c != '>' && c != ' ' && c != '\t') res += c;
- }
- return res;
-}
-
-void readFile(istream &fin){
- int cnt[4] = {}, id = -1, oldNpos = npos;
- string line;
- while (getline(fin, line)){
- if (line[0] == '>') {
- if (id != -1 && npos < tripInit.seq[id].size()) npos = tripInit.seq[id].size();
- id = name2id[formatName(line)];
- }
- else{
- for (char c: line){
- if (c == 'A' || c == 'a') { tripInit.seq[id].push_back(0); cnt[0]++; }
- if (c == 'C' || c == 'c') { tripInit.seq[id].push_back(1); cnt[1]++; }
- if (c == 'G' || c == 'g') { tripInit.seq[id].push_back(2); cnt[2]++; }
- if (c == 'T' || c == 't') { tripInit.seq[id].push_back(3); cnt[3]++; }
- if (c == 'X' || c == 'x' || c == 'N' || c == 'n' || c == '-') { tripInit.seq[id].push_back(-1); }
- }
- }
- if (npos < tripInit.seq[id].size()) npos = tripInit.seq[id].size();
- }
- for (id = 0; id < tripInit.seq.size(); id++){
- while (tripInit.seq[id].size() < npos) tripInit.seq[id].push_back(-1);
- }
- score_t cntsum = cnt[0] + cnt[1] + cnt[2] + cnt[3];
- while (tripInit.pi.size() < npos) tripInit.pi.push_back({cnt[0] / cntsum, cnt[1] / cntsum, cnt[2] / cntsum, cnt[3] / cntsum});
- for (int p = oldNpos; p < npos; p++){
- int pcnt[4] = {};
- for (id = 0; id < tripInit.seq.size(); id++){
- if (tripInit.seq[id][p] != -1) pcnt[tripInit.seq[id][p]]++;
- }
- tripInit.weight.push_back(pcnt[0] + pcnt[1] + pcnt[2] + pcnt[3] - max({pcnt[0], pcnt[1], pcnt[2], pcnt[3]}) > 1);
- }
-}
-
-void readPhilip(istream &fin){
- string line;
- int nTaxa, L;
- while (fin >> nTaxa){
- int cnt[4] = {}, oldNpos = npos;
- fin >> L;
- for (int i = 0; i < nTaxa; i++){
- fin >> line;
- int id = name2id[line];
- getline(fin, line);
- for (char c: line){
- if (c == 'A' || c == 'a') { tripInit.seq[id].push_back(0); cnt[0]++; }
- if (c == 'C' || c == 'c') { tripInit.seq[id].push_back(1); cnt[1]++; }
- if (c == 'G' || c == 'g') { tripInit.seq[id].push_back(2); cnt[2]++; }
- if (c == 'T' || c == 't') { tripInit.seq[id].push_back(3); cnt[3]++; }
- if (c == 'X' || c == 'x' || c == 'N' || c == 'n' || c == '-') { tripInit.seq[id].push_back(-1); }
- }
- if (npos < tripInit.seq[id].size()) npos = tripInit.seq[id].size();
- }
- for (int id = 0; id < tripInit.seq.size(); id++){
- while (tripInit.seq[id].size() < npos) tripInit.seq[id].push_back(-1);
- }
- score_t cntsum = cnt[0] + cnt[1] + cnt[2] + cnt[3];
- while (tripInit.pi.size() < npos) tripInit.pi.push_back({cnt[0] / cntsum, cnt[1] / cntsum, cnt[2] / cntsum, cnt[3] / cntsum});
- for (int p = oldNpos; p < npos; p++){
- int pcnt[4] = {};
- for (int id = 0; id < tripInit.seq.size(); id++){
- if (tripInit.seq[id][p] != -1) pcnt[tripInit.seq[id][p]]++;
- }
- tripInit.weight.push_back(pcnt[0] + pcnt[1] + pcnt[2] + pcnt[3] - max({pcnt[0], pcnt[1], pcnt[2], pcnt[3]}) > 1);
- }
- }
-}
-
-string helpText = R"V0G0N(feast [-o oFilePath -r nRound -s nSample -p probability -t nThread -y] inputList
--o path to output file (default: stdout)
--r number of total rounds of placements (default: 5)
--s number of total rounds of subsampling (default: 0)
--p subsampling probability of keeping each taxon (default: 0.5)
--t number of threads (default: 1)
--y take one input in PHYLIP format instead of a list of inputs in FASTA format
-inputList: the path to a file containing a list of paths to input aligned gene files, one file per line
-Gene files must be in FASTA format. The header line should be ">Species_Name".
-)V0G0N";
-
-int main(int argc, char** argv){
- vector<string> files;
-
- int nThreads = 1, nRounds = 4, nSample = 0;
- bool phylip = false;
- double p = 0.5;
- string outputFile;
- ofstream fileOut;
- if (argc == 1) {cerr << helpText; return 0;}
- for (int i = 1; i < argc; i += 2){
- if (strcmp(argv[i], "-y") == 0) {phylip = true; i--; continue;}
-
- if (strcmp(argv[i], "-o") == 0) outputFile = argv[i + 1];
- if (strcmp(argv[i], "-r") == 0) sscanf(argv[i + 1], "%d", &nRounds);
- if (strcmp(argv[i], "-s") == 0) sscanf(argv[i + 1], "%d", &nSample);
- if (strcmp(argv[i], "-p") == 0) sscanf(argv[i + 1], "%lf", &p);
- if (strcmp(argv[i], "-t") == 0) sscanf(argv[i + 1], "%d", &nThreads);
- if (strcmp(argv[i], "-h") == 0) {cerr << helpText; return 0;}
- }
- ostream &fout = (outputFile == "") ? cout : fileOut;
- if (outputFile != "") fileOut.open(outputFile);
-
- if (nRounds < nThreads){
- tripInit.nThreads = nThreads / nRounds;
- nThreads = nRounds;
- }
-
- if (phylip) {
- {
- ifstream fin(argv[argc - 1]);
- int n, L;
- string line;
- while (fin >> n){
- fin >> L;
- for (int i = 0; i < n; i++){
- string s;
- fin >> s;
- getline(fin, line);
- if(name2id.count(s) == 0) {
- name2id[s] = names.size();
- names.push_back(s);
- tripInit.seq.push_back({});
- }
- }
- }
- }
- {
- ifstream fin(argv[argc - 1]);
- readPhilip(fin);
- }
- }
- else {
- ifstream listIn(argv[argc - 1]);
- for (string file; getline(listIn, file);){
- files.push_back(file);
- }
-
- for (string file: files){
- ifstream fin(file);
- string line;
- while (getline(fin, line)){
- if (line[0] != '>') continue;
- string s = formatName(line);
- if(name2id.count(s) == 0) {
- name2id[s] = names.size();
- names.push_back(s);
- tripInit.seq.push_back({});
- }
- }
- }
- for (string file: files){
- ifstream fin(file);
- readFile(fin);
- }
- }
-
- tripInit.npos = npos;
- cerr << "#Species: " << names.size() << endl;
- cerr << "#Bases: " << npos << endl;
- cerr << "#Rounds: " << nRounds << endl;
- cerr << "#Samples: " << nSample << endl;
- cerr << "#Threads: " << nThreads << "x" << tripInit.nThreads << endl;
- cerr << "p = " << p << endl;
-
- ConstrainedOptimizationAlgorithm alg(names.size(), tripInit, names);
- auto res = alg.run(nRounds, nThreads);
- cerr << "Score: " << (double) res.first << endl;
- cerr << res.second << endl;
-
- res = alg.run(nSample, nThreads, p);
- cerr << "Score: " << (double) res.first << endl;
- fout << res.second << endl;
- return 0;
-}
diff --git a/addons/ASTER/feast.exe b/addons/ASTER/feast.exe
deleted file mode 100644
index db041d1181227550cbeb5a0efc13af2e652eff7a..0000000000000000000000000000000000000000
Binary files a/addons/ASTER/feast.exe and /dev/null differ
diff --git a/addons/ASTER/genetree.hpp b/addons/ASTER/genetree.hpp
deleted file mode 100644
index 3d896867d96bcfea8e310d8dd42d09a1d0fe6b46..0000000000000000000000000000000000000000
--- a/addons/ASTER/genetree.hpp
+++ /dev/null
@@ -1,1024 +0,0 @@
-#include<vector>
-#include<array>
-#include<thread>
-
-using namespace std;
-
-struct TripartitionInitializer{
- struct Node{
- int up = -1, down = -1; // -1 for dummy!
- int maxChild = -1, max2Child = -1, downMost = -1;
- int maxHeight = 0, max2Height = 0, path = 0;
- };
-
- int nTaxa;
- vector<vector<int> > roots;
- vector<vector<vector<pair<int, int> > > > parentChild;
-};
-
-struct Tripartition{
- struct Partition{
- struct Node{
- score_t X = 0, Y = 0, Z = 0,
- sX = 0, sY = 0, sZ = 0, sXY = 0, sYZ = 0, sXZ = 0, sX2 = 0, sY2 = 0, sZ2 = 0,
- sX2Y = 0, sX2Z = 0, sY2X = 0, sY2Z = 0, sZ2X = 0, sZ2Y = 0, sX2YZ = 0, sY2XZ = 0, sZ2XY = 0,
- sTx = 0, sTxX = 0, sTy = 0, sTyY = 0, sTz = 0, sTzZ = 0, sQ = 0,
- Tx = 0, Txuy = 0, Txuz = 0,
- Ty = 0, Tyux = 0, Tyuz = 0,
- Tz = 0, Tzux = 0, Tzuy = 0,
- Q = 0, Qux = 0, Quy = 0, Quz = 0, Quxy = 0, Quxz = 0, Quyz = 0, Qux2 = 0, Quy2 = 0, Quz2 = 0; //QuQ === 1
- int up = -1, down = -1; // -1 for dummy!
-
- void testAdd(Node &v){
- const score_t vX2 = v.X*(v.X-1)/2, vY2 = v.Y*(v.Y-1)/2, vZ2 = v.Z*(v.Z-1)/2;
-
- Node &u = *this;
- u.sX += v.X;
- u.sY += v.Y;
- u.sZ += v.Z;
- u.sXY += v.X * v.Y;
- u.sXZ += v.X * v.Z;
- u.sYZ += v.Y * v.Z;
- u.sX2 += vX2;
- u.sY2 += vY2;
- u.sZ2 += vZ2;
- u.sX2Y += vX2 * v.Y;
- u.sX2Z += vX2 * v.Z;
- u.sY2X += vY2 * v.X;
- u.sY2Z += vY2 * v.Z;
- u.sZ2X += vZ2 * v.X;
- u.sZ2Y += vZ2 * v.Y;
- u.sX2YZ += vX2 * v.Y * v.Z;
- u.sY2XZ += vY2 * v.X * v.Z;
- u.sZ2XY += vZ2 * v.X * v.Y;
- u.sTx += v.Tx;
- u.sTxX += v.Tx * v.X;
- u.sTy += v.Ty;
- u.sTyY += v.Ty * v.Y;
- u.sTz += v.Tz;
- u.sTzZ += v.Tz * v.Z;
- u.sQ += v.Q;
- }
-
- void testRmv(Node &v){
- const score_t vX2 = v.X*(v.X-1)/2, vY2 = v.Y*(v.Y-1)/2, vZ2 = v.Z*(v.Z-1)/2;
-
- Node &u = *this;
- u.sX -= v.X;
- u.sY -= v.Y;
- u.sZ -= v.Z;
- u.sXY -= v.X * v.Y;
- u.sXZ -= v.X * v.Z;
- u.sYZ -= v.Y * v.Z;
- u.sX2 -= vX2;
- u.sY2 -= vY2;
- u.sZ2 -= vZ2;
- u.sX2Y -= vX2 * v.Y;
- u.sX2Z -= vX2 * v.Z;
- u.sY2X -= vY2 * v.X;
- u.sY2Z -= vY2 * v.Z;
- u.sZ2X -= vZ2 * v.X;
- u.sZ2Y -= vZ2 * v.Y;
- u.sX2YZ -= vX2 * v.Y * v.Z;
- u.sY2XZ -= vY2 * v.X * v.Z;
- u.sZ2XY -= vZ2 * v.X * v.Y;
- u.sTx -= v.Tx;
- u.sTxX -= v.Tx * v.X;
- u.sTy -= v.Ty;
- u.sTyY -= v.Ty * v.Y;
- u.sTz -= v.Tz;
- u.sTzZ -= v.Tz * v.Z;
- u.sQ -= v.Q;
- }
-
- void testAddSpecial(Node &w){
- Node &u = *this;
- score_t usX_c2 = u.sX*(u.sX-1)/2, usY_c2 = u.sY*(u.sY-1)/2, usZ_c2 = u.sZ*(u.sZ-1)/2;
-
- u.X += w.X;
- u.Y += w.Y;
- u.Z += w.Z;
- u.Q += w.Q + w.Qux*u.sX + w.Quy*u.sY + w.Quz*u.sZ + w.Quxy*u.sX*u.sY + w.Quxz*u.sX*u.sZ + w.Quyz*u.sY*u.sZ + w.Qux2*usX_c2 + w.Quy2*usY_c2 + w.Quz2*usZ_c2
- + 2*w.X*(u.sTx + u.sY*u.sZ2 + u.sY2*u.sZ - u.sZ2Y - u.sY2Z) + 2*w.Y*(u.sTy + u.sX*u.sZ2 + u.sX2*u.sZ - u.sZ2X - u.sX2Z) + 2*w.Z*(u.sTz + u.sX*u.sY2 + u.sX2*u.sY - u.sX2Y - u.sY2X);
- u.Qux += 2*w.Y*u.sZ2 + 2*w.Z*u.sY2 + w.Qux + w.Qux2*u.sX + w.Quxy*u.sY + w.Quxz*u.sZ;
- u.Quy += 2*w.X*u.sZ2 + 2*w.Z*u.sX2 + w.Quy + w.Quxy*u.sX + w.Quy2*u.sY + w.Quyz*u.sZ;
- u.Quz += 2*w.X*u.sY2 + 2*w.Y*u.sX2 + w.Quz + w.Quxz*u.sX + w.Quyz*u.sY + w.Quz2*u.sZ;
- u.Quxy += w.Quxy;
- u.Quxz += w.Quxz;
- u.Quyz += w.Quyz;
- u.Qux2 += 2*w.Y*u.sZ + 2*w.Z*u.sY + w.Qux2;
- u.Quy2 += 2*w.X*u.sZ + 2*w.Z*u.sX + w.Quy2;
- u.Quz2 += 2*w.X*u.sY + 2*w.Y*u.sX + w.Quz2;
- u.Tx += w.Tx + w.Txuy*u.sY + w.Z*usY_c2 + w.Txuz*u.sZ + w.Y*usZ_c2;
- u.Txuy += w.Txuy + w.Z*u.sY;
- u.Txuz += w.Txuz + w.Y*u.sZ;
- u.Ty += w.Ty + w.Tyux*u.sX + w.Z*usX_c2 + w.Tyuz*u.sZ + w.X*usZ_c2;
- u.Tyux += w.Tyux + w.Z*u.sX;
- u.Tyuz += w.Tyuz + w.X*u.sZ;
- u.Tz += w.Tz + w.Tzux*u.sX + w.Y*usX_c2 + w.Tzuy*u.sY + w.X*usY_c2;
- u.Tzux += w.Tzux + w.Y*u.sX;
- u.Tzuy += w.Tzuy + w.X*u.sY;
-
- }
-
- void testRmvSpecial(Node &w){
- Node &u = *this;
- score_t usX_c2 = u.sX*(u.sX-1)/2, usY_c2 = u.sY*(u.sY-1)/2, usZ_c2 = u.sZ*(u.sZ-1)/2;
-
- u.X -= w.X;
- u.Y -= w.Y;
- u.Z -= w.Z;
- u.Q -= w.Q + w.Qux*u.sX + w.Quy*u.sY + w.Quz*u.sZ + w.Quxy*u.sX*u.sY + w.Quxz*u.sX*u.sZ + w.Quyz*u.sY*u.sZ + w.Qux2*usX_c2 + w.Quy2*usY_c2 + w.Quz2*usZ_c2
- + 2*w.X*(u.sTx + u.sY*u.sZ2 + u.sY2*u.sZ - u.sZ2Y - u.sY2Z) + 2*w.Y*(u.sTy + u.sX*u.sZ2 + u.sX2*u.sZ - u.sZ2X - u.sX2Z) + 2*w.Z*(u.sTz + u.sX*u.sY2 + u.sX2*u.sY - u.sX2Y - u.sY2X);
- u.Qux -= 2*w.Y*u.sZ2 + 2*w.Z*u.sY2 + w.Qux + w.Qux2*u.sX + w.Quxy*u.sY + w.Quxz*u.sZ;
- u.Quy -= 2*w.X*u.sZ2 + 2*w.Z*u.sX2 + w.Quy + w.Quxy*u.sX + w.Quy2*u.sY + w.Quyz*u.sZ;
- u.Quz -= 2*w.X*u.sY2 + 2*w.Y*u.sX2 + w.Quz + w.Quxz*u.sX + w.Quyz*u.sY + w.Quz2*u.sZ;
- u.Quxy -= w.Quxy;
- u.Quxz -= w.Quxz;
- u.Quyz -= w.Quyz;
- u.Qux2 -= 2*w.Y*u.sZ + 2*w.Z*u.sY + w.Qux2;
- u.Quy2 -= 2*w.X*u.sZ + 2*w.Z*u.sX + w.Quy2;
- u.Quz2 -= 2*w.X*u.sY + 2*w.Y*u.sX + w.Quz2;
- u.Tx -= w.Tx + w.Txuy*u.sY + w.Z*usY_c2 + w.Txuz*u.sZ + w.Y*usZ_c2;
- u.Txuy -= w.Txuy + w.Z*u.sY;
- u.Txuz -= w.Txuz + w.Y*u.sZ;
- u.Ty -= w.Ty + w.Tyux*u.sX + w.Z*usX_c2 + w.Tyuz*u.sZ + w.X*usZ_c2;
- u.Tyux -= w.Tyux + w.Z*u.sX;
- u.Tyuz -= w.Tyuz + w.X*u.sZ;
- u.Tz -= w.Tz + w.Tzux*u.sX + w.Y*usX_c2 + w.Tzuy*u.sY + w.X*usY_c2;
- u.Tzux -= w.Tzux + w.Y*u.sX;
- u.Tzuy -= w.Tzuy + w.X*u.sY;
- }
-
- void testCalc(Node &w){
- Node &u = *this;
- /*
- 3*sx2yz + 3*sy2xz + 3*sz2xy - 2*sx*sy2z - 2*sx2z*sy - sx2*syz - sxz*sy2 - 2*sx*sz2y - 2*sx2y*sz - sxy*sz2 - 2*sy*sz2x - 2*sy2x*sz + 2*sx*sy*sz2 + 2*sx*sy2*sz + 2*sx2*sy*sz
- + 2*sy*sz2*ux + 2*sy2*sz*ux - 2*sy2z*ux - 2*sz2y*ux
- + 2*sy*sz*ux2 - syz*ux2
- + 2*sx*sz2*uy + 2*sx2*sz*uy - 2*sx2z*uy - 2*sz2x*uy
- + 2*sx*sz*uy2 - sxz*uy2
- + 2*sx*sy2*uz + 2*sx2*sy*uz - 2*sx2y*uz - 2*sy2x*uz
- + 2*sx*sy*uz2 - sxy*uz2
- + sx2*uy*uz + sy2*ux*uz + sz2*ux*uy
- tx = sy*sz2 + sy2*sz - sz2y - sy2z + sy2*uz + sz2*uy + sy*uz2 + sz*uy2 + stx + utx
- ty = sx*sz2 + sx2*sz - sz2x - sx2z + sx2*uz + sz2*ux + sx*uz2 + sz*ux2 + sty + uty
- tz = sx*sy2 + sx2*sy - sy2x - sx2y + sx2*uy + sy2*ux + sx*uy2 + sy*ux2 + stz + utz
- Tx = tx + w.Tx
- Ty = ty + w.Ty
- Tz = tz + w.Tz
-
- ux -> sx + ux
- ux2 -> sx_c2 + sx * ux + ux2
- uxy -> sx * sy + sx * uy + sy * ux + uxy
- utx -> sy*sz2 + sy2*sz - sz2y - sy2z + sy2*uz + sz2*uy + sy*uz2 + sz*uy2 + stx + utx
- */
- score_t usX_c2 = u.sX*(u.sX-1)/2, usY_c2 = u.sY*(u.sY-1)/2, usZ_c2 = u.sZ*(u.sZ-1)/2;
-
- u.X = u.sX + w.X;
- u.Y = u.sY + w.Y;
- u.Z = u.sZ + w.Z;
- u.Q = u.sQ + w.Q + w.Qux*u.sX + w.Quy*u.sY + w.Quz*u.sZ + w.Quxy*u.sX*u.sY + w.Quxz*u.sX*u.sZ + w.Quyz*u.sY*u.sZ + w.Qux2*usX_c2 + w.Quy2*usY_c2 + w.Quz2*usZ_c2
- + 2*w.X*(u.sTx + u.sY*u.sZ2 + u.sY2*u.sZ - u.sZ2Y - u.sY2Z) + 2*w.Y*(u.sTy + u.sX*u.sZ2 + u.sX2*u.sZ - u.sZ2X - u.sX2Z) + 2*w.Z*(u.sTz + u.sX*u.sY2 + u.sX2*u.sY - u.sX2Y - u.sY2X)
- + 3*u.sX2YZ + 3*u.sY2XZ + 3*u.sZ2XY - 2*u.sX*u.sY2Z - 2*u.sX2Z*u.sY - u.sX2*u.sYZ - u.sXZ*u.sY2 - 2*u.sX*u.sZ2Y - 2*u.sX2Y*u.sZ - u.sXY*u.sZ2 - 2*u.sY*u.sZ2X
- - 2*u.sY2X*u.sZ + 2*u.sX*u.sY*u.sZ2 + 2*u.sX*u.sY2*u.sZ + 2*u.sX2*u.sY*u.sZ
- + 2*u.sTx*u.sX - 2*u.sTxX + 2*u.sTy*u.sY - 2*u.sTyY + 2*u.sTz*u.sZ - 2*u.sTzZ;
- u.Qux = 2*w.Y*u.sZ2 + 2*w.Z*u.sY2 + w.Qux + w.Qux2*u.sX + w.Quxy*u.sY + w.Quxz*u.sZ + 2*u.sY*u.sZ2 + 2*u.sY2*u.sZ - 2*u.sY2Z - 2*u.sZ2Y + 2*u.sTx;
- u.Quy = 2*w.X*u.sZ2 + 2*w.Z*u.sX2 + w.Quy + w.Quxy*u.sX + w.Quy2*u.sY + w.Quyz*u.sZ + 2*u.sX*u.sZ2 + 2*u.sX2*u.sZ - 2*u.sX2Z - 2*u.sZ2X + 2*u.sTy;
- u.Quz = 2*w.X*u.sY2 + 2*w.Y*u.sX2 + w.Quz + w.Quxz*u.sX + w.Quyz*u.sY + w.Quz2*u.sZ + 2*u.sX*u.sY2 + 2*u.sX2*u.sY - 2*u.sX2Y - 2*u.sY2X + 2*u.sTz;
- u.Quxy = w.Quxy + u.sZ2;
- u.Quxz = w.Quxz + u.sY2;
- u.Quyz = w.Quyz + u.sX2;
- u.Qux2 = 2*w.Y*u.sZ + 2*w.Z*u.sY + w.Qux2 + 2*u.sY*u.sZ - u.sYZ;
- u.Quy2 = 2*w.X*u.sZ + 2*w.Z*u.sX + w.Quy2 + 2*u.sX*u.sZ - u.sXZ;
- u.Quz2 = 2*w.X*u.sY + 2*w.Y*u.sX + w.Quz2 + 2*u.sX*u.sY - u.sXY;
- u.Tx = w.Tx + w.Txuy*u.sY + w.Z*usY_c2 + w.Txuz*u.sZ + w.Y*usZ_c2 + u.sTx + u.sY*u.sZ2 + u.sY2*u.sZ - u.sZ2Y - u.sY2Z;
- u.Txuy = w.Txuy + w.Z*u.sY + u.sZ2;
- u.Txuz = w.Txuz + w.Y*u.sZ + u.sY2;
- u.Ty = w.Ty + w.Tyux*u.sX + w.Z*usX_c2 + w.Tyuz*u.sZ + w.X*usZ_c2 + u.sTy + u.sX*u.sZ2 + u.sX2*u.sZ - u.sZ2X - u.sX2Z;
- u.Tyux = w.Tyux + w.Z*u.sX + u.sZ2;
- u.Tyuz = w.Tyuz + w.X*u.sZ + u.sX2;
- u.Tz = w.Tz + w.Tzux*u.sX + w.Y*usX_c2 + w.Tzuy*u.sY + w.X*usY_c2 + u.sTz + u.sX*u.sY2 + u.sX2*u.sY - u.sX2Y - u.sY2X;
- u.Tzux = w.Tzux + w.Y*u.sX + u.sY2;
- u.Tzuy = w.Tzuy + w.X*u.sY + u.sX2;
- }
-
- bool verify(Node &w){
- Node v = *this;
- testCalc(w);
- return memcmp(this, &v, sizeof(Node));
- }
- };
-
- void Xnormal(Node& u, Node& v, Node& o, Node& w){
- const score_t vX=v.X-o.X, vX2=(v.X*(v.X-1)-o.X*(o.X-1))/2, vY=v.Y, vY2=v.Y*(v.Y-1)/2, vZ=v.Z, vZ2=v.Z*(v.Z-1)/2, vQ=v.Q-o.Q, vTx=v.Tx, vTy=v.Ty-o.Ty, vTz=v.Tz-o.Tz;
-
- const score_t dusX_c2=((u.sX+vX)*(u.sX+vX-1)-u.sX*(u.sX-1))/2;
- u.X += vX;
- u.Q += vQ + w.Qux*vX + w.Quxy*vX*u.sY + w.Quxz*vX*u.sZ + w.Qux2*dusX_c2
- + 2*w.Y*(vTy + vX*u.sZ2 + vX2*u.sZ - vZ2*vX - vX2*vZ) + 2*w.Z*(vTz + vX*u.sY2 + vX2*u.sY - vX2*vY - vY2*vX)
- + 3*vX2*vY*vZ + 3*vY2*vX*vZ + 3*vZ2*vX*vY - 2*vX*u.sY2Z - 2*vX2*vZ*u.sY - vX2*u.sYZ - vX*vZ*u.sY2 - 2*vX*u.sZ2Y - 2*vX2*vY*u.sZ - vX*vY*u.sZ2 - 2*u.sY*vZ2*vX
- - 2*vY2*vX*u.sZ + 2*vX*u.sY*u.sZ2 + 2*vX*u.sY2*u.sZ + 2*vX2*u.sY*u.sZ
- + 2*u.sTx*vX - 2*vTx*vX + 2*vTy*u.sY - 2*vTy*vY + 2*vTz*u.sZ - 2*vTz*vZ;
- u.Qux += w.Qux2*vX;
- u.Quy += 2*w.Z*vX2 + w.Quxy*vX + 2*vX*u.sZ2 + 2*vX2*u.sZ - 2*vX2*vZ - 2*vZ2*vX + 2*vTy;
- u.Quz += 2*w.Y*vX2 + w.Quxz*vX + 2*vX*u.sY2 + 2*vX2*u.sY - 2*vX2*vY - 2*vY2*vX + 2*vTz;
- u.Quyz += vX2;
- u.Quy2 += 2*w.Z*vX + 2*vX*u.sZ - vX*vZ;
- u.Quz2 += 2*w.Y*vX + 2*vX*u.sY - vX*vY;
- u.Ty += w.Tyux*vX + w.Z*dusX_c2 + vTy + vX*u.sZ2 + vX2*u.sZ - vZ2*vX - vX2*vZ;
- u.Tyux += w.Z*vX;
- u.Tyuz += vX2;
- u.Tz += w.Tzux*vX + w.Y*dusX_c2 + vTz + vX*u.sY2 + vX2*u.sY - vX2*vY - vY2*vX;
- u.Tzux += w.Y*vX;
- u.Tzuy += vX2;
-
- u.sX += vX;
- u.sXY += vX * vY;
- u.sXZ += vX * vZ;
- u.sX2 += vX2;
- u.sX2Y += vX2 * vY;
- u.sX2Z += vX2 * vZ;
- u.sY2X += vY2 * vX;
- u.sZ2X += vZ2 * vX;
- u.sX2YZ += vX2 * vY * vZ;
- u.sY2XZ += vY2 * vX * vZ;
- u.sZ2XY += vZ2 * vX * vY;
- u.sTxX += vTx * vX;
- u.sTy += vTy;
- u.sTyY += vTy * vY;
- u.sTz += vTz;
- u.sTzZ += vTz * vZ;
- u.sQ += vQ;
- }
-
- void Ynormal(Node& u, Node& v, Node& o, Node& w){
- const score_t vX=v.X, vX2=v.X*(v.X-1)/2, vY=v.Y-o.Y, vY2=(v.Y*(v.Y-1)-o.Y*(o.Y-1))/2, vZ=v.Z, vZ2=v.Z*(v.Z-1)/2, vQ=v.Q-o.Q, vTx=v.Tx-o.Tx, vTy=v.Ty, vTz=v.Tz-o.Tz;
-
- const score_t dusY_c2=((u.sY+vY)*(u.sY+vY-1)-u.sY*(u.sY-1))/2;
- u.Y += vY;
- u.Q += vQ + w.Quy*vY + w.Quxy*u.sX*vY + w.Quyz*vY*u.sZ + w.Quy2*dusY_c2
- + 2*w.X*(vTx + vY*u.sZ2 + vY2*u.sZ - vZ2*vY - vY2*vZ) + 2*w.Z*(vTz + u.sX*vY2 + u.sX2*vY - vX2*vY - vY2*vX)
- + 3*vX2*vY*vZ + 3*vY2*vX*vZ + 3*vZ2*vX*vY - 2*u.sX*vY2*vZ - 2*u.sX2Z*vY - u.sX2*vY*vZ - u.sXZ*vY2 - 2*u.sX*vZ2*vY - 2*vX2*vY*u.sZ - vX*vY*u.sZ2 - 2*vY*u.sZ2X
- - 2*vY2*vX*u.sZ + 2*u.sX*vY*u.sZ2 + 2*u.sX*vY2*u.sZ + 2*u.sX2*vY*u.sZ
- + 2*vTx*u.sX - 2*vTx*vX + 2*u.sTy*vY - 2*vTy*vY + 2*vTz*u.sZ - 2*vTz*vZ;
- u.Qux += 2*w.Z*vY2 + w.Quxy*vY + 2*vY*u.sZ2 + 2*vY2*u.sZ - 2*vY2*vZ - 2*vZ2*vY + 2*vTx;
- u.Quy += w.Quy2*vY;
- u.Quz += 2*w.X*vY2 + w.Quyz*vY + 2*u.sX*vY2 + 2*u.sX2*vY - 2*vX2*vY - 2*vY2*vX + 2*vTz;
- u.Quxz += vY2;
- u.Qux2 += 2*w.Z*vY + 2*vY*u.sZ - vY*vZ;
- u.Quz2 += 2*w.X*vY + 2*u.sX*vY - vX*vY;
- u.Tx += w.Txuy*vY + w.Z*dusY_c2 + vTx + vY*u.sZ2 + vY2*u.sZ - vZ2*vY - vY2*vZ;
- u.Txuy += w.Z*vY;
- u.Txuz += vY2;
- u.Tz += w.Tzuy*vY + w.X*dusY_c2 + vTz + u.sX*vY2 + u.sX2*vY - vX2*vY - vY2*vX;
- u.Tzux += vY2;
- u.Tzuy += w.X*vY;
-
- u.sY += vY;
- u.sXY += vX * vY;
- u.sYZ += vY * vZ;
- u.sY2 += vY2;
- u.sX2Y += vX2 * vY;
- u.sY2X += vY2 * vX;
- u.sY2Z += vY2 * vZ;
- u.sZ2Y += vZ2 * vY;
- u.sX2YZ += vX2 * vY * vZ;
- u.sY2XZ += vY2 * vX * vZ;
- u.sZ2XY += vZ2 * vX * vY;
- u.sTx += vTx;
- u.sTxX += vTx * vX;
- u.sTyY += vTy * vY;
- u.sTz += vTz;
- u.sTzZ += vTz * vZ;
- u.sQ += vQ;
- }
-
- void Znormal(Node& u, Node& v, Node& o, Node& w){
- const score_t vX=v.X, vX2=v.X*(v.X-1)/2, vY=v.Y, vY2=v.Y*(v.Y-1)/2, vZ=v.Z-o.Z, vZ2=(v.Z*(v.Z-1)-o.Z*(o.Z-1))/2, vQ=v.Q-o.Q, vTx=v.Tx-o.Tx, vTy=v.Ty-o.Ty, vTz=v.Tz;
-
- const score_t dusZ_c2=((u.sZ+vZ)*(u.sZ+vZ-1)-u.sZ*(u.sZ-1))/2;
- u.Z += vZ;
- u.Q += vQ + w.Quz*vZ + w.Quxz*u.sX*vZ + w.Quyz*u.sY*vZ + w.Quz2*dusZ_c2
- + 2*w.X*(vTx + u.sY*vZ2 + u.sY2*vZ - vZ2*vY - vY2*vZ) + 2*w.Y*(vTy + u.sX*vZ2 + u.sX2*vZ - vZ2*vX - vX2*vZ)
- + 3*vX2*vY*vZ + 3*vY2*vX*vZ + 3*vZ2*vX*vY - 2*u.sX*vY2*vZ - 2*vX2*vZ*u.sY - u.sX2*vY*vZ - vX*vZ*u.sY2 - 2*u.sX*vZ2*vY - 2*u.sX2Y*vZ - u.sXY*vZ2 - 2*u.sY*vZ2*vX
- - 2*u.sY2X*vZ + 2*u.sX*u.sY*vZ2 + 2*u.sX*u.sY2*vZ + 2*u.sX2*u.sY*vZ
- + 2*vTx*u.sX - 2*vTx*vX + 2*vTy*u.sY - 2*vTy*vY + 2*u.sTz*vZ - 2*vTz*vZ;
- u.Qux += 2*w.Y*vZ2 + w.Quxz*vZ + 2*u.sY*vZ2 + 2*u.sY2*vZ - 2*vY2*vZ - 2*vZ2*vY + 2*vTx;
- u.Quy += 2*w.X*vZ2 + w.Quyz*vZ + 2*u.sX*vZ2 + 2*u.sX2*vZ - 2*vX2*vZ - 2*vZ2*vX + 2*vTy;
- u.Quz += w.Quz2*vZ;
- u.Quxy += vZ2;
- u.Qux2 += 2*w.Y*vZ + 2*u.sY*vZ - vY*vZ;
- u.Quy2 += 2*w.X*vZ + 2*u.sX*vZ - vX*vZ;
- u.Tx += w.Txuz*vZ + w.Y*dusZ_c2 + vTx + u.sY*vZ2 + u.sY2*vZ - vZ2*vY - vY2*vZ;
- u.Txuy += vZ2;
- u.Txuz += w.Y*vZ;
- u.Ty += w.Tyuz*vZ + w.X*dusZ_c2 + vTy + u.sX*vZ2 + u.sX2*vZ - vZ2*vX - vX2*vZ;
- u.Tyux += vZ2;
- u.Tyuz += w.X*vZ;
-
- u.sZ += vZ;
- u.sXZ += vX * vZ;
- u.sYZ += vY * vZ;
- u.sZ2 += vZ2;
- u.sX2Z += vX2 * vZ;
- u.sY2Z += vY2 * vZ;
- u.sZ2X += vZ2 * vX;
- u.sZ2Y += vZ2 * vY;
- u.sX2YZ += vX2 * vY * vZ;
- u.sY2XZ += vY2 * vX * vZ;
- u.sZ2XY += vZ2 * vX * vY;
- u.sTx += vTx;
- u.sTxX += vTx * vX;
- u.sTy += vTy;
- u.sTyY += vTy * vY;
- u.sTzZ += vTz * vZ;
- u.sQ += vQ;
- }
-
- void Xspecial(Node& u, Node& w, Node& o){
- const score_t usY_c2 = u.sY*(u.sY-1)/2, usZ_c2 = u.sZ*(u.sZ-1)/2;
- const score_t wQ=w.Q-o.Q, wQux=w.Qux-o.Qux, wQuy=w.Quy-o.Quy, wQuz=w.Quz-o.Quz;
- const score_t wX=w.X-o.X, wQuy2=w.Quy2-o.Quy2, wQuz2=w.Quz2-o.Quz2, wQuyz=w.Quyz-o.Quyz;
- const score_t wTy=w.Ty-o.Ty, wTz=w.Tz-o.Tz, wTyux=w.Tyux-o.Tyux, wTyuz=w.Tyuz-o.Tyuz, wTzux=w.Tzux-o.Tzux, wTzuy=w.Tzuy-o.Tzuy;
-
- u.X += wX;
- u.Q += wQ + wQux*u.sX + wQuy*u.sY + wQuz*u.sZ + wQuyz*u.sY*u.sZ + wQuy2*usY_c2 + wQuz2*usZ_c2
- + 2*wX*(u.sTx + u.sY*u.sZ2 + u.sY2*u.sZ - u.sZ2Y - u.sY2Z);
- u.Qux += wQux;
- u.Quy += 2*wX*u.sZ2 + wQuy + wQuy2*u.sY + wQuyz*u.sZ;
- u.Quz += 2*wX*u.sY2 + wQuz + wQuyz*u.sY + wQuz2*u.sZ;
- u.Quyz += wQuyz;
- u.Quy2 += 2*wX*u.sZ + wQuy2;
- u.Quz2 += 2*wX*u.sY + wQuz2;
- u.Ty += wTy + wTyux*u.sX + wTyuz*u.sZ + wX*usZ_c2;
- u.Tyux += wTyux;
- u.Tyuz += wTyuz + wX*u.sZ;
- u.Tz += wTz + wTzux*u.sX + wTzuy*u.sY + wX*usY_c2;
- u.Tzux += wTzux;
- u.Tzuy += wTzuy + wX*u.sY;
- }
-
- void Yspecial(Node& u, Node& w, Node& o){
- const score_t usX_c2 = u.sX*(u.sX-1)/2, usZ_c2 = u.sZ*(u.sZ-1)/2;
- const score_t wQ=w.Q-o.Q, wQux=w.Qux-o.Qux, wQuy=w.Quy-o.Quy, wQuz=w.Quz-o.Quz;
- const score_t wY=w.Y-o.Y, wQux2=w.Qux2-o.Qux2, wQuz2=w.Quz2-o.Quz2, wQuxz=w.Quxz-o.Quxz;
- const score_t wTx=w.Tx-o.Tx, wTz=w.Tz-o.Tz, wTxuy=w.Txuy-o.Txuy, wTxuz=w.Txuz-o.Txuz, wTzux=w.Tzux-o.Tzux, wTzuy=w.Tzuy-o.Tzuy;
-
- u.Y += wY;
- u.Q += wQ + wQux*u.sX + wQuy*u.sY + wQuz*u.sZ + wQuxz*u.sX*u.sZ + wQux2*usX_c2 + wQuz2*usZ_c2
- + 2*wY*(u.sTy + u.sX*u.sZ2 + u.sX2*u.sZ - u.sZ2X - u.sX2Z);
- u.Qux += 2*wY*u.sZ2 + wQux + wQux2*u.sX + wQuxz*u.sZ;
- u.Quy += wQuy;
- u.Quz += 2*wY*u.sX2 + wQuz + wQuxz*u.sX + wQuz2*u.sZ;
- u.Quxz += wQuxz;
- u.Qux2 += 2*wY*u.sZ + wQux2;
- u.Quz2 += 2*wY*u.sX + wQuz2;
- u.Tx += wTx + wTxuy*u.sY + wTxuz*u.sZ + wY*usZ_c2;
- u.Txuy += wTxuy;
- u.Txuz += wTxuz + wY*u.sZ;
- u.Tz += wTz + wTzux*u.sX + wY*usX_c2 + wTzuy*u.sY;
- u.Tzux += wTzux + wY*u.sX;
- u.Tzuy += wTzuy;
- }
-
- void Zspecial(Node& u, Node& w, Node& o){
- const score_t usX_c2 = u.sX*(u.sX-1)/2, usY_c2 = u.sY*(u.sY-1)/2;
- const score_t wQ=w.Q-o.Q, wQux=w.Qux-o.Qux, wQuy=w.Quy-o.Quy, wQuz=w.Quz-o.Quz;
- const score_t wZ=w.Z-o.Z, wQux2=w.Qux2-o.Qux2, wQuy2=w.Quy2-o.Quy2, wQuxy=w.Quxy-o.Quxy;
- const score_t wTx=w.Tx-o.Tx, wTy=w.Ty-o.Ty, wTxuy=w.Txuy-o.Txuy, wTxuz=w.Txuz-o.Txuz, wTyux=w.Tyux-o.Tyux, wTyuz=w.Tyuz-o.Tyuz;
-
- u.Z += wZ;
- u.Q += wQ + wQux*u.sX + wQuy*u.sY + wQuz*u.sZ + wQuxy*u.sX*u.sY + wQux2*usX_c2 + wQuy2*usY_c2
- + 2*wZ*(u.sTz + u.sX*u.sY2 + u.sX2*u.sY - u.sX2Y - u.sY2X);
- u.Qux += 2*wZ*u.sY2 + wQux + wQux2*u.sX + wQuxy*u.sY;
- u.Quy += 2*wZ*u.sX2 + wQuy + wQuxy*u.sX + wQuy2*u.sY;
- u.Quz += wQuz;
- u.Quxy += wQuxy;
- u.Qux2 += 2*wZ*u.sY + wQux2;
- u.Quy2 += 2*wZ*u.sX + wQuy2;
- u.Tx += wTx + wTxuy*u.sY + wZ*usY_c2 + wTxuz*u.sZ;
- u.Txuy += wTxuy + wZ*u.sY;
- u.Txuz += wTxuz;
- u.Ty += wTy + wTyux*u.sX + wZ*usX_c2 + wTyuz*u.sZ;
- u.Tyux += wTyux + wZ*u.sX;
- u.Tyuz += wTyuz;
- }
-
- void doXnormal(Node& u, Node& v, Node& o, Node& w){
- const score_t vX=1, vX2=(v.X*(v.X-1)-o.X*(o.X-1))/2, vY=v.Y, vY2=v.Y*(v.Y-1)/2, vZ=v.Z, vZ2=v.Z*(v.Z-1)/2, vQ=v.Q-o.Q, vTx=v.Tx, vTy=v.Ty-o.Ty, vTz=v.Tz-o.Tz;
-
- const score_t dusX_c2=((u.sX+vX)*(u.sX+vX-1)-u.sX*(u.sX-1))/2;
- u.X += vX;
- u.Q += vQ + w.Qux*vX + w.Quxy*vX*u.sY + w.Quxz*vX*u.sZ + w.Qux2*dusX_c2
- + 2*w.Y*(vTy + vX*u.sZ2 + vX2*u.sZ - vZ2*vX - vX2*vZ) + 2*w.Z*(vTz + vX*u.sY2 + vX2*u.sY - vX2*vY - vY2*vX)
- + 3*vX2*vY*vZ + 3*vY2*vX*vZ + 3*vZ2*vX*vY - 2*vX*u.sY2Z - 2*vX2*vZ*u.sY - vX2*u.sYZ - vX*vZ*u.sY2 - 2*vX*u.sZ2Y - 2*vX2*vY*u.sZ - vX*vY*u.sZ2 - 2*u.sY*vZ2*vX
- - 2*vY2*vX*u.sZ + 2*vX*u.sY*u.sZ2 + 2*vX*u.sY2*u.sZ + 2*vX2*u.sY*u.sZ
- + 2*u.sTx*vX - 2*vTx*vX + 2*vTy*u.sY - 2*vTy*vY + 2*vTz*u.sZ - 2*vTz*vZ;
- u.Qux += w.Qux2*vX;
- u.Quy += 2*w.Z*vX2 + w.Quxy*vX + 2*vX*u.sZ2 + 2*vX2*u.sZ - 2*vX2*vZ - 2*vZ2*vX + 2*vTy;
- u.Quz += 2*w.Y*vX2 + w.Quxz*vX + 2*vX*u.sY2 + 2*vX2*u.sY - 2*vX2*vY - 2*vY2*vX + 2*vTz;
- u.Quyz += vX2;
- u.Quy2 += 2*w.Z*vX + 2*vX*u.sZ - vX*vZ;
- u.Quz2 += 2*w.Y*vX + 2*vX*u.sY - vX*vY;
- u.Ty += w.Tyux*vX + w.Z*dusX_c2 + vTy + vX*u.sZ2 + vX2*u.sZ - vZ2*vX - vX2*vZ;
- u.Tyux += w.Z*vX;
- u.Tyuz += vX2;
- u.Tz += w.Tzux*vX + w.Y*dusX_c2 + vTz + vX*u.sY2 + vX2*u.sY - vX2*vY - vY2*vX;
- u.Tzux += w.Y*vX;
- u.Tzuy += vX2;
-
- u.sX += vX;
- u.sXY += vX * vY;
- u.sXZ += vX * vZ;
- u.sX2 += vX2;
- u.sX2Y += vX2 * vY;
- u.sX2Z += vX2 * vZ;
- u.sY2X += vY2 * vX;
- u.sZ2X += vZ2 * vX;
- u.sX2YZ += vX2 * vY * vZ;
- u.sY2XZ += vY2 * vX * vZ;
- u.sZ2XY += vZ2 * vX * vY;
- u.sTxX += vTx * vX;
- u.sTy += vTy;
- u.sTyY += vTy * vY;
- u.sTz += vTz;
- u.sTzZ += vTz * vZ;
- u.sQ += vQ;
- }
-
- void doYnormal(Node& u, Node& v, Node& o, Node& w){
- const score_t vX=v.X, vX2=v.X*(v.X-1)/2, vY=1, vY2=(v.Y*(v.Y-1)-o.Y*(o.Y-1))/2, vZ=v.Z, vZ2=v.Z*(v.Z-1)/2, vQ=v.Q-o.Q, vTx=v.Tx-o.Tx, vTy=v.Ty, vTz=v.Tz-o.Tz;
-
- const score_t dusY_c2=((u.sY+vY)*(u.sY+vY-1)-u.sY*(u.sY-1))/2;
- u.Y += vY;
- u.Q += vQ + w.Quy*vY + w.Quxy*u.sX*vY + w.Quyz*vY*u.sZ + w.Quy2*dusY_c2
- + 2*w.X*(vTx + vY*u.sZ2 + vY2*u.sZ - vZ2*vY - vY2*vZ) + 2*w.Z*(vTz + u.sX*vY2 + u.sX2*vY - vX2*vY - vY2*vX)
- + 3*vX2*vY*vZ + 3*vY2*vX*vZ + 3*vZ2*vX*vY - 2*u.sX*vY2*vZ - 2*u.sX2Z*vY - u.sX2*vY*vZ - u.sXZ*vY2 - 2*u.sX*vZ2*vY - 2*vX2*vY*u.sZ - vX*vY*u.sZ2 - 2*vY*u.sZ2X
- - 2*vY2*vX*u.sZ + 2*u.sX*vY*u.sZ2 + 2*u.sX*vY2*u.sZ + 2*u.sX2*vY*u.sZ
- + 2*vTx*u.sX - 2*vTx*vX + 2*u.sTy*vY - 2*vTy*vY + 2*vTz*u.sZ - 2*vTz*vZ;
- u.Qux += 2*w.Z*vY2 + w.Quxy*vY + 2*vY*u.sZ2 + 2*vY2*u.sZ - 2*vY2*vZ - 2*vZ2*vY + 2*vTx;
- u.Quy += w.Quy2*vY;
- u.Quz += 2*w.X*vY2 + w.Quyz*vY + 2*u.sX*vY2 + 2*u.sX2*vY - 2*vX2*vY - 2*vY2*vX + 2*vTz;
- u.Quxz += vY2;
- u.Qux2 += 2*w.Z*vY + 2*vY*u.sZ - vY*vZ;
- u.Quz2 += 2*w.X*vY + 2*u.sX*vY - vX*vY;
- u.Tx += w.Txuy*vY + w.Z*dusY_c2 + vTx + vY*u.sZ2 + vY2*u.sZ - vZ2*vY - vY2*vZ;
- u.Txuy += w.Z*vY;
- u.Txuz += vY2;
- u.Tz += w.Tzuy*vY + w.X*dusY_c2 + vTz + u.sX*vY2 + u.sX2*vY - vX2*vY - vY2*vX;
- u.Tzux += vY2;
- u.Tzuy += w.X*vY;
-
- u.sY += vY;
- u.sXY += vX * vY;
- u.sYZ += vY * vZ;
- u.sY2 += vY2;
- u.sX2Y += vX2 * vY;
- u.sY2X += vY2 * vX;
- u.sY2Z += vY2 * vZ;
- u.sZ2Y += vZ2 * vY;
- u.sX2YZ += vX2 * vY * vZ;
- u.sY2XZ += vY2 * vX * vZ;
- u.sZ2XY += vZ2 * vX * vY;
- u.sTx += vTx;
- u.sTxX += vTx * vX;
- u.sTyY += vTy * vY;
- u.sTz += vTz;
- u.sTzZ += vTz * vZ;
- u.sQ += vQ;
- }
-
- void doZnormal(Node& u, Node& v, Node& o, Node& w){
- const score_t vX=v.X, vX2=v.X*(v.X-1)/2, vY=v.Y, vY2=v.Y*(v.Y-1)/2, vZ=1, vZ2=(v.Z*(v.Z-1)-o.Z*(o.Z-1))/2, vQ=v.Q-o.Q, vTx=v.Tx-o.Tx, vTy=v.Ty-o.Ty, vTz=v.Tz;
-
- const score_t dusZ_c2=((u.sZ+vZ)*(u.sZ+vZ-1)-u.sZ*(u.sZ-1))/2;
- u.Z += vZ;
- u.Q += vQ + w.Quz*vZ + w.Quxz*u.sX*vZ + w.Quyz*u.sY*vZ + w.Quz2*dusZ_c2
- + 2*w.X*(vTx + u.sY*vZ2 + u.sY2*vZ - vZ2*vY - vY2*vZ) + 2*w.Y*(vTy + u.sX*vZ2 + u.sX2*vZ - vZ2*vX - vX2*vZ)
- + 3*vX2*vY*vZ + 3*vY2*vX*vZ + 3*vZ2*vX*vY - 2*u.sX*vY2*vZ - 2*vX2*vZ*u.sY - u.sX2*vY*vZ - vX*vZ*u.sY2 - 2*u.sX*vZ2*vY - 2*u.sX2Y*vZ - u.sXY*vZ2 - 2*u.sY*vZ2*vX
- - 2*u.sY2X*vZ + 2*u.sX*u.sY*vZ2 + 2*u.sX*u.sY2*vZ + 2*u.sX2*u.sY*vZ
- + 2*vTx*u.sX - 2*vTx*vX + 2*vTy*u.sY - 2*vTy*vY + 2*u.sTz*vZ - 2*vTz*vZ;
- u.Qux += 2*w.Y*vZ2 + w.Quxz*vZ + 2*u.sY*vZ2 + 2*u.sY2*vZ - 2*vY2*vZ - 2*vZ2*vY + 2*vTx;
- u.Quy += 2*w.X*vZ2 + w.Quyz*vZ + 2*u.sX*vZ2 + 2*u.sX2*vZ - 2*vX2*vZ - 2*vZ2*vX + 2*vTy;
- u.Quz += w.Quz2*vZ;
- u.Quxy += vZ2;
- u.Qux2 += 2*w.Y*vZ + 2*u.sY*vZ - vY*vZ;
- u.Quy2 += 2*w.X*vZ + 2*u.sX*vZ - vX*vZ;
- u.Tx += w.Txuz*vZ + w.Y*dusZ_c2 + vTx + u.sY*vZ2 + u.sY2*vZ - vZ2*vY - vY2*vZ;
- u.Txuy += vZ2;
- u.Txuz += w.Y*vZ;
- u.Ty += w.Tyuz*vZ + w.X*dusZ_c2 + vTy + u.sX*vZ2 + u.sX2*vZ - vZ2*vX - vX2*vZ;
- u.Tyux += vZ2;
- u.Tyuz += w.X*vZ;
-
- u.sZ += vZ;
- u.sXZ += vX * vZ;
- u.sYZ += vY * vZ;
- u.sZ2 += vZ2;
- u.sX2Z += vX2 * vZ;
- u.sY2Z += vY2 * vZ;
- u.sZ2X += vZ2 * vX;
- u.sZ2Y += vZ2 * vY;
- u.sX2YZ += vX2 * vY * vZ;
- u.sY2XZ += vY2 * vX * vZ;
- u.sZ2XY += vZ2 * vX * vY;
- u.sTx += vTx;
- u.sTxX += vTx * vX;
- u.sTy += vTy;
- u.sTyY += vTy * vY;
- u.sTzZ += vTz * vZ;
- u.sQ += vQ;
- }
-
- void doXspecial(Node& u, Node& w, Node& o){
- const score_t usY_c2 = u.sY*(u.sY-1)/2, usZ_c2 = u.sZ*(u.sZ-1)/2;
- const score_t wQ=w.Q-o.Q, wQux=w.Qux-o.Qux, wQuy=w.Quy-o.Quy, wQuz=w.Quz-o.Quz;
- const score_t wX=1, wQuy2=w.Quy2-o.Quy2, wQuz2=w.Quz2-o.Quz2, wQuyz=w.Quyz-o.Quyz;
- const score_t wTy=w.Ty-o.Ty, wTz=w.Tz-o.Tz, wTyux=w.Tyux-o.Tyux, wTyuz=w.Tyuz-o.Tyuz, wTzux=w.Tzux-o.Tzux, wTzuy=w.Tzuy-o.Tzuy;
-
- u.X += wX;
- u.Q += wQ + wQux*u.sX + wQuy*u.sY + wQuz*u.sZ + wQuyz*u.sY*u.sZ + wQuy2*usY_c2 + wQuz2*usZ_c2
- + 2*wX*(u.sTx + u.sY*u.sZ2 + u.sY2*u.sZ - u.sZ2Y - u.sY2Z);
- u.Qux += wQux;
- u.Quy += 2*wX*u.sZ2 + wQuy + wQuy2*u.sY + wQuyz*u.sZ;
- u.Quz += 2*wX*u.sY2 + wQuz + wQuyz*u.sY + wQuz2*u.sZ;
- u.Quyz += wQuyz;
- u.Quy2 += 2*wX*u.sZ + wQuy2;
- u.Quz2 += 2*wX*u.sY + wQuz2;
- u.Ty += wTy + wTyux*u.sX + wTyuz*u.sZ + wX*usZ_c2;
- u.Tyux += wTyux;
- u.Tyuz += wTyuz + wX*u.sZ;
- u.Tz += wTz + wTzux*u.sX + wTzuy*u.sY + wX*usY_c2;
- u.Tzux += wTzux;
- u.Tzuy += wTzuy + wX*u.sY;
- }
-
- void doYspecial(Node& u, Node& w, Node& o){
- const score_t usX_c2 = u.sX*(u.sX-1)/2, usZ_c2 = u.sZ*(u.sZ-1)/2;
- const score_t wQ=w.Q-o.Q, wQux=w.Qux-o.Qux, wQuy=w.Quy-o.Quy, wQuz=w.Quz-o.Quz;
- const score_t wY=1, wQux2=w.Qux2-o.Qux2, wQuz2=w.Quz2-o.Quz2, wQuxz=w.Quxz-o.Quxz;
- const score_t wTx=w.Tx-o.Tx, wTz=w.Tz-o.Tz, wTxuy=w.Txuy-o.Txuy, wTxuz=w.Txuz-o.Txuz, wTzux=w.Tzux-o.Tzux, wTzuy=w.Tzuy-o.Tzuy;
-
- u.Y += wY;
- u.Q += wQ + wQux*u.sX + wQuy*u.sY + wQuz*u.sZ + wQuxz*u.sX*u.sZ + wQux2*usX_c2 + wQuz2*usZ_c2
- + 2*wY*(u.sTy + u.sX*u.sZ2 + u.sX2*u.sZ - u.sZ2X - u.sX2Z);
- u.Qux += 2*wY*u.sZ2 + wQux + wQux2*u.sX + wQuxz*u.sZ;
- u.Quy += wQuy;
- u.Quz += 2*wY*u.sX2 + wQuz + wQuxz*u.sX + wQuz2*u.sZ;
- u.Quxz += wQuxz;
- u.Qux2 += 2*wY*u.sZ + wQux2;
- u.Quz2 += 2*wY*u.sX + wQuz2;
- u.Tx += wTx + wTxuy*u.sY + wTxuz*u.sZ + wY*usZ_c2;
- u.Txuy += wTxuy;
- u.Txuz += wTxuz + wY*u.sZ;
- u.Tz += wTz + wTzux*u.sX + wY*usX_c2 + wTzuy*u.sY;
- u.Tzux += wTzux + wY*u.sX;
- u.Tzuy += wTzuy;
- }
-
- void doZspecial(Node& u, Node& w, Node& o){
- const score_t usX_c2 = u.sX*(u.sX-1)/2, usY_c2 = u.sY*(u.sY-1)/2;
- const score_t wQ=w.Q-o.Q, wQux=w.Qux-o.Qux, wQuy=w.Quy-o.Quy, wQuz=w.Quz-o.Quz;
- const score_t wZ=1, wQux2=w.Qux2-o.Qux2, wQuy2=w.Quy2-o.Quy2, wQuxy=w.Quxy-o.Quxy;
- const score_t wTx=w.Tx-o.Tx, wTy=w.Ty-o.Ty, wTxuy=w.Txuy-o.Txuy, wTxuz=w.Txuz-o.Txuz, wTyux=w.Tyux-o.Tyux, wTyuz=w.Tyuz-o.Tyuz;
-
- u.Z += wZ;
- u.Q += wQ + wQux*u.sX + wQuy*u.sY + wQuz*u.sZ + wQuxy*u.sX*u.sY + wQux2*usX_c2 + wQuy2*usY_c2
- + 2*wZ*(u.sTz + u.sX*u.sY2 + u.sX2*u.sY - u.sX2Y - u.sY2X);
- u.Qux += 2*wZ*u.sY2 + wQux + wQux2*u.sX + wQuxy*u.sY;
- u.Quy += 2*wZ*u.sX2 + wQuy + wQuxy*u.sX + wQuy2*u.sY;
- u.Quz += wQuz;
- u.Quxy += wQuxy;
- u.Qux2 += 2*wZ*u.sY + wQux2;
- u.Quy2 += 2*wZ*u.sX + wQuy2;
- u.Tx += wTx + wTxuy*u.sY + wZ*usY_c2 + wTxuz*u.sZ;
- u.Txuy += wTxuy + wZ*u.sY;
- u.Txuz += wTxuz;
- u.Ty += wTy + wTyux*u.sX + wZ*usX_c2 + wTyuz*u.sZ;
- u.Tyux += wTyux + wZ*u.sX;
- u.Tyuz += wTyuz;
- }
-
- void undoXnormal(Node& u, Node& v, Node& o, Node& w){
- const score_t vX=-1, vX2=(v.X*(v.X-1)-o.X*(o.X-1))/2, vY=v.Y, vY2=v.Y*(v.Y-1)/2, vZ=v.Z, vZ2=v.Z*(v.Z-1)/2, vQ=v.Q-o.Q, vTx=v.Tx, vTy=v.Ty-o.Ty, vTz=v.Tz-o.Tz;
-
- const score_t dusX_c2=((u.sX+vX)*(u.sX+vX-1)-u.sX*(u.sX-1))/2;
- u.X += vX;
- u.Q += vQ + w.Qux*vX + w.Quxy*vX*u.sY + w.Quxz*vX*u.sZ + w.Qux2*dusX_c2
- + 2*w.Y*(vTy + vX*u.sZ2 + vX2*u.sZ - vZ2*vX - vX2*vZ) + 2*w.Z*(vTz + vX*u.sY2 + vX2*u.sY - vX2*vY - vY2*vX)
- + 3*vX2*vY*vZ + 3*vY2*vX*vZ + 3*vZ2*vX*vY - 2*vX*u.sY2Z - 2*vX2*vZ*u.sY - vX2*u.sYZ - vX*vZ*u.sY2 - 2*vX*u.sZ2Y - 2*vX2*vY*u.sZ - vX*vY*u.sZ2 - 2*u.sY*vZ2*vX
- - 2*vY2*vX*u.sZ + 2*vX*u.sY*u.sZ2 + 2*vX*u.sY2*u.sZ + 2*vX2*u.sY*u.sZ
- + 2*u.sTx*vX - 2*vTx*vX + 2*vTy*u.sY - 2*vTy*vY + 2*vTz*u.sZ - 2*vTz*vZ;
- u.Qux += w.Qux2*vX;
- u.Quy += 2*w.Z*vX2 + w.Quxy*vX + 2*vX*u.sZ2 + 2*vX2*u.sZ - 2*vX2*vZ - 2*vZ2*vX + 2*vTy;
- u.Quz += 2*w.Y*vX2 + w.Quxz*vX + 2*vX*u.sY2 + 2*vX2*u.sY - 2*vX2*vY - 2*vY2*vX + 2*vTz;
- u.Quyz += vX2;
- u.Quy2 += 2*w.Z*vX + 2*vX*u.sZ - vX*vZ;
- u.Quz2 += 2*w.Y*vX + 2*vX*u.sY - vX*vY;
- u.Ty += w.Tyux*vX + w.Z*dusX_c2 + vTy + vX*u.sZ2 + vX2*u.sZ - vZ2*vX - vX2*vZ;
- u.Tyux += w.Z*vX;
- u.Tyuz += vX2;
- u.Tz += w.Tzux*vX + w.Y*dusX_c2 + vTz + vX*u.sY2 + vX2*u.sY - vX2*vY - vY2*vX;
- u.Tzux += w.Y*vX;
- u.Tzuy += vX2;
-
- u.sX += vX;
- u.sXY += vX * vY;
- u.sXZ += vX * vZ;
- u.sX2 += vX2;
- u.sX2Y += vX2 * vY;
- u.sX2Z += vX2 * vZ;
- u.sY2X += vY2 * vX;
- u.sZ2X += vZ2 * vX;
- u.sX2YZ += vX2 * vY * vZ;
- u.sY2XZ += vY2 * vX * vZ;
- u.sZ2XY += vZ2 * vX * vY;
- u.sTxX += vTx * vX;
- u.sTy += vTy;
- u.sTyY += vTy * vY;
- u.sTz += vTz;
- u.sTzZ += vTz * vZ;
- u.sQ += vQ;
- }
-
- void undoYnormal(Node& u, Node& v, Node& o, Node& w){
- const score_t vX=v.X, vX2=v.X*(v.X-1)/2, vY=-1, vY2=(v.Y*(v.Y-1)-o.Y*(o.Y-1))/2, vZ=v.Z, vZ2=v.Z*(v.Z-1)/2, vQ=v.Q-o.Q, vTx=v.Tx-o.Tx, vTy=v.Ty, vTz=v.Tz-o.Tz;
-
- const score_t dusY_c2=((u.sY+vY)*(u.sY+vY-1)-u.sY*(u.sY-1))/2;
- u.Y += vY;
- u.Q += vQ + w.Quy*vY + w.Quxy*u.sX*vY + w.Quyz*vY*u.sZ + w.Quy2*dusY_c2
- + 2*w.X*(vTx + vY*u.sZ2 + vY2*u.sZ - vZ2*vY - vY2*vZ) + 2*w.Z*(vTz + u.sX*vY2 + u.sX2*vY - vX2*vY - vY2*vX)
- + 3*vX2*vY*vZ + 3*vY2*vX*vZ + 3*vZ2*vX*vY - 2*u.sX*vY2*vZ - 2*u.sX2Z*vY - u.sX2*vY*vZ - u.sXZ*vY2 - 2*u.sX*vZ2*vY - 2*vX2*vY*u.sZ - vX*vY*u.sZ2 - 2*vY*u.sZ2X
- - 2*vY2*vX*u.sZ + 2*u.sX*vY*u.sZ2 + 2*u.sX*vY2*u.sZ + 2*u.sX2*vY*u.sZ
- + 2*vTx*u.sX - 2*vTx*vX + 2*u.sTy*vY - 2*vTy*vY + 2*vTz*u.sZ - 2*vTz*vZ;
- u.Qux += 2*w.Z*vY2 + w.Quxy*vY + 2*vY*u.sZ2 + 2*vY2*u.sZ - 2*vY2*vZ - 2*vZ2*vY + 2*vTx;
- u.Quy += w.Quy2*vY;
- u.Quz += 2*w.X*vY2 + w.Quyz*vY + 2*u.sX*vY2 + 2*u.sX2*vY - 2*vX2*vY - 2*vY2*vX + 2*vTz;
- u.Quxz += vY2;
- u.Qux2 += 2*w.Z*vY + 2*vY*u.sZ - vY*vZ;
- u.Quz2 += 2*w.X*vY + 2*u.sX*vY - vX*vY;
- u.Tx += w.Txuy*vY + w.Z*dusY_c2 + vTx + vY*u.sZ2 + vY2*u.sZ - vZ2*vY - vY2*vZ;
- u.Txuy += w.Z*vY;
- u.Txuz += vY2;
- u.Tz += w.Tzuy*vY + w.X*dusY_c2 + vTz + u.sX*vY2 + u.sX2*vY - vX2*vY - vY2*vX;
- u.Tzux += vY2;
- u.Tzuy += w.X*vY;
-
- u.sY += vY;
- u.sXY += vX * vY;
- u.sYZ += vY * vZ;
- u.sY2 += vY2;
- u.sX2Y += vX2 * vY;
- u.sY2X += vY2 * vX;
- u.sY2Z += vY2 * vZ;
- u.sZ2Y += vZ2 * vY;
- u.sX2YZ += vX2 * vY * vZ;
- u.sY2XZ += vY2 * vX * vZ;
- u.sZ2XY += vZ2 * vX * vY;
- u.sTx += vTx;
- u.sTxX += vTx * vX;
- u.sTyY += vTy * vY;
- u.sTz += vTz;
- u.sTzZ += vTz * vZ;
- u.sQ += vQ;
- }
-
- void undoZnormal(Node& u, Node& v, Node& o, Node& w){
- const score_t vX=v.X, vX2=v.X*(v.X-1)/2, vY=v.Y, vY2=v.Y*(v.Y-1)/2, vZ=-1, vZ2=(v.Z*(v.Z-1)-o.Z*(o.Z-1))/2, vQ=v.Q-o.Q, vTx=v.Tx-o.Tx, vTy=v.Ty-o.Ty, vTz=v.Tz;
-
- const score_t dusZ_c2=((u.sZ+vZ)*(u.sZ+vZ-1)-u.sZ*(u.sZ-1))/2;
- u.Z += vZ;
- u.Q += vQ + w.Quz*vZ + w.Quxz*u.sX*vZ + w.Quyz*u.sY*vZ + w.Quz2*dusZ_c2
- + 2*w.X*(vTx + u.sY*vZ2 + u.sY2*vZ - vZ2*vY - vY2*vZ) + 2*w.Y*(vTy + u.sX*vZ2 + u.sX2*vZ - vZ2*vX - vX2*vZ)
- + 3*vX2*vY*vZ + 3*vY2*vX*vZ + 3*vZ2*vX*vY - 2*u.sX*vY2*vZ - 2*vX2*vZ*u.sY - u.sX2*vY*vZ - vX*vZ*u.sY2 - 2*u.sX*vZ2*vY - 2*u.sX2Y*vZ - u.sXY*vZ2 - 2*u.sY*vZ2*vX
- - 2*u.sY2X*vZ + 2*u.sX*u.sY*vZ2 + 2*u.sX*u.sY2*vZ + 2*u.sX2*u.sY*vZ
- + 2*vTx*u.sX - 2*vTx*vX + 2*vTy*u.sY - 2*vTy*vY + 2*u.sTz*vZ - 2*vTz*vZ;
- u.Qux += 2*w.Y*vZ2 + w.Quxz*vZ + 2*u.sY*vZ2 + 2*u.sY2*vZ - 2*vY2*vZ - 2*vZ2*vY + 2*vTx;
- u.Quy += 2*w.X*vZ2 + w.Quyz*vZ + 2*u.sX*vZ2 + 2*u.sX2*vZ - 2*vX2*vZ - 2*vZ2*vX + 2*vTy;
- u.Quz += w.Quz2*vZ;
- u.Quxy += vZ2;
- u.Qux2 += 2*w.Y*vZ + 2*u.sY*vZ - vY*vZ;
- u.Quy2 += 2*w.X*vZ + 2*u.sX*vZ - vX*vZ;
- u.Tx += w.Txuz*vZ + w.Y*dusZ_c2 + vTx + u.sY*vZ2 + u.sY2*vZ - vZ2*vY - vY2*vZ;
- u.Txuy += vZ2;
- u.Txuz += w.Y*vZ;
- u.Ty += w.Tyuz*vZ + w.X*dusZ_c2 + vTy + u.sX*vZ2 + u.sX2*vZ - vZ2*vX - vX2*vZ;
- u.Tyux += vZ2;
- u.Tyuz += w.X*vZ;
-
- u.sZ += vZ;
- u.sXZ += vX * vZ;
- u.sYZ += vY * vZ;
- u.sZ2 += vZ2;
- u.sX2Z += vX2 * vZ;
- u.sY2Z += vY2 * vZ;
- u.sZ2X += vZ2 * vX;
- u.sZ2Y += vZ2 * vY;
- u.sX2YZ += vX2 * vY * vZ;
- u.sY2XZ += vY2 * vX * vZ;
- u.sZ2XY += vZ2 * vX * vY;
- u.sTx += vTx;
- u.sTxX += vTx * vX;
- u.sTy += vTy;
- u.sTyY += vTy * vY;
- u.sTzZ += vTz * vZ;
- u.sQ += vQ;
- }
-
- void undoXspecial(Node& u, Node& w, Node& o){
- const score_t usY_c2 = u.sY*(u.sY-1)/2, usZ_c2 = u.sZ*(u.sZ-1)/2;
- const score_t wQ=w.Q-o.Q, wQux=w.Qux-o.Qux, wQuy=w.Quy-o.Quy, wQuz=w.Quz-o.Quz;
- const score_t wX=-1, wQuy2=w.Quy2-o.Quy2, wQuz2=w.Quz2-o.Quz2, wQuyz=w.Quyz-o.Quyz;
- const score_t wTy=w.Ty-o.Ty, wTz=w.Tz-o.Tz, wTyux=w.Tyux-o.Tyux, wTyuz=w.Tyuz-o.Tyuz, wTzux=w.Tzux-o.Tzux, wTzuy=w.Tzuy-o.Tzuy;
-
- u.X += wX;
- u.Q += wQ + wQux*u.sX + wQuy*u.sY + wQuz*u.sZ + wQuyz*u.sY*u.sZ + wQuy2*usY_c2 + wQuz2*usZ_c2
- + 2*wX*(u.sTx + u.sY*u.sZ2 + u.sY2*u.sZ - u.sZ2Y - u.sY2Z);
- u.Qux += wQux;
- u.Quy += 2*wX*u.sZ2 + wQuy + wQuy2*u.sY + wQuyz*u.sZ;
- u.Quz += 2*wX*u.sY2 + wQuz + wQuyz*u.sY + wQuz2*u.sZ;
- u.Quyz += wQuyz;
- u.Quy2 += 2*wX*u.sZ + wQuy2;
- u.Quz2 += 2*wX*u.sY + wQuz2;
- u.Ty += wTy + wTyux*u.sX + wTyuz*u.sZ + wX*usZ_c2;
- u.Tyux += wTyux;
- u.Tyuz += wTyuz + wX*u.sZ;
- u.Tz += wTz + wTzux*u.sX + wTzuy*u.sY + wX*usY_c2;
- u.Tzux += wTzux;
- u.Tzuy += wTzuy + wX*u.sY;
- }
-
- void undoYspecial(Node& u, Node& w, Node& o){
- const score_t usX_c2 = u.sX*(u.sX-1)/2, usZ_c2 = u.sZ*(u.sZ-1)/2;
- const score_t wQ=w.Q-o.Q, wQux=w.Qux-o.Qux, wQuy=w.Quy-o.Quy, wQuz=w.Quz-o.Quz;
- const score_t wY=-1, wQux2=w.Qux2-o.Qux2, wQuz2=w.Quz2-o.Quz2, wQuxz=w.Quxz-o.Quxz;
- const score_t wTx=w.Tx-o.Tx, wTz=w.Tz-o.Tz, wTxuy=w.Txuy-o.Txuy, wTxuz=w.Txuz-o.Txuz, wTzux=w.Tzux-o.Tzux, wTzuy=w.Tzuy-o.Tzuy;
-
- u.Y += wY;
- u.Q += wQ + wQux*u.sX + wQuy*u.sY + wQuz*u.sZ + wQuxz*u.sX*u.sZ + wQux2*usX_c2 + wQuz2*usZ_c2
- + 2*wY*(u.sTy + u.sX*u.sZ2 + u.sX2*u.sZ - u.sZ2X - u.sX2Z);
- u.Qux += 2*wY*u.sZ2 + wQux + wQux2*u.sX + wQuxz*u.sZ;
- u.Quy += wQuy;
- u.Quz += 2*wY*u.sX2 + wQuz + wQuxz*u.sX + wQuz2*u.sZ;
- u.Quxz += wQuxz;
- u.Qux2 += 2*wY*u.sZ + wQux2;
- u.Quz2 += 2*wY*u.sX + wQuz2;
- u.Tx += wTx + wTxuy*u.sY + wTxuz*u.sZ + wY*usZ_c2;
- u.Txuy += wTxuy;
- u.Txuz += wTxuz + wY*u.sZ;
- u.Tz += wTz + wTzux*u.sX + wY*usX_c2 + wTzuy*u.sY;
- u.Tzux += wTzux + wY*u.sX;
- u.Tzuy += wTzuy;
- }
-
- void undoZspecial(Node& u, Node& w, Node& o){
- const score_t usX_c2 = u.sX*(u.sX-1)/2, usY_c2 = u.sY*(u.sY-1)/2;
- const score_t wQ=w.Q-o.Q, wQux=w.Qux-o.Qux, wQuy=w.Quy-o.Quy, wQuz=w.Quz-o.Quz;
- const score_t wZ=-1, wQux2=w.Qux2-o.Qux2, wQuy2=w.Quy2-o.Quy2, wQuxy=w.Quxy-o.Quxy;
- const score_t wTx=w.Tx-o.Tx, wTy=w.Ty-o.Ty, wTxuy=w.Txuy-o.Txuy, wTxuz=w.Txuz-o.Txuz, wTyux=w.Tyux-o.Tyux, wTyuz=w.Tyuz-o.Tyuz;
-
- u.Z += wZ;
- u.Q += wQ + wQux*u.sX + wQuy*u.sY + wQuz*u.sZ + wQuxy*u.sX*u.sY + wQux2*usX_c2 + wQuy2*usY_c2
- + 2*wZ*(u.sTz + u.sX*u.sY2 + u.sX2*u.sY - u.sX2Y - u.sY2X);
- u.Qux += 2*wZ*u.sY2 + wQux + wQux2*u.sX + wQuxy*u.sY;
- u.Quy += 2*wZ*u.sX2 + wQuy + wQuxy*u.sX + wQuy2*u.sY;
- u.Quz += wQuz;
- u.Quxy += wQuxy;
- u.Qux2 += 2*wZ*u.sY + wQux2;
- u.Quy2 += 2*wZ*u.sX + wQuy2;
- u.Tx += wTx + wTxuy*u.sY + wZ*usY_c2 + wTxuz*u.sZ;
- u.Txuy += wTxuy + wZ*u.sY;
- u.Txuz += wTxuz;
- u.Ty += wTy + wTyux*u.sX + wZ*usX_c2 + wTyuz*u.sZ;
- u.Tyux += wTyux + wZ*u.sX;
- u.Tyuz += wTyuz;
- }
-
-
- vector<vector<int> > leafParent;
- score_t totalScore = 0;
- Node dummy, nodeX, nodeY, nodeZ;
- vector<vector<Node> > nodes, nodesTotal;
- vector<int> roots;
- vector<int> color;
-
- int buildTree(int v, vector<TripartitionInitializer::Node> &iNodes, vector<vector<int> > &children){
- for (int c: children[v]){
- int u = buildTree(c, iNodes, children);
- iNodes[u].up = v;
- if (iNodes[u].maxHeight + 1 > iNodes[u].maxHeight){
- int t = iNodes[v].maxChild;
- iNodes[v].maxChild = u;
- iNodes[v].maxHeight = iNodes[u].maxHeight + 1;
- u = t;
- }
- if (u != -1 && iNodes[u].max2Height + 1 > iNodes[u].maxHeight){
- iNodes[v].max2Child = u;
- iNodes[v].max2Height = iNodes[u].maxHeight + 1;
- }
- }
- int u = iNodes[v].maxChild;
- if (u != -1 && iNodes[u].maxHeight >= iNodes[u].path + 1 + iNodes[v].max2Height){
- iNodes[u].up = -1;
- if (iNodes[u].downMost == -1){
- iNodes[v].up = u;
- iNodes[u].down = v;
- }
- else {
- iNodes[v].up = iNodes[u].downMost;
- iNodes[iNodes[u].downMost].down = v;
- }
- iNodes[u].downMost = v;
- iNodes[u].path += 1 + iNodes[v].max2Height;
- return u;
- }
- else return v;
- }
-
- Partition(const TripartitionInitializer &init, int k): nodes(init.roots[k].size()), leafParent(init.roots[k].size(), vector<int>(init.nTaxa, -1)),
- nodesTotal(init.roots[k].size()), color(init.nTaxa, -1){
- nodeX.X = 1;
- nodeY.Y = 1;
- nodeZ.Z = 1;
-
- //cerr << "here1!" << endl;
- for (int i = 0; i < init.roots[k].size(); i++){
- int nInternal = 0;
- for (const pair<int, int> pc: init.parentChild[k][i]){
- if (pc.first - init.nTaxa + 1 > nInternal) nInternal = pc.first - init.nTaxa + 1;
- }
- vector<TripartitionInitializer::Node> iNodes(nInternal);
- vector<vector<int> > children(nInternal);
- for (const pair<int, int> pc: init.parentChild[k][i]){
- if (pc.second < init.nTaxa) leafParent[i][pc.second] = pc.first - init.nTaxa;
- else children[pc.first - init.nTaxa].push_back(pc.second - init.nTaxa);
- }
- //cerr << init.roots[i] - init.nTaxa << endl;
- /*for (int i = 0; i < children.size(); i++){
- for (int j: children[i]){
- cerr << i << " " << j << endl;
- }
- }*/
- //for (int j = 0; j < init.nTaxa; j++) cerr << j << "->" << leafParent[i][j] << endl;
- roots.push_back(buildTree(init.roots[k][i] - init.nTaxa, iNodes, children));
- for (int j = 0; j < nInternal; j++){
- nodes[i].emplace_back();
- nodes[i][j].up = iNodes[j].up;
- nodes[i][j].down = iNodes[j].down;
- nodesTotal[i].emplace_back();
- nodesTotal[i][j].up = iNodes[j].up;
- nodesTotal[i][j].down = iNodes[j].down;
- //cerr << j << " " << nodes[i][j].up << " " << nodes[i][j].down << endl;
- }
- }
- //cerr << "Init finished\n";
- }
-
- void add(int x, int i){
- //cerr << nodes[0][0].X << " " << nodes[0][0].Y << " " << nodes[0][0].Z << ":" << nodes[0][0].Q << "|" << nodes[0][1].X << " " << nodes[0][1].Y << " " << nodes[0][1].Z << ":" << nodes[0][1].Q << "|" << nodes[0][2].X << " " << nodes[0][2].Y << " " << nodes[0][2].Z << ":" << nodes[0][2].Q << "|" << nodes[0][3].X << " " << nodes[0][3].Y << " " << nodes[0][3].Z << ":" << nodes[0][3].Q << endl << endl;
- totalScore = 0;
- for (int k = 0; k < leafParent.size(); k++){
- int u = leafParent[k][i], v = -2;
- Node *pv = (x == 0) ? &nodeZ : (x == 1) ? &nodeX : &nodeY;
- Node vOld = dummy;
- if (u == -1){
- totalScore += nodes[k][roots[k]].Q;
- }
- while (u != -1){
- Node *pu = &nodes[k][u];
- Node uOld = *pu;
- if (pu->down == v){
- if (x == 0) doZspecial(*pu, *pv, vOld);//{undoZspecial(*pu, vOld); doZspecial(*pu, *pv);}
- else if (x == 1) doXspecial(*pu, *pv, vOld);//{undoXspecial(*pu, vOld); doXspecial(*pu, *pv);}
- else doYspecial(*pu, *pv, vOld);//{undoYspecial(*pu, vOld); doYspecial(*pu, *pv);}
-
- //if (pu->verify(*pv)) cerr << "ERROR!";
- }
- else {
- Node &w = (pu->down == -1) ? dummy : nodes[k][pu->down];
- if (x == 0) doZnormal(*pu, *pv, vOld, w);//{undoZnormal(*pu, vOld, w); doZnormal(*pu, *pv, w);}
- else if (x == 1) doXnormal(*pu, *pv, vOld, w);//{undoXnormal(*pu, vOld, w); doXnormal(*pu, *pv, w);}
- else doYnormal(*pu, *pv, vOld, w);//{undoYnormal(*pu, vOld, w); doYnormal(*pu, *pv, w);}
-
- //if (pu->verify(w)) cerr << "ERROR!";
- }
- vOld = uOld;
- v = u;
- pv = pu;
- u = pu->up;
- }
- totalScore += pv->Q;
- }
- //cerr << nodes[0][0].X << " " << nodes[0][0].Y << " " << nodes[0][0].Z << ":" << nodes[0][0].Q << "|" << nodes[0][1].X << " " << nodes[0][1].Y << " " << nodes[0][1].Z << ":" << nodes[0][1].Q << "|" << nodes[0][2].X << " " << nodes[0][2].Y << " " << nodes[0][2].Z << ":" << nodes[0][2].Q << "|" << nodes[0][3].X << " " << nodes[0][3].Y << " " << nodes[0][3].Z << ":" << nodes[0][3].Q << endl << endl;
- }
-
- void rmv(int x, int i){
- totalScore = 0;
- for (int k = 0; k < leafParent.size(); k++){
- int u = leafParent[k][i], v = -2;
- Node *pv = &dummy;
- Node vOld = (x == 0) ? nodeZ : (x == 1) ? nodeX : nodeY;
- if (u == -1){
- totalScore += nodes[k][roots[k]].Q;
- }
- while (u != -1){
- Node *pu = &nodes[k][u];
- Node uOld = *pu;
- if (pu->down == v){
- if (x == 0) undoZspecial(*pu, *pv, vOld);//{undoZspecial(*pu, vOld); doZspecial(*pu, *pv);}
- else if (x == 1) undoXspecial(*pu, *pv, vOld);//{undoXspecial(*pu, vOld); doXspecial(*pu, *pv);}
- else undoYspecial(*pu, *pv, vOld);//{undoYspecial(*pu, vOld); doYspecial(*pu, *pv);}
- }
- else {
- Node &w = (pu->down == -1) ? dummy : nodes[k][pu->down];
- if (x == 0) undoZnormal(*pu, *pv, vOld, w);//{undoZnormal(*pu, vOld, w); doZnormal(*pu, *pv, w);}
- else if (x == 1) undoXnormal(*pu, *pv, vOld, w);//{undoXnormal(*pu, vOld, w); doXnormal(*pu, *pv, w);}
- else undoYnormal(*pu, *pv, vOld, w);//{undoYnormal(*pu, vOld, w); doYnormal(*pu, *pv, w);}
- }
- vOld = uOld;
- v = u;
- pv = pu;
- u = pu->up;
- }
- totalScore += pv->Q;
- }
- }
-
- void update(int x, int i){
- int y = color[i];
- if (x == y) return;
- color[i] = x;
- if (y == -1){
- add(x, i);
- return;
- }
- if (x == -1){
- rmv(y, i);
- return;
- }
- totalScore = 0;
- for (int k = 0; k < leafParent.size(); k++){
- int u = leafParent[k][i], v = -2;
- Node *pv = (x == 0) ? &nodeZ : (x == 1) ? &nodeX : &nodeY;
- Node vMid = dummy;
- Node vOld = (y == 0) ? nodeZ : (y == 1) ? nodeX : nodeY;
- if (u == -1){
- totalScore += nodes[k][roots[k]].Q;
- }
- while (u != -1){
- Node *pu = &nodes[k][u];
- Node uOld = *pu, uMid;
- if (pu->down == v){
- if (y == 0) undoZspecial(*pu, vMid, vOld);
- else if (y == 1) undoXspecial(*pu, vMid, vOld);
- else undoYspecial(*pu, vMid, vOld);
- uMid = *pu;
- if (x == 0) doZspecial(*pu, *pv, vMid);
- else if (x == 1) doXspecial(*pu, *pv, vMid);
- else doYspecial(*pu, *pv, vMid);
- }
- else {
- Node &w = (pu->down == -1) ? dummy : nodes[k][pu->down];
- if (y == 0) undoZnormal(*pu, vMid, vOld, w);
- else if (y == 1) undoXnormal(*pu, vMid, vOld, w);
- else undoYnormal(*pu, vMid, vOld, w);
- uMid = *pu;
- if (x == 0) doZnormal(*pu, *pv, vMid, w);
- else if (x == 1) doXnormal(*pu, *pv, vMid, w);
- else doYnormal(*pu, *pv, vMid, w);
- }
- vOld = uOld;
- vMid = uMid;
- v = u;
- pv = pu;
- u = pu->up;
- }
- totalScore += pv->Q;
- }
- }
-
- score_t score(){
- return totalScore;
- }
- };
-
- vector<Partition> parts;
-
- Tripartition(const TripartitionInitializer &init){
- for (int p = 0; p < init.roots.size(); p++) parts.emplace_back(init, p);
- }
-
- void update(int x, int i){
- vector<thread> thrds;
- for (int p = 1; p < parts.size(); p++) thrds.emplace_back(&Partition::update, &parts[p], x, i);
- parts[0].update(x, i);
- for (thread &t: thrds) t.join();
- }
-
- score_t score(){
- score_t res = 0;
- for (int p = 0; p < parts.size(); p++) res += parts[p].score();
- return res;
- }
-};
diff --git a/addons/ASTER/genetreewithbinaryweight.hpp b/addons/ASTER/genetreewithbinaryweight.hpp
deleted file mode 100644
index 65dfb9e2f50c43e409c562cef1c1600b75b693a5..0000000000000000000000000000000000000000
--- a/addons/ASTER/genetreewithbinaryweight.hpp
+++ /dev/null
@@ -1,366 +0,0 @@
-#include<vector>
-#include<array>
-#include<thread>
-
-#define SUPPORT
-
-using namespace std;
-
-struct TripartitionInitializer{
- struct Node{
- int up = -1, small = -1, large = -1;
- score_t weight = 1;
- };
-
- vector<vector<Node> > nodes;
- vector<vector<vector<int> > > leafParent;
-};
-
-struct Tripartition{
- struct Partition{
- struct Node{
- score_t x = 0, y = 0, z = 0, tx = 0, ty = 0, tz = 0, q = 0;
- score_t x2a = 0, y2a = 0, z2a = 0, xya = 0, xza = 0, yza = 0;
- score_t x2b = 0, y2b = 0, z2b = 0, xyb = 0, xzb = 0, yzb = 0;
-
- int up = -1, small = -1, large = -1; // -1 for dummy!
- score_t weight = 1;
-
- };
-
- score_t normal(Node& w){
- Node& u = nodes[w.small];
- Node& v = nodes[w.large];
- //u.update(version, totalZ[w.small]);
- //v.update(version, totalZ[w.large]);
-
- w.x = u.x + v.x;
- w.y = u.y + v.y;
- w.z = u.z + v.z;
- w.x2a = u.x2a + v.x2a + u.x * v.x;
- w.y2a = u.y2a + v.y2a + u.y * v.y;
- w.z2a = u.z2a + v.z2a + u.z * v.z;
- w.xya = u.xya + v.xya + u.x * v.y + u.y * v.x;
- w.xza = u.xza + v.xza + u.x * v.z + u.z * v.x;
- w.yza = u.yza + v.yza + u.y * v.z + u.z * v.y;
- w.x2b = (u.x2b + v.x2b + u.x * v.x) * (1 - w.weight);
- w.y2b = (u.y2b + v.y2b + u.y * v.y) * (1 - w.weight);
- w.z2b = (u.z2b + v.z2b + u.z * v.z) * (1 - w.weight);
- w.xyb = (u.xyb + v.xyb + u.x * v.y + u.y * v.x) * (1 - w.weight);
- w.xzb = (u.xzb + v.xzb + u.x * v.z + u.z * v.x) * (1 - w.weight);
- w.yzb = (u.yzb + v.yzb + u.y * v.z + u.z * v.y) * (1 - w.weight);
-
-
- w.tx = u.tx + v.tx + u.y * (v.z2a - v.z2b) + (u.z2a - u.z2b) * v.y + u.z * (v.y2a - v.y2b) + (u.y2a - u.y2b) * v.z;
- w.ty = u.ty + v.ty + u.x * (v.z2a - v.z2b) + (u.z2a - u.z2b) * v.x + u.z * (v.x2a - v.x2b) + (u.x2a - u.x2b) * v.z;
- w.tz = u.tz + v.tz + u.x * (v.y2a - v.y2b) + (u.y2a - u.y2b) * v.x + u.y * (v.x2a - v.x2b) + (u.x2a - u.x2b) * v.y;
- score_t oldQ = w.q;
- w.q = u.x * v.tx + u.y * v.ty + u.z * v.tz + v.x * u.tx + v.y * u.ty + v.z * u.tz
- + u.x2a * v.yza - u.x2b * v.yzb
- + u.y2a * v.xza - u.y2b * v.xzb
- + u.z2a * v.xya - u.z2b * v.xyb;
- return w.q - oldQ;
- }
-
- vector<vector<int> > leafParent;
- score_t totalScore = 0;
- vector<Node> nodes;
- vector<int> color;
-
- Partition(TripartitionInitializer init, int p): leafParent(init.leafParent[p]), nodes(init.nodes[p].size()), color(init.leafParent[p].size(), -1){
- for (int i = 0; i < nodes.size(); i++){
- nodes[i].up = init.nodes[p][i].up;
- nodes[i].small = init.nodes[p][i].small;
- nodes[i].large = init.nodes[p][i].large;
- nodes[i].weight = init.nodes[p][i].weight;
- }
- }
- /*
- void reset(){
- totalScore = 0;
- version++;
- }
-
- void addTotal(int i){
- for (int w: leafParent[i]){
- totalZ[w].z++;
- w = totalZ[w].up;
- while (w != -1){
- Node& u = totalZ[totalZ[w].small];
- Node& v = totalZ[totalZ[w].large];
- totalZ[w].z = u.z + v.z;
- totalZ[w].z2a = u.z2a + v.z2a + u.z * v.z;
- totalZ[w].z2b = (u.z2b + v.z2b + u.z * v.z) * (1 - totalZ[w].weight);
- w = totalZ[w].up;
- }
- }
- }
-
- void rmvTotal(int i){
- for (int w: leafParent[i]){
- totalZ[w].z--;
- w = totalZ[w].up;
- while (w != -1){
- Node& u = totalZ[totalZ[w].small];
- Node& v = totalZ[totalZ[w].large];
- totalZ[w].z = u.z + v.z;
- totalZ[w].z2a = u.z2a + v.z2a + u.z * v.z;
- totalZ[w].z2b = (u.z2b + v.z2b + u.z * v.z) * (1 - totalZ[w].weight);
- w = totalZ[w].up;
- }
- }
- }
-
- void add(int x, int i){
- for (int u: leafParent[i]){
- nodes[u].update(version, totalZ[u]);
- ((x == 0) ? nodes[u].z : (x == 1) ? nodes[u].x : nodes[u].y)++;
- int w = nodes[u].up;
- while (w != -1){
- nodes[w].update(version, totalZ[w]);
- totalScore += normal(nodes[w]);
- u = w;
- w = nodes[u].up;
- }
- }
- }
-
- void rmv(int x, int i){
- for (int u: leafParent[i]){
- nodes[u].update(version, totalZ[u]);
- ((x == 0) ? nodes[u].z : (x == 1) ? nodes[u].x : nodes[u].y)--;
- int w = nodes[u].up;
- while (w != -1){
- nodes[w].update(version, totalZ[w]);
- totalScore += normal(nodes[w]);
- u = w;
- w = nodes[u].up;
- }
- }
- }
- */
- void update(int x, int i){
- int y = color[i];
- if (x == y) return;
- for (int u: leafParent[i]){
- if (y != -1) ((y == 0) ? nodes[u].z : (y == 1) ? nodes[u].x : nodes[u].y)--;
- if (x != -1) ((x == 0) ? nodes[u].z : (x == 1) ? nodes[u].x : nodes[u].y)++;
- int w = nodes[u].up;
- while (w != -1){
- totalScore += normal(nodes[w]);
- u = w;
- w = nodes[u].up;
- }
- }
- color[i] = x;
- }
-
- score_t score(){
- return totalScore;
- }
- };
-
- vector<Partition> parts;
-
- Tripartition(const TripartitionInitializer &init){
- for (int p = 0; p < init.nodes.size(); p++) parts.emplace_back(init, p);
- }
- /*
- void reset(){
- for (int p = 0; p < parts.size(); p++) parts[p].reset();
- }
-
- void addTotal(int i){
- vector<thread> thrds;
- for (int p = 1; p < parts.size(); p++) thrds.emplace_back(&Partition::addTotal, &parts[p], i);
- parts[0].addTotal(i);
- for (thread &t: thrds) t.join();
- }
-
- void rmvTotal(int i){
- vector<thread> thrds;
- for (int p = 1; p < parts.size(); p++) thrds.emplace_back(&Partition::rmvTotal, &parts[p], i);
- parts[0].rmvTotal(i);
- for (thread &t: thrds) t.join();
- }
-
- void add(int x, int i){
- vector<thread> thrds;
- for (int p = 1; p < parts.size(); p++) thrds.emplace_back(&Partition::add, &parts[p], x, i);
- parts[0].add(x, i);
- for (thread &t: thrds) t.join();
- }
-
- void rmv(int x, int i){
- vector<thread> thrds;
- for (int p = 1; p < parts.size(); p++) thrds.emplace_back(&Partition::rmv, &parts[p], x, i);
- parts[0].rmv(x, i);
- for (thread &t: thrds) t.join();
- }
- */
-
- void update(int x, int i){
- vector<thread> thrds;
- for (int p = 1; p < parts.size(); p++) thrds.emplace_back(&Partition::update, &parts[p], x, i);
- parts[0].update(x, i);
- for (thread &t: thrds) t.join();
- }
-
- score_t score(){
- score_t res = 0;
- for (int p = 0; p < parts.size(); p++) res += parts[p].score();
- return res;
- }
-};
-
-struct Quadrupartition{
- struct Partition{
- struct Node{
- score_t a = 0, b = 0, c = 0, d = 0;
- score_t ab_c = 0, ab_d = 0, a_cd = 0, b_cd = 0;
- score_t ac_b = 0, a_bd = 0, ac_d = 0, c_bd = 0;
- score_t a_bc = 0, ad_b = 0, ad_c = 0, d_bc = 0;
- score_t abx = 0, acx = 0, adx = 0, bcx = 0, bdx = 0, cdx = 0;
- score_t aby = 0, acy = 0, ady = 0, bcy = 0, bdy = 0, cdy = 0;
- //score_t abx = 0, cdx = 0, aby = 0, cdy = 0;
-
- score_t ab_cd = 0, ac_bd = 0, ad_bc = 0;
-
- int up = -1, small = -1, large = -1; // -1 for dummy!
- score_t weight = 1;
- };
-
- array<score_t, 3> normal(Node& w){
- Node& u = nodes[w.small];
- Node& v = nodes[w.large];
-
- w.a = u.a + v.a;
- w.b = u.b + v.b;
- w.c = u.c + v.c;
- w.d = u.d + v.d;
- w.abx = u.abx + v.abx + u.a * v.b + v.a * u.b;
- w.acx = u.acx + v.acx + u.a * v.c + v.a * u.c;
- w.adx = u.adx + v.adx + u.a * v.d + v.a * u.d;
- w.bcx = u.bcx + v.bcx + u.b * v.c + v.b * u.c;
- w.bdx = u.bdx + v.bdx + u.b * v.d + v.b * u.d;
- w.cdx = u.cdx + v.cdx + u.c * v.d + v.c * u.d;
- w.aby = (u.aby + v.aby + u.a * v.b + v.a * u.b) * (1 - w.weight);
- w.acy = (u.acy + v.acy + u.a * v.c + v.a * u.c) * (1 - w.weight);
- w.ady = (u.ady + v.ady + u.a * v.d + v.a * u.d) * (1 - w.weight);
- w.bcy = (u.bcy + v.bcy + u.b * v.c + v.b * u.c) * (1 - w.weight);
- w.bdy = (u.bdy + v.bdy + u.b * v.d + v.b * u.d) * (1 - w.weight);
- w.cdy = (u.cdy + v.cdy + u.c * v.d + v.c * u.d) * (1 - w.weight);
-
- w.ab_c = u.ab_c + v.ab_c + u.c * (v.abx - v.aby) + (u.abx - u.aby) * v.c;
- w.ab_d = u.ab_d + v.ab_d + u.d * (v.abx - v.aby) + (u.abx - u.aby) * v.d;
- w.a_cd = u.a_cd + v.a_cd + u.a * (v.cdx - v.cdy) + (u.cdx - u.cdy) * v.a;
- w.b_cd = u.b_cd + v.b_cd + u.b * (v.cdx - v.cdy) + (u.cdx - u.cdy) * v.b;
-
- w.ac_b = u.ac_b + v.ac_b + u.b * (v.acx - v.acy) + (u.acx - u.acy) * v.b;
- w.ac_d = u.ac_d + v.ac_d + u.d * (v.acx - v.acy) + (u.acx - u.acy) * v.d;
- w.a_bd = u.a_bd + v.a_bd + u.a * (v.bdx - v.bdy) + (u.bdx - u.bdy) * v.a;
- w.c_bd = u.c_bd + v.c_bd + u.c * (v.bdx - v.bdy) + (u.bdx - u.bdy) * v.c;
-
- w.ad_b = u.ad_b + v.ad_b + u.b * (v.adx - v.ady) + (u.adx - u.ady) * v.b;
- w.ad_c = u.ad_c + v.ad_c + u.c * (v.adx - v.ady) + (u.adx - u.ady) * v.c;
- w.a_bc = u.a_bc + v.a_bc + u.a * (v.bcx - v.bcy) + (u.bcx - u.bcy) * v.a;
- w.d_bc = u.d_bc + v.d_bc + u.d * (v.bcx - v.bcy) + (u.bcx - u.bcy) * v.d;
-
- score_t ab_cd = w.ab_cd, ac_bd = w.ac_bd, ad_bc = w.ad_bc;
- w.ab_cd = u.abx * v.cdx - u.aby * v.cdy + v.abx * u.cdx - v.aby * u.cdy
- + u.ab_c * v.d + v.ab_c * u.d
- + u.ab_d * v.c + v.ab_d * u.c
- + u.a_cd * v.b + v.a_cd * u.b
- + u.b_cd * v.a + v.b_cd * u.a;
- w.ac_bd = u.acx * v.bdx - u.acy * v.bdy + v.acx * u.bdx - v.acy * u.bdy
- + u.ac_b * v.d + v.ac_b * u.d
- + u.a_bd * v.c + v.a_bd * u.c
- + u.ac_d * v.b + v.ac_d * u.b
- + u.c_bd * v.a + v.c_bd * u.a;
- w.ad_bc = u.adx * v.bcx - u.ady * v.bcy + v.adx * u.bcx - v.ady * u.bcy
- + u.a_bc * v.d + v.a_bc * u.d
- + u.ad_b * v.c + v.ad_b * u.c
- + u.ad_c * v.b + v.ad_c * u.b
- + u.d_bc * v.a + v.d_bc * u.a;
- return {w.ab_cd - ab_cd, w.ac_bd - ac_bd, w.ad_bc - ad_bc};
- }
-
- vector<vector<int> > leafParent;
- vector<score_t> score1, score2, score3, prod;
- double totalScore1 = 0, totalScore2 = 0, totalScore3 = 0;
- vector<Node> nodes;
- vector<int> color;
-
- Partition(TripartitionInitializer init, int p): leafParent(init.leafParent[p]), nodes(init.nodes[p].size()),
- prod(init.nodes[p].size()), score1(init.nodes[p].size()), score2(init.nodes[p].size()), score3(init.nodes[p].size()), color(init.leafParent[p].size(), -1){
- for (int i = 0; i < nodes.size(); i++){
- nodes[i].up = init.nodes[p][i].up;
- nodes[i].small = init.nodes[p][i].small;
- nodes[i].large = init.nodes[p][i].large;
- nodes[i].weight = init.nodes[p][i].weight;
- }
- }
-
- void update(int x, int i){
- int y = color[i];
- if (x == y) return;
- for (int u: leafParent[i]){
- score_t s1 = 0, s2 = 0, s3 = 0;
- if (y != -1) ((y == 0) ? nodes[u].a : (y == 1) ? nodes[u].b : (y == 2) ? nodes[u].c : nodes[u].d)--;
- if (x != -1) ((x == 0) ? nodes[u].a : (x == 1) ? nodes[u].b : (x == 2) ? nodes[u].c : nodes[u].d)++;
- int w = nodes[u].up;
- while (w != -1){
- array<score_t, 3> s = normal(nodes[w]);
- s1 += s[0]; s2 += s[1]; s3 += s[2];
- u = w;
- w = nodes[u].up;
- }
- double t = score1[u] + score2[u] + score3[u];
- if (t > 0){
- totalScore1 -= score1[u] / t;
- totalScore2 -= score2[u] / t;
- totalScore3 -= score3[u] / t;
- }
- score1[u] += s1; score2[u] += s2; score3[u] += s3;
- t = score1[u] + score2[u] + score3[u];
- if (t > 0){
- totalScore1 += score1[u] / t;
- totalScore2 += score2[u] / t;
- totalScore3 += score3[u] / t;
- }
- }
- color[i] = x;
- }
-
- array<double, 3> score(){
- return {(double) totalScore1, (double) totalScore2, (double) totalScore3};
- }
- };
-
- vector<Partition> parts;
-
- Quadrupartition(const TripartitionInitializer &init){
- for (int p = 0; p < init.nodes.size(); p++) parts.emplace_back(init, p);
- }
-
- void update(int x, int i){
- vector<thread> thrds;
- for (int p = 1; p < parts.size(); p++) thrds.emplace_back(&Partition::update, &parts[p], x, i);
- parts[0].update(x, i);
- for (thread &t: thrds) t.join();
- }
-
- array<double, 3> score(){
- array<double, 3> res;
- res[0] = 0;
- res[1] = 0;
- res[2] = 0;
- for (int p = 0; p < parts.size(); p++){
- auto t = parts[p].score();
- res[0] += t[0];
- res[1] += t[1];
- res[2] += t[2];
- }
- return res;
- }
-};
diff --git a/addons/ASTER/genetreewithhybridweight.hpp b/addons/ASTER/genetreewithhybridweight.hpp
deleted file mode 100644
index b61424147173a9456b32ed6b3f17d205c87c51f1..0000000000000000000000000000000000000000
--- a/addons/ASTER/genetreewithhybridweight.hpp
+++ /dev/null
@@ -1,357 +0,0 @@
-#include<vector>
-#include<array>
-#include<thread>
-
-#define SUPPORT
-
-using namespace std;
-
-struct TripartitionInitializer{
- struct Node{
- int up = -1, small = -1, large = -1;
- score_t weight = 1, length = 1;
- };
-
- vector<vector<Node> > nodes;
- vector<vector<vector<int> > > leafParent;
-};
-
-struct Tripartition{
- struct Partition{
- struct Node{
- score_t x = 0, y = 0, z = 0, tx = 0, ty = 0, tz = 0, q = 0;
- score_t x2a = 0, y2a = 0, z2a = 0, xya = 0, xza = 0, yza = 0;
- score_t x2b = 0, y2b = 0, z2b = 0, xyb = 0, xzb = 0, yzb = 0;
-
- int up = -1, small = -1, large = -1; // -1 for dummy!
- score_t weight = 1, length = 1;
- };
-
- score_t normal(Node& w){
- Node& u = nodes[w.small];
- Node& v = nodes[w.large];
- //u.update(version, totalZ[w.small]);
- //v.update(version, totalZ[w.large]);
-
- w.x = (u.x + v.x) * w.length;
- w.y = (u.y + v.y) * w.length;
- w.z = (u.z + v.z) * w.length;
- w.x2a = u.x2a + v.x2a + u.x * v.x;
- w.y2a = u.y2a + v.y2a + u.y * v.y;
- w.z2a = u.z2a + v.z2a + u.z * v.z;
- w.xya = u.xya + v.xya + u.x * v.y + u.y * v.x;
- w.xza = u.xza + v.xza + u.x * v.z + u.z * v.x;
- w.yza = u.yza + v.yza + u.y * v.z + u.z * v.y;
- w.x2b = (u.x2b + v.x2b + u.x * v.x) * (1 - w.weight);
- w.y2b = (u.y2b + v.y2b + u.y * v.y) * (1 - w.weight);
- w.z2b = (u.z2b + v.z2b + u.z * v.z) * (1 - w.weight);
- w.xyb = (u.xyb + v.xyb + u.x * v.y + u.y * v.x) * (1 - w.weight);
- w.xzb = (u.xzb + v.xzb + u.x * v.z + u.z * v.x) * (1 - w.weight);
- w.yzb = (u.yzb + v.yzb + u.y * v.z + u.z * v.y) * (1 - w.weight);
-
-
- w.tx = (u.tx + v.tx + u.y * (v.z2a - v.z2b) + (u.z2a - u.z2b) * v.y + u.z * (v.y2a - v.y2b) + (u.y2a - u.y2b) * v.z) * w.length;
- w.ty = (u.ty + v.ty + u.x * (v.z2a - v.z2b) + (u.z2a - u.z2b) * v.x + u.z * (v.x2a - v.x2b) + (u.x2a - u.x2b) * v.z) * w.length;
- w.tz = (u.tz + v.tz + u.x * (v.y2a - v.y2b) + (u.y2a - u.y2b) * v.x + u.y * (v.x2a - v.x2b) + (u.x2a - u.x2b) * v.y) * w.length;
- score_t oldQ = w.q;
- w.q = u.x * v.tx + u.y * v.ty + u.z * v.tz + v.x * u.tx + v.y * u.ty + v.z * u.tz
- + u.x2a * v.yza - u.x2b * v.yzb
- + u.y2a * v.xza - u.y2b * v.xzb
- + u.z2a * v.xya - u.z2b * v.xyb;
- return w.q - oldQ;
- }
-
- vector<vector<int> > leafParent;
- score_t totalScore = 0;
- vector<Node> nodes;
- vector<int> color;
-
- Partition(TripartitionInitializer init, int p): leafParent(init.leafParent[p]), nodes(init.nodes[p].size()), color(init.leafParent[p].size(), -1){
- for (int i = 0; i < nodes.size(); i++){
- nodes[i].up = init.nodes[p][i].up;
- nodes[i].small = init.nodes[p][i].small;
- nodes[i].large = init.nodes[p][i].large;
- nodes[i].weight = init.nodes[p][i].weight;
- nodes[i].length = init.nodes[p][i].length;
- }
- }
- /*
- void reset(){
- totalScore = 0;
- version++;
- }
-
- void addTotal(int i){
- for (int w: leafParent[i]){
- totalZ[w].z += totalZ[w].length;
- w = totalZ[w].up;
- while (w != -1){
- Node& u = totalZ[totalZ[w].small];
- Node& v = totalZ[totalZ[w].large];
- totalZ[w].z = (u.z + v.z) * totalZ[w].length;
- totalZ[w].z2a = u.z2a + v.z2a + u.z * v.z;
- totalZ[w].z2b = (u.z2b + v.z2b + u.z * v.z) * (1 - totalZ[w].weight);
- w = totalZ[w].up;
- }
- }
- }
-
- void rmvTotal(int i){
- for (int w: leafParent[i]){
- totalZ[w].z -= totalZ[w].length;
- w = totalZ[w].up;
- while (w != -1){
- Node& u = totalZ[totalZ[w].small];
- Node& v = totalZ[totalZ[w].large];
- totalZ[w].z = (u.z + v.z) * totalZ[w].length;
- totalZ[w].z2a = u.z2a + v.z2a + u.z * v.z;
- totalZ[w].z2b = (u.z2b + v.z2b + u.z * v.z) * (1 - totalZ[w].weight);
- w = totalZ[w].up;
- }
- }
- }
-
- void add(int x, int i){
- for (int u: leafParent[i]){
- nodes[u].update(version, totalZ[u]);
- ((x == 0) ? nodes[u].z : (x == 1) ? nodes[u].x : nodes[u].y) += nodes[u].length;
- int w = nodes[u].up;
- while (w != -1){
- nodes[w].update(version, totalZ[w]);
- totalScore += normal(nodes[w]);
- u = w;
- w = nodes[u].up;
- }
- }
- }
-
- void rmv(int x, int i){
- for (int u: leafParent[i]){
- nodes[u].update(version, totalZ[u]);
- ((x == 0) ? nodes[u].z : (x == 1) ? nodes[u].x : nodes[u].y) -= nodes[u].length;
- int w = nodes[u].up;
- while (w != -1){
- nodes[w].update(version, totalZ[w]);
- totalScore += normal(nodes[w]);
- u = w;
- w = nodes[u].up;
- }
- }
- }
- */
- void update(int x, int i){
- int y = color[i];
- if (x == y) return;
- for (int u: leafParent[i]){
- if (y != -1) ((y == 0) ? nodes[u].z : (y == 1) ? nodes[u].x : nodes[u].y) -= nodes[u].length;
- if (x != -1) ((x == 0) ? nodes[u].z : (x == 1) ? nodes[u].x : nodes[u].y) += nodes[u].length;
- int w = nodes[u].up;
- while (w != -1){
- totalScore += normal(nodes[w]);
- u = w;
- w = nodes[u].up;
- }
- }
- color[i] = x;
- }
-
- score_t score(){
- return totalScore;
- }
- };
-
- vector<Partition> parts;
-
- Tripartition(const TripartitionInitializer &init){
- for (int p = 0; p < init.nodes.size(); p++) parts.emplace_back(init, p);
- }
- /*
- void reset(){
- for (int p = 0; p < parts.size(); p++) parts[p].reset();
- }
-
- void addTotal(int i){
- vector<thread> thrds;
- for (int p = 1; p < parts.size(); p++) thrds.emplace_back(&Partition::addTotal, &parts[p], i);
- parts[0].addTotal(i);
- for (thread &t: thrds) t.join();
- }
-
- void rmvTotal(int i){
- vector<thread> thrds;
- for (int p = 1; p < parts.size(); p++) thrds.emplace_back(&Partition::rmvTotal, &parts[p], i);
- parts[0].rmvTotal(i);
- for (thread &t: thrds) t.join();
- }
-
- void add(int x, int i){
- vector<thread> thrds;
- for (int p = 1; p < parts.size(); p++) thrds.emplace_back(&Partition::add, &parts[p], x, i);
- parts[0].add(x, i);
- for (thread &t: thrds) t.join();
- }
-
- void rmv(int x, int i){
- vector<thread> thrds;
- for (int p = 1; p < parts.size(); p++) thrds.emplace_back(&Partition::rmv, &parts[p], x, i);
- parts[0].rmv(x, i);
- for (thread &t: thrds) t.join();
- }
- */
- void update(int x, int i){
- vector<thread> thrds;
- for (int p = 1; p < parts.size(); p++) thrds.emplace_back(&Partition::update, &parts[p], x, i);
- parts[0].update(x, i);
- for (thread &t: thrds) t.join();
- }
-
- score_t score(){
- score_t res = 0;
- for (int p = 0; p < parts.size(); p++) res += parts[p].score();
- return res;
- }
-};
-
-struct Quadrupartition{
- struct Partition{
- struct Node{
- score_t a = 0, b = 0, c = 0, d = 0;
- score_t ab_c = 0, ab_d = 0, a_cd = 0, b_cd = 0;
- score_t ac_b = 0, a_bd = 0, ac_d = 0, c_bd = 0;
- score_t a_bc = 0, ad_b = 0, ad_c = 0, d_bc = 0;
- score_t abx = 0, acx = 0, adx = 0, bcx = 0, bdx = 0, cdx = 0;
- score_t aby = 0, acy = 0, ady = 0, bcy = 0, bdy = 0, cdy = 0;
- //score_t abx = 0, cdx = 0, aby = 0, cdy = 0;
-
- score_t ab_cd = 0, ac_bd = 0, ad_bc = 0;
-
- int up = -1, small = -1, large = -1; // -1 for dummy!
- score_t weight = 1, length = 1;
- };
-
- array<score_t, 3> normal(Node& w){
- Node& u = nodes[w.small];
- Node& v = nodes[w.large];
-
- w.a = (u.a + v.a) * w.length;
- w.b = (u.b + v.b) * w.length;
- w.c = (u.c + v.c) * w.length;
- w.d = (u.d + v.d) * w.length;
- w.abx = u.abx + v.abx + u.a * v.b + v.a * u.b;
- w.acx = u.acx + v.acx + u.a * v.c + v.a * u.c;
- w.adx = u.adx + v.adx + u.a * v.d + v.a * u.d;
- w.bcx = u.bcx + v.bcx + u.b * v.c + v.b * u.c;
- w.bdx = u.bdx + v.bdx + u.b * v.d + v.b * u.d;
- w.cdx = u.cdx + v.cdx + u.c * v.d + v.c * u.d;
- w.aby = (u.aby + v.aby + u.a * v.b + v.a * u.b) * (1 - w.weight);
- w.acy = (u.acy + v.acy + u.a * v.c + v.a * u.c) * (1 - w.weight);
- w.ady = (u.ady + v.ady + u.a * v.d + v.a * u.d) * (1 - w.weight);
- w.bcy = (u.bcy + v.bcy + u.b * v.c + v.b * u.c) * (1 - w.weight);
- w.bdy = (u.bdy + v.bdy + u.b * v.d + v.b * u.d) * (1 - w.weight);
- w.cdy = (u.cdy + v.cdy + u.c * v.d + v.c * u.d) * (1 - w.weight);
-
- w.ab_c = (u.ab_c + v.ab_c + u.c * (v.abx - v.aby) + (u.abx - u.aby) * v.c) * w.length;
- w.ab_d = (u.ab_d + v.ab_d + u.d * (v.abx - v.aby) + (u.abx - u.aby) * v.d) * w.length;
- w.a_cd = (u.a_cd + v.a_cd + u.a * (v.cdx - v.cdy) + (u.cdx - u.cdy) * v.a) * w.length;
- w.b_cd = (u.b_cd + v.b_cd + u.b * (v.cdx - v.cdy) + (u.cdx - u.cdy) * v.b) * w.length;
-
- w.ac_b = (u.ac_b + v.ac_b + u.b * (v.acx - v.acy) + (u.acx - u.acy) * v.b) * w.length;
- w.ac_d = (u.ac_d + v.ac_d + u.d * (v.acx - v.acy) + (u.acx - u.acy) * v.d) * w.length;
- w.a_bd = (u.a_bd + v.a_bd + u.a * (v.bdx - v.bdy) + (u.bdx - u.bdy) * v.a) * w.length;
- w.c_bd = (u.c_bd + v.c_bd + u.c * (v.bdx - v.bdy) + (u.bdx - u.bdy) * v.c) * w.length;
-
- w.ad_b = (u.ad_b + v.ad_b + u.b * (v.adx - v.ady) + (u.adx - u.ady) * v.b) * w.length;
- w.ad_c = (u.ad_c + v.ad_c + u.c * (v.adx - v.ady) + (u.adx - u.ady) * v.c) * w.length;
- w.a_bc = (u.a_bc + v.a_bc + u.a * (v.bcx - v.bcy) + (u.bcx - u.bcy) * v.a) * w.length;
- w.d_bc = (u.d_bc + v.d_bc + u.d * (v.bcx - v.bcy) + (u.bcx - u.bcy) * v.d) * w.length;
-
- score_t ab_cd = w.ab_cd, ac_bd = w.ac_bd, ad_bc = w.ad_bc;
- w.ab_cd = u.abx * v.cdx - u.aby * v.cdy + v.abx * u.cdx - v.aby * u.cdy
- + u.ab_c * v.d + v.ab_c * u.d
- + u.ab_d * v.c + v.ab_d * u.c
- + u.a_cd * v.b + v.a_cd * u.b
- + u.b_cd * v.a + v.b_cd * u.a;
- w.ac_bd = u.acx * v.bdx - u.acy * v.bdy + v.acx * u.bdx - v.acy * u.bdy
- + u.ac_b * v.d + v.ac_b * u.d
- + u.a_bd * v.c + v.a_bd * u.c
- + u.ac_d * v.b + v.ac_d * u.b
- + u.c_bd * v.a + v.c_bd * u.a;
- w.ad_bc = u.adx * v.bcx - u.ady * v.bcy + v.adx * u.bcx - v.ady * u.bcy
- + u.a_bc * v.d + v.a_bc * u.d
- + u.ad_b * v.c + v.ad_b * u.c
- + u.ad_c * v.b + v.ad_c * u.b
- + u.d_bc * v.a + v.d_bc * u.a;
- return {w.ab_cd - ab_cd, w.ac_bd - ac_bd, w.ad_bc - ad_bc};
- }
-
- vector<vector<int> > leafParent;
- score_t totalScore1 = 0, totalScore2 = 0, totalScore3 = 0, cnt[4] = {};
- vector<Node> nodes;
- vector<int> color;
-
- Partition(TripartitionInitializer init, int p): leafParent(init.leafParent[p]), nodes(init.nodes[p].size()), color(init.leafParent[p].size(), -1){
- for (int i = 0; i < nodes.size(); i++){
- nodes[i].up = init.nodes[p][i].up;
- nodes[i].small = init.nodes[p][i].small;
- nodes[i].large = init.nodes[p][i].large;
- nodes[i].weight = init.nodes[p][i].weight;
- nodes[i].length = init.nodes[p][i].length;
- }
- }
-
- void update(int x, int i){
- int y = color[i];
- if (x == y) return;
- if (y != -1) cnt[y]--;
- if (x != -1) cnt[x]++;
- for (int u: leafParent[i]){
- score_t s1 = 0, s2 = 0, s3 = 0;
- if (y != -1) ((y == 0) ? nodes[u].a : (y == 1) ? nodes[u].b : (y == 2) ? nodes[u].c : nodes[u].d) -= nodes[u].length;
- if (x != -1) ((x == 0) ? nodes[u].a : (x == 1) ? nodes[u].b : (x == 2) ? nodes[u].c : nodes[u].d) += nodes[u].length;
- int w = nodes[u].up;
- while (w != -1){
- array<score_t, 3> s = normal(nodes[w]);
- s1 += s[0]; s2 += s[1]; s3 += s[2];
- u = w;
- w = nodes[u].up;
- }
- totalScore1 += s1;
- totalScore2 += s2;
- totalScore3 += s3;
- }
- color[i] = x;
- }
-
- array<double, 3> score(){
- double prod = cnt[0] * cnt[1] * cnt[2] * cnt[3];
- return {totalScore1 / prod, totalScore2 / prod, totalScore3 / prod};
- }
- };
-
- vector<Partition> parts;
-
- Quadrupartition(const TripartitionInitializer &init){
- for (int p = 0; p < init.nodes.size(); p++) parts.emplace_back(init, p);
- }
-
- void update(int x, int i){
- vector<thread> thrds;
- for (int p = 1; p < parts.size(); p++) thrds.emplace_back(&Partition::update, &parts[p], x, i);
- parts[0].update(x, i);
- for (thread &t: thrds) t.join();
- }
-
- array<double, 3> score(){
- array<double, 3> res;
- res[0] = 0;
- res[1] = 0;
- res[2] = 0;
- for (int p = 0; p < parts.size(); p++){
- auto t = parts[p].score();
- res[0] += t[0];
- res[1] += t[1];
- res[2] += t[2];
- }
- return res;
- }
-};
diff --git a/addons/ASTER/genetreewithlength.hpp b/addons/ASTER/genetreewithlength.hpp
deleted file mode 100644
index 52cf42b22675862bd603dfc95341d06a5eddbb02..0000000000000000000000000000000000000000
--- a/addons/ASTER/genetreewithlength.hpp
+++ /dev/null
@@ -1,211 +0,0 @@
-#include<vector>
-#include<array>
-#include<thread>
-
-using namespace std;
-
-struct TripartitionInitializer{
- struct Node{
- int up = -1, small = -1, large = -1;
- score_t weight = 1;
- };
-
- vector<vector<Node> > nodes;
- vector<vector<vector<int> > > leafParent;
-};
-
-struct Tripartition{
- struct Partition{
- struct Node{
- score_t x = 0, y = 0, z = 0, tx = 0, ty = 0, tz = 0, q = 0;
- score_t x2a = 0, y2a = 0, z2a = 0, xya = 0, xza = 0, yza = 0;
- score_t x2b = 0, y2b = 0, z2b = 0, xyb = 0, xzb = 0, yzb = 0;
-
- int version = 0, up = -1, small = -1, large = -1; // -1 for dummy!
- score_t weight = 1;
-
- };
-
- score_t normal(Node& w){
- Node& u = nodes[w.small];
- Node& v = nodes[w.large];
- //u.update(version, totalZ[w.small]);
- //v.update(version, totalZ[w.large]);
-
- w.x = (u.x + v.x) * w.weight;
- w.y = (u.y + v.y) * w.weight;
- w.z = (u.z + v.z) * w.weight;
- w.x2a = u.x2a + v.x2a + u.x * v.x;
- w.y2a = u.y2a + v.y2a + u.y * v.y;
- w.z2a = u.z2a + v.z2a + u.z * v.z;
- w.xya = u.xya + v.xya + u.x * v.y + u.y * v.x;
- w.xza = u.xza + v.xza + u.x * v.z + u.z * v.x;
- w.yza = u.yza + v.yza + u.y * v.z + u.z * v.y;
- w.x2b = (u.x2b + v.x2b + u.x * v.x) * w.weight * w.weight;
- w.y2b = (u.y2b + v.y2b + u.y * v.y) * w.weight * w.weight;
- w.z2b = (u.z2b + v.z2b + u.z * v.z) * w.weight * w.weight;
- w.xyb = (u.xyb + v.xyb + u.x * v.y + u.y * v.x) * w.weight * w.weight;
- w.xzb = (u.xzb + v.xzb + u.x * v.z + u.z * v.x) * w.weight * w.weight;
- w.yzb = (u.yzb + v.yzb + u.y * v.z + u.z * v.y) * w.weight * w.weight;
-
-
- w.tx = (u.tx + v.tx + u.y * (v.z2a - v.z2b) + (u.z2a - u.z2b) * v.y + u.z * (v.y2a - v.y2b) + (u.y2a - u.y2b) * v.z) * w.weight;
- w.ty = (u.ty + v.ty + u.x * (v.z2a - v.z2b) + (u.z2a - u.z2b) * v.x + u.z * (v.x2a - v.x2b) + (u.x2a - u.x2b) * v.z) * w.weight;
- w.tz = (u.tz + v.tz + u.x * (v.y2a - v.y2b) + (u.y2a - u.y2b) * v.x + u.y * (v.x2a - v.x2b) + (u.x2a - u.x2b) * v.y) * w.weight;
- score_t oldQ = w.q;
- w.q = u.x * v.tx + u.y * v.ty + u.z * v.tz + v.x * u.tx + v.y * u.ty + v.z * u.tz
- + u.x2a * v.yza - u.x2b * v.yzb
- + u.y2a * v.xza - u.y2b * v.xzb
- + u.z2a * v.xya - u.z2b * v.xyb;
- return w.q - oldQ;
- }
-
- vector<vector<int> > leafParent;
- score_t totalScore = 0;
- vector<Node> nodes;
- vector<int> color;
-
- Partition(TripartitionInitializer init, int p): leafParent(init.leafParent[p]), nodes(init.nodes[p].size()), color(init.leafParent[p].size(), -1){
- for (int i = 0; i < nodes.size(); i++){
- nodes[i].up = init.nodes[p][i].up;
- nodes[i].small = init.nodes[p][i].small;
- nodes[i].large = init.nodes[p][i].large;
- nodes[i].weight = init.nodes[p][i].weight;
- }
- }
- /*
- void reset(){
- totalScore = 0;
- version++;
- }
-
- void addTotal(int i){
- for (int w: leafParent[i]){
- totalZ[w].z += totalZ[w].weight;
- w = totalZ[w].up;
- while (w != -1){
- Node& u = totalZ[totalZ[w].small];
- Node& v = totalZ[totalZ[w].large];
- totalZ[w].z = (u.z + v.z) * totalZ[w].weight;
- totalZ[w].z2a = u.z2a + v.z2a + u.z * v.z;
- totalZ[w].z2b = (u.z2b + v.z2b + u.z * v.z) * totalZ[w].weight * totalZ[w].weight;
- w = totalZ[w].up;
- }
- }
- }
-
- void rmvTotal(int i){
- for (int w: leafParent[i]){
- totalZ[w].z -= totalZ[w].weight;
- w = totalZ[w].up;
- while (w != -1){
- Node& u = totalZ[totalZ[w].small];
- Node& v = totalZ[totalZ[w].large];
- totalZ[w].z = (u.z + v.z) * totalZ[w].weight;
- totalZ[w].z2a = u.z2a + v.z2a + u.z * v.z;
- totalZ[w].z2b = (u.z2b + v.z2b + u.z * v.z) * totalZ[w].weight * totalZ[w].weight;
- w = totalZ[w].up;
- }
- }
- }
-
- void add(int x, int i){
- for (int u: leafParent[i]){
- nodes[u].update(version, totalZ[u]);
- if (x == 0) nodes[u].z += nodes[u].weight; else if (x == 1) nodes[u].x += nodes[u].weight; else nodes[u].y += nodes[u].weight;
- int w = nodes[u].up;
- while (w != -1){
- nodes[w].update(version, totalZ[w]);
- totalScore += normal(nodes[w]);
- u = w;
- w = nodes[u].up;
- }
- }
- }
-
- void rmv(int x, int i){
- for (int u: leafParent[i]){
- nodes[u].update(version, totalZ[u]);
- if (x == 0) nodes[u].z -= nodes[u].weight; else if (x == 1) nodes[u].x -= nodes[u].weight; else nodes[u].y -= nodes[u].weight;
- int w = nodes[u].up;
- while (w != -1){
- nodes[w].update(version, totalZ[w]);
- totalScore += normal(nodes[w]);
- u = w;
- w = nodes[u].up;
- }
- }
- }
- */
- void update(int x, int i){
- int y = color[i];
- if (x == y) return;
- for (int u: leafParent[i]){
- if (y != -1) ((y == 0) ? nodes[u].z : (y == 1) ? nodes[u].x : nodes[u].y) -= nodes[u].weight;
- if (x != -1) ((x == 0) ? nodes[u].z : (x == 1) ? nodes[u].x : nodes[u].y) += nodes[u].weight;
- int w = nodes[u].up;
- while (w != -1){
- totalScore += normal(nodes[w]);
- u = w;
- w = nodes[u].up;
- }
- }
- color[i] = x;
- }
-
- score_t score(){
- return totalScore;
- }
- };
-
- vector<Partition> parts;
-
- Tripartition(const TripartitionInitializer &init){
- for (int p = 0; p < init.nodes.size(); p++) parts.emplace_back(init, p);
- }
- /*
- void reset(){
- for (int p = 0; p < parts.size(); p++) parts[p].reset();
- }
-
- void addTotal(int i){
- vector<thread> thrds;
- for (int p = 1; p < parts.size(); p++) thrds.emplace_back(&Partition::addTotal, &parts[p], i);
- parts[0].addTotal(i);
- for (thread &t: thrds) t.join();
- }
-
- void rmvTotal(int i){
- vector<thread> thrds;
- for (int p = 1; p < parts.size(); p++) thrds.emplace_back(&Partition::rmvTotal, &parts[p], i);
- parts[0].rmvTotal(i);
- for (thread &t: thrds) t.join();
- }
-
- void add(int x, int i){
- vector<thread> thrds;
- for (int p = 1; p < parts.size(); p++) thrds.emplace_back(&Partition::add, &parts[p], x, i);
- parts[0].add(x, i);
- for (thread &t: thrds) t.join();
- }
-
- void rmv(int x, int i){
- vector<thread> thrds;
- for (int p = 1; p < parts.size(); p++) thrds.emplace_back(&Partition::rmv, &parts[p], x, i);
- parts[0].rmv(x, i);
- for (thread &t: thrds) t.join();
- }
- */
- void update(int x, int i){
- vector<thread> thrds;
- for (int p = 1; p < parts.size(); p++) thrds.emplace_back(&Partition::update, &parts[p], x, i);
- parts[0].update(x, i);
- for (thread &t: thrds) t.join();
- }
-
- score_t score(){
- score_t res = 0;
- for (int p = 0; p < parts.size(); p++) res += parts[p].score();
- return res;
- }
-};
diff --git a/addons/ASTER/genetreewithweight.hpp b/addons/ASTER/genetreewithweight.hpp
deleted file mode 100644
index 823aeb0f5e00e7451e39c37e349b6b9310c8f509..0000000000000000000000000000000000000000
--- a/addons/ASTER/genetreewithweight.hpp
+++ /dev/null
@@ -1,367 +0,0 @@
-#include<vector>
-#include<array>
-#include<thread>
-
-#define SUPPORT
-
-using namespace std;
-
-struct TripartitionInitializer{
- struct Node{
- int up = -1, small = -1, large = -1;
- score_t weight = 1;
- };
-
- vector<vector<Node> > nodes;
- vector<vector<vector<int> > > leafParent;
-};
-
-struct Tripartition{
- struct Partition{
- struct Node{
- score_t x = 0, y = 0, z = 0, tx = 0, ty = 0, tz = 0, q = 0;
- score_t x2a = 0, y2a = 0, z2a = 0, xya = 0, xza = 0, yza = 0;
- score_t x2b = 0, y2b = 0, z2b = 0, xyb = 0, xzb = 0, yzb = 0;
-
- int up = -1, small = -1, large = -1; // -1 for dummy!
- score_t weight = 1;
-
- };
-
- score_t normal(Node& w){
- Node& u = nodes[w.small];
- Node& v = nodes[w.large];
- //u.update(version, totalZ[w.small]);
- //v.update(version, totalZ[w.large]);
-
- w.x = u.x + v.x;
- w.y = u.y + v.y;
- w.z = u.z + v.z;
- w.x2a = u.x2a + v.x2a + u.x * v.x;
- w.y2a = u.y2a + v.y2a + u.y * v.y;
- w.z2a = u.z2a + v.z2a + u.z * v.z;
- w.xya = u.xya + v.xya + u.x * v.y + u.y * v.x;
- w.xza = u.xza + v.xza + u.x * v.z + u.z * v.x;
- w.yza = u.yza + v.yza + u.y * v.z + u.z * v.y;
- w.x2b = (u.x2b + v.x2b + u.x * v.x) * (1 - w.weight);
- w.y2b = (u.y2b + v.y2b + u.y * v.y) * (1 - w.weight);
- w.z2b = (u.z2b + v.z2b + u.z * v.z) * (1 - w.weight);
- w.xyb = (u.xyb + v.xyb + u.x * v.y + u.y * v.x) * (1 - w.weight);
- w.xzb = (u.xzb + v.xzb + u.x * v.z + u.z * v.x) * (1 - w.weight);
- w.yzb = (u.yzb + v.yzb + u.y * v.z + u.z * v.y) * (1 - w.weight);
-
-
- w.tx = u.tx + v.tx + u.y * (v.z2a - v.z2b) + (u.z2a - u.z2b) * v.y + u.z * (v.y2a - v.y2b) + (u.y2a - u.y2b) * v.z;
- w.ty = u.ty + v.ty + u.x * (v.z2a - v.z2b) + (u.z2a - u.z2b) * v.x + u.z * (v.x2a - v.x2b) + (u.x2a - u.x2b) * v.z;
- w.tz = u.tz + v.tz + u.x * (v.y2a - v.y2b) + (u.y2a - u.y2b) * v.x + u.y * (v.x2a - v.x2b) + (u.x2a - u.x2b) * v.y;
- score_t oldQ = w.q;
- w.q = u.x * v.tx + u.y * v.ty + u.z * v.tz + v.x * u.tx + v.y * u.ty + v.z * u.tz
- + u.x2a * v.yza - u.x2b * v.yzb
- + u.y2a * v.xza - u.y2b * v.xzb
- + u.z2a * v.xya - u.z2b * v.xyb;
- return w.q - oldQ;
- }
-
- vector<vector<int> > leafParent;
- score_t totalScore = 0;
- vector<Node> nodes;
- vector<int> color;
-
- Partition(TripartitionInitializer init, int p): leafParent(init.leafParent[p]), nodes(init.nodes[p].size()), color(init.leafParent[p].size(), -1){
- for (int i = 0; i < nodes.size(); i++){
- nodes[i].up = init.nodes[p][i].up;
- nodes[i].small = init.nodes[p][i].small;
- nodes[i].large = init.nodes[p][i].large;
- nodes[i].weight = init.nodes[p][i].weight;
- }
- }
- /*
- void reset(){
- totalScore = 0;
- version++;
- }
-
- void addTotal(int i){
- for (int w: leafParent[i]){
- totalZ[w].z++;
- w = totalZ[w].up;
- while (w != -1){
- Node& u = totalZ[totalZ[w].small];
- Node& v = totalZ[totalZ[w].large];
- totalZ[w].z = u.z + v.z;
- totalZ[w].z2a = u.z2a + v.z2a + u.z * v.z;
- totalZ[w].z2b = (u.z2b + v.z2b + u.z * v.z) * (1 - totalZ[w].weight);
- w = totalZ[w].up;
- }
- }
- }
-
- void rmvTotal(int i){
- for (int w: leafParent[i]){
- totalZ[w].z--;
- w = totalZ[w].up;
- while (w != -1){
- Node& u = totalZ[totalZ[w].small];
- Node& v = totalZ[totalZ[w].large];
- totalZ[w].z = u.z + v.z;
- totalZ[w].z2a = u.z2a + v.z2a + u.z * v.z;
- totalZ[w].z2b = (u.z2b + v.z2b + u.z * v.z) * (1 - totalZ[w].weight);
- w = totalZ[w].up;
- }
- }
- }
-
- void add(int x, int i){
- for (int u: leafParent[i]){
- nodes[u].update(version, totalZ[u]);
- ((x == 0) ? nodes[u].z : (x == 1) ? nodes[u].x : nodes[u].y)++;
- int w = nodes[u].up;
- while (w != -1){
- nodes[w].update(version, totalZ[w]);
- totalScore += normal(nodes[w]);
- u = w;
- w = nodes[u].up;
- }
- }
- }
-
- void rmv(int x, int i){
- for (int u: leafParent[i]){
- nodes[u].update(version, totalZ[u]);
- ((x == 0) ? nodes[u].z : (x == 1) ? nodes[u].x : nodes[u].y)--;
- int w = nodes[u].up;
- while (w != -1){
- nodes[w].update(version, totalZ[w]);
- totalScore += normal(nodes[w]);
- u = w;
- w = nodes[u].up;
- }
- }
- }
- */
- void update(int x, int i){
- int y = color[i];
- if (x == y) return;
- for (int u: leafParent[i]){
- if (y != -1) ((y == 0) ? nodes[u].z : (y == 1) ? nodes[u].x : nodes[u].y)--;
- if (x != -1) ((x == 0) ? nodes[u].z : (x == 1) ? nodes[u].x : nodes[u].y)++;
- int w = nodes[u].up;
- while (w != -1){
- totalScore += normal(nodes[w]);
- u = w;
- w = nodes[u].up;
- }
- }
- color[i] = x;
- }
-
- score_t score(){
- return totalScore;
- }
- };
-
- vector<Partition> parts;
-
- Tripartition(const TripartitionInitializer &init){
- for (int p = 0; p < init.nodes.size(); p++) parts.emplace_back(init, p);
- }
- /*
- void reset(){
- for (int p = 0; p < parts.size(); p++) parts[p].reset();
- }
-
- void addTotal(int i){
- vector<thread> thrds;
- for (int p = 1; p < parts.size(); p++) thrds.emplace_back(&Partition::addTotal, &parts[p], i);
- parts[0].addTotal(i);
- for (thread &t: thrds) t.join();
- }
-
- void rmvTotal(int i){
- vector<thread> thrds;
- for (int p = 1; p < parts.size(); p++) thrds.emplace_back(&Partition::rmvTotal, &parts[p], i);
- parts[0].rmvTotal(i);
- for (thread &t: thrds) t.join();
- }
-
- void add(int x, int i){
- vector<thread> thrds;
- for (int p = 1; p < parts.size(); p++) thrds.emplace_back(&Partition::add, &parts[p], x, i);
- parts[0].add(x, i);
- for (thread &t: thrds) t.join();
- }
-
- void rmv(int x, int i){
- vector<thread> thrds;
- for (int p = 1; p < parts.size(); p++) thrds.emplace_back(&Partition::rmv, &parts[p], x, i);
- parts[0].rmv(x, i);
- for (thread &t: thrds) t.join();
- }
- */
-
- void update(int x, int i){
- vector<thread> thrds;
- for (int p = 1; p < parts.size(); p++) thrds.emplace_back(&Partition::update, &parts[p], x, i);
- parts[0].update(x, i);
- for (thread &t: thrds) t.join();
- }
-
- score_t score(){
- score_t res = 0;
- for (int p = 0; p < parts.size(); p++) res += parts[p].score();
- return res;
- }
-};
-
-struct Quadrupartition{
- struct Partition{
- struct Node{
- score_t a = 0, b = 0, c = 0, d = 0;
- score_t ab_c = 0, ab_d = 0, a_cd = 0, b_cd = 0;
- score_t ac_b = 0, a_bd = 0, ac_d = 0, c_bd = 0;
- score_t a_bc = 0, ad_b = 0, ad_c = 0, d_bc = 0;
- score_t abx = 0, acx = 0, adx = 0, bcx = 0, bdx = 0, cdx = 0;
- score_t aby = 0, acy = 0, ady = 0, bcy = 0, bdy = 0, cdy = 0;
- //score_t abx = 0, cdx = 0, aby = 0, cdy = 0;
-
- score_t ab_cd = 0, ac_bd = 0, ad_bc = 0;
-
- int up = -1, small = -1, large = -1; // -1 for dummy!
- score_t weight = 1;
- };
-
- array<score_t, 3> normal(Node& w){
- Node& u = nodes[w.small];
- Node& v = nodes[w.large];
-
- w.a = u.a + v.a;
- w.b = u.b + v.b;
- w.c = u.c + v.c;
- w.d = u.d + v.d;
- w.abx = u.abx + v.abx + u.a * v.b + v.a * u.b;
- w.acx = u.acx + v.acx + u.a * v.c + v.a * u.c;
- w.adx = u.adx + v.adx + u.a * v.d + v.a * u.d;
- w.bcx = u.bcx + v.bcx + u.b * v.c + v.b * u.c;
- w.bdx = u.bdx + v.bdx + u.b * v.d + v.b * u.d;
- w.cdx = u.cdx + v.cdx + u.c * v.d + v.c * u.d;
- w.aby = (u.aby + v.aby + u.a * v.b + v.a * u.b) * (1 - w.weight);
- w.acy = (u.acy + v.acy + u.a * v.c + v.a * u.c) * (1 - w.weight);
- w.ady = (u.ady + v.ady + u.a * v.d + v.a * u.d) * (1 - w.weight);
- w.bcy = (u.bcy + v.bcy + u.b * v.c + v.b * u.c) * (1 - w.weight);
- w.bdy = (u.bdy + v.bdy + u.b * v.d + v.b * u.d) * (1 - w.weight);
- w.cdy = (u.cdy + v.cdy + u.c * v.d + v.c * u.d) * (1 - w.weight);
-
- w.ab_c = u.ab_c + v.ab_c + u.c * (v.abx - v.aby) + (u.abx - u.aby) * v.c;
- w.ab_d = u.ab_d + v.ab_d + u.d * (v.abx - v.aby) + (u.abx - u.aby) * v.d;
- w.a_cd = u.a_cd + v.a_cd + u.a * (v.cdx - v.cdy) + (u.cdx - u.cdy) * v.a;
- w.b_cd = u.b_cd + v.b_cd + u.b * (v.cdx - v.cdy) + (u.cdx - u.cdy) * v.b;
-
- w.ac_b = u.ac_b + v.ac_b + u.b * (v.acx - v.acy) + (u.acx - u.acy) * v.b;
- w.ac_d = u.ac_d + v.ac_d + u.d * (v.acx - v.acy) + (u.acx - u.acy) * v.d;
- w.a_bd = u.a_bd + v.a_bd + u.a * (v.bdx - v.bdy) + (u.bdx - u.bdy) * v.a;
- w.c_bd = u.c_bd + v.c_bd + u.c * (v.bdx - v.bdy) + (u.bdx - u.bdy) * v.c;
-
- w.ad_b = u.ad_b + v.ad_b + u.b * (v.adx - v.ady) + (u.adx - u.ady) * v.b;
- w.ad_c = u.ad_c + v.ad_c + u.c * (v.adx - v.ady) + (u.adx - u.ady) * v.c;
- w.a_bc = u.a_bc + v.a_bc + u.a * (v.bcx - v.bcy) + (u.bcx - u.bcy) * v.a;
- w.d_bc = u.d_bc + v.d_bc + u.d * (v.bcx - v.bcy) + (u.bcx - u.bcy) * v.d;
-
- score_t ab_cd = w.ab_cd, ac_bd = w.ac_bd, ad_bc = w.ad_bc;
- w.ab_cd = u.abx * v.cdx - u.aby * v.cdy + v.abx * u.cdx - v.aby * u.cdy
- + u.ab_c * v.d + v.ab_c * u.d
- + u.ab_d * v.c + v.ab_d * u.c
- + u.a_cd * v.b + v.a_cd * u.b
- + u.b_cd * v.a + v.b_cd * u.a;
- w.ac_bd = u.acx * v.bdx - u.acy * v.bdy + v.acx * u.bdx - v.acy * u.bdy
- + u.ac_b * v.d + v.ac_b * u.d
- + u.a_bd * v.c + v.a_bd * u.c
- + u.ac_d * v.b + v.ac_d * u.b
- + u.c_bd * v.a + v.c_bd * u.a;
- w.ad_bc = u.adx * v.bcx - u.ady * v.bcy + v.adx * u.bcx - v.ady * u.bcy
- + u.a_bc * v.d + v.a_bc * u.d
- + u.ad_b * v.c + v.ad_b * u.c
- + u.ad_c * v.b + v.ad_c * u.b
- + u.d_bc * v.a + v.d_bc * u.a;
- return {w.ab_cd - ab_cd, w.ac_bd - ac_bd, w.ad_bc - ad_bc};
- }
-
- vector<vector<int> > leafParent;
- vector<score_t> score1, score2, score3, prod;
- score_t totalScore1 = 0, totalScore2 = 0, totalScore3 = 0;
- vector<Node> nodes;
- vector<int> color;
-
- Partition(TripartitionInitializer init, int p): leafParent(init.leafParent[p]), nodes(init.nodes[p].size()),
- prod(init.nodes[p].size()), score1(init.nodes[p].size()), score2(init.nodes[p].size()), score3(init.nodes[p].size()), color(init.leafParent[p].size(), -1){
- for (int i = 0; i < nodes.size(); i++){
- nodes[i].up = init.nodes[p][i].up;
- nodes[i].small = init.nodes[p][i].small;
- nodes[i].large = init.nodes[p][i].large;
- nodes[i].weight = init.nodes[p][i].weight;
- }
- }
-
- void update(int x, int i){
- int y = color[i];
- if (x == y) return;
- for (int u: leafParent[i]){
- score_t s1 = 0, s2 = 0, s3 = 0;
- if (y != -1) ((y == 0) ? nodes[u].a : (y == 1) ? nodes[u].b : (y == 2) ? nodes[u].c : nodes[u].d)--;
- if (x != -1) ((x == 0) ? nodes[u].a : (x == 1) ? nodes[u].b : (x == 2) ? nodes[u].c : nodes[u].d)++;
- int w = nodes[u].up;
- while (w != -1){
- array<score_t, 3> s = normal(nodes[w]);
- s1 += s[0]; s2 += s[1]; s3 += s[2];
- u = w;
- w = nodes[u].up;
- }
- score_t t = score1[u] + score2[u] + score3[u];
- if (prod[u] > 1e-8){
- totalScore1 -= (score1[u] + (prod[u] - t) / 3) / prod[u];
- totalScore2 -= (score2[u] + (prod[u] - t) / 3) / prod[u];
- totalScore3 -= (score3[u] + (prod[u] - t) / 3) / prod[u];
- }
- score1[u] += s1; score2[u] += s2; score3[u] += s3;
- prod[u] = nodes[u].a * nodes[u].b * nodes[u].c * nodes[u].d;
- t = score1[u] + score2[u] + score3[u];
- if (prod[u] > 1e-8){
- totalScore1 += (score1[u] + (prod[u] - t) / 3) / prod[u];
- totalScore2 += (score2[u] + (prod[u] - t) / 3) / prod[u];
- totalScore3 += (score3[u] + (prod[u] - t) / 3) / prod[u];
- }
- }
- color[i] = x;
- }
-
- array<double, 3> score(){
- return {(double) totalScore1, (double) totalScore2, (double) totalScore3};
- }
- };
-
- vector<Partition> parts;
-
- Quadrupartition(const TripartitionInitializer &init){
- for (int p = 0; p < init.nodes.size(); p++) parts.emplace_back(init, p);
- }
-
- void update(int x, int i){
- vector<thread> thrds;
- for (int p = 1; p < parts.size(); p++) thrds.emplace_back(&Partition::update, &parts[p], x, i);
- parts[0].update(x, i);
- for (thread &t: thrds) t.join();
- }
-
- array<double, 3> score(){
- array<double, 3> res;
- res[0] = 0;
- res[1] = 0;
- res[2] = 0;
- for (int p = 0; p < parts.size(); p++){
- auto t = parts[p].score();
- res[0] += t[0];
- res[1] += t[1];
- res[2] += t[2];
- }
- return res;
- }
-};
diff --git a/addons/ASTER/incbeta.c b/addons/ASTER/incbeta.c
deleted file mode 100644
index 7a01dd78a8cdbdb5b1ebd3ec62b41aab81d687ae..0000000000000000000000000000000000000000
--- a/addons/ASTER/incbeta.c
+++ /dev/null
@@ -1,79 +0,0 @@
-/*
- * zlib License
- *
- * Regularized Incomplete Beta Function
- *
- * Copyright (c) 2016, 2017 Lewis Van Winkle
- * http://CodePlea.com
- *
- * This software is provided 'as-is', without any express or implied
- * warranty. In no event will the authors be held liable for any damages
- * arising from the use of this software.
- *
- * Permission is granted to anyone to use this software for any purpose,
- * including commercial applications, and to alter it and redistribute it
- * freely, subject to the following restrictions:
- *
- * 1. The origin of this software must not be misrepresented; you must not
- * claim that you wrote the original software. If you use this software
- * in a product, an acknowledgement in the product documentation would be
- * appreciated but is not required.
- * 2. Altered source versions must be plainly marked as such, and must not be
- * misrepresented as being the original software.
- * 3. This notice may not be removed or altered from any source distribution.
- */
-
-
-#include <math.h>
-
-#define STOP 1.0e-8
-#define TINY 1.0e-30
-
-double incbeta(double a, double b, double x) {
- if (x < 0.0 || x > 1.0) return 1.0/0.0;
-
- /*The continued fraction converges nicely for x < (a+1)/(a+b+2)*/
- if (x > (a+1.0)/(a+b+2.0)) {
- return (1.0-incbeta(b,a,1.0-x)); /*Use the fact that beta is symmetrical.*/
- }
-
- /*Find the first part before the continued fraction.*/
- const double lbeta_ab = lgamma(a)+lgamma(b)-lgamma(a+b);
- const double front = exp(log(x)*a+log(1.0-x)*b-lbeta_ab) / a;
-
- /*Use Lentz's algorithm to evaluate the continued fraction.*/
- double f = 1.0, c = 1.0, d = 0.0;
-
- int i, m;
- for (i = 0; i <= 200; ++i) {
- m = i/2;
-
- double numerator;
- if (i == 0) {
- numerator = 1.0; /*First numerator is 1.0.*/
- } else if (i % 2 == 0) {
- numerator = (m*(b-m)*x)/((a+2.0*m-1.0)*(a+2.0*m)); /*Even term.*/
- } else {
- numerator = -((a+m)*(a+b+m)*x)/((a+2.0*m)*(a+2.0*m+1)); /*Odd term.*/
- }
-
- /*Do an iteration of Lentz's algorithm.*/
- d = 1.0 + numerator * d;
- if (fabs(d) < TINY) d = TINY;
- d = 1.0 / d;
-
- c = 1.0 + numerator / c;
- if (fabs(c) < TINY) c = TINY;
-
- const double cd = c*d;
- f *= cd;
-
- /*Check for stop.*/
- if (fabs(1.0-cd) < STOP) {
- return front * (f-1.0);
- }
- }
-
- return 1.0/0.0; /*Needed more loops, did not converge.*/
-}
-
diff --git a/addons/ASTER/multitree.hpp b/addons/ASTER/multitree.hpp
deleted file mode 100644
index 760493b5a7e40072b1db2c30e19b65d614d6eb4d..0000000000000000000000000000000000000000
--- a/addons/ASTER/multitree.hpp
+++ /dev/null
@@ -1,392 +0,0 @@
-#include<vector>
-#include<array>
-#include<thread>
-
-#define SUPPORT
-
-using namespace std;
-
-score_t NUM_EQ_CLASSES = 0;
-
-struct TripartitionInitializer{
- struct Node{
- int up = -1, small = -1, large = -1;
- bool dup = false;
- };
-
- vector<vector<Node> > nodes;
- vector<vector<vector<int> > > leafParent;
-};
-
-struct Tripartition{
- struct Partition{
- struct Node{
- score_t x = 0, y = 0, z = 0, tx = 0, ty = 0, tz = 0, q = 0;
- int up = -1, small = -1, large = -1; // -1 for dummy!
- bool dup = false;
- };
-
- score_t normal(Node& w){
- Node& u = nodes[w.small];
- Node& v = nodes[w.large];
- w.tx = u.tx + v.tx + u.y * v.z * (u.y + v.z - 2) + u.z * v.y * (u.z + v.y - 2);
- w.ty = u.ty + v.ty + u.x * v.z * (u.x + v.z - 2) + u.z * v.x * (u.z + v.x - 2);
- w.tz = u.tz + v.tz + u.x * v.y * (u.x + v.y - 2) + u.y * v.x * (u.y + v.x - 2);
- score_t oldQ = w.q;
- w.q = u.x * v.tx + u.y * v.ty + u.z * v.tz + v.x * u.tx + v.y * u.ty + v.z * u.tz
- + (u.x - 1) * u.x * v.y * v.z //+ (v.x - 1) * v.x * u.y * u.z
- + (u.y - 1) * u.y * v.x * v.z //+ (v.y - 1) * v.y * u.x * u.z
- + (u.z - 1) * u.z * v.x * v.y //+ (v.z - 1) * v.z * u.x * u.y
- ;
- return w.q - oldQ;
- }
-
- void special(Node& w){
- Node& u = nodes[w.small];
- Node& v = nodes[w.large];
- w.tx = u.tx + v.tx;
- w.ty = u.ty + v.ty;
- w.tz = u.tz + v.tz;
- }
-
- vector<vector<int> > leafParent;
- score_t totalScore = 0;
- vector<Node> nodes;
- vector<int> color;
-
- Partition(const TripartitionInitializer &init, int p): leafParent(init.leafParent[p]), nodes(init.nodes[p].size()), color(init.leafParent[p].size(), -1){
- for (int i = 0; i < nodes.size(); i++){
- nodes[i].up = init.nodes[p][i].up;
- nodes[i].small = init.nodes[p][i].small;
- nodes[i].large = init.nodes[p][i].large;
- nodes[i].dup = init.nodes[p][i].dup;
- }
- }
- /*
- void reset(){
- totalScore = 0;
- version++;
- }
-
- void addTotal(int i){
- for (int u: leafParent[i]){
- totalZ[u]++;
- int w = nodes[u].up;
- while (w != -1 && (nodes[w].dup == false || nodes[w].large == u)){
- totalZ[w]++;
- u = w;
- w = nodes[u].up;
- }
- }
- }
-
- void rmvTotal(int i){
- for (int u: leafParent[i]){
- totalZ[u]--;
- int w = nodes[u].up;
- while (w != -1 && (nodes[w].dup == false || nodes[w].large == u)){
- totalZ[w]--;
- u = w;
- w = nodes[u].up;
- }
- }
- }
-
- void add(int x, int i){
- for (int u: leafParent[i]){
- nodes[u].update(version, totalZ[u]);
- if (x == 0) nodes[u].z++; else if (x == 1) nodes[u].x++; else nodes[u].y++;
- int w = nodes[u].up;
- while (w != -1 && (nodes[w].dup == false || nodes[w].large == u)){
- nodes[w].update(version, totalZ[w]);
- if (x == 0) nodes[w].z++; else if (x == 1) nodes[w].x++; else nodes[w].y++;
- if (nodes[w].dup) special(nodes[w]); else totalScore += normal(nodes[w]);
- u = w;
- w = nodes[u].up;
- }
- if (w != -1){
- nodes[w].update(version, totalZ[w]);
- special(nodes[w]);
- }
- }
- }
-
- void rmv(int x, int i){
- for (int u: leafParent[i]){
- nodes[u].update(version, totalZ[u]);
- if (x == 0) nodes[u].z--; else if (x == 1) nodes[u].x--; else nodes[u].y--;
- int w = nodes[u].up;
- while (w != -1 && (nodes[w].dup == false || nodes[w].large == u)){
- nodes[w].update(version, totalZ[w]);
- if (x == 0) nodes[w].z--; else if (x == 1) nodes[w].x--; else nodes[w].y--;
- if (nodes[w].dup) special(nodes[w]); else totalScore += normal(nodes[w]);
- u = w;
- w = nodes[u].up;
- }
- if (w != -1){
- nodes[w].update(version, totalZ[w]);
- special(nodes[w]);
- }
- }
- }
- */
- void update(int x, int i){
- int y = color[i];
- if (x == y) return;
- for (int u: leafParent[i]){
- if (y != -1) ((y == 0) ? nodes[u].z : (y == 1) ? nodes[u].x : nodes[u].y)--;
- if (x != -1) ((x == 0) ? nodes[u].z : (x == 1) ? nodes[u].x : nodes[u].y)++;
- int w = nodes[u].up;
- while (w != -1 && (nodes[w].dup == false || nodes[w].large == u)){
- if (y != -1) ((y == 0) ? nodes[w].z : (y == 1) ? nodes[w].x : nodes[w].y)--;
- if (x != -1) ((x == 0) ? nodes[w].z : (x == 1) ? nodes[w].x : nodes[w].y)++;
- if (nodes[w].dup) special(nodes[w]); else totalScore += normal(nodes[w]);
- u = w;
- w = nodes[u].up;
- }
- if (w != -1){
- special(nodes[w]);
- }
- }
- color[i] = x;
- }
-
- score_t score(){
- return totalScore / 2;
- }
- };
-
- vector<Partition> parts;
-
- struct Node{
- score_t x = 0, t = 0, q = 0;
- int version = 0, up = -1, small = -1, large = -1; // -1 for dummy!
- bool dup = false;
- };
-
- Tripartition(const TripartitionInitializer &init){
- score_t s = 0;
-
- for (int p = 0; p < init.nodes.size(); p++){
- const vector<TripartitionInitializer::Node> &nodes = init.nodes[p];
- const vector<vector<int> > &leafParent = init.leafParent[p];
- vector<score_t> x(nodes.size()), t(nodes.size()), q(nodes.size());
- for (int i = 0; i < leafParent.size(); i++){
- for (int u: leafParent[i]){
- x[u]++;
- int w = nodes[u].up;
- while (w != -1 && (nodes[w].dup == false || nodes[w].large == u)){
- x[w]++;
- if (nodes[w].dup) t[w] = t[nodes[w].small] + t[nodes[w].large];
- else {
- int v = (nodes[w].small == u) ? nodes[w].large : nodes[w].small;
- t[w] = t[u] + t[v] + x[u] * x[v] * (x[u] + x[v] - 2) / 2;
- s -= q[w];
- q[w] = x[u] * t[v] + x[v] * t[u] + (x[u] - 1) * x[u] * (x[v] - 1) * x[v] / 4;
- s += q[w];
- }
- u = w;
- w = nodes[u].up;
- }
- if (w != -1) t[w] = t[nodes[w].small] + t[nodes[w].large];
- }
- }
- }
-
- NUM_EQ_CLASSES = s;
-
- for (int p = 0; p < init.nodes.size(); p++) parts.emplace_back(init, p);
- }
- /*
- void reset(){
- for (int p = 0; p < parts.size(); p++) parts[p].reset();
- }
-
- void addTotal(int i){
- vector<thread> thrds;
- for (int p = 1; p < parts.size(); p++) thrds.emplace_back(&Partition::addTotal, &parts[p], i);
- parts[0].addTotal(i);
- for (thread &t: thrds) t.join();
- }
-
- void rmvTotal(int i){
- vector<thread> thrds;
- for (int p = 1; p < parts.size(); p++) thrds.emplace_back(&Partition::rmvTotal, &parts[p], i);
- parts[0].rmvTotal(i);
- for (thread &t: thrds) t.join();
- }
-
- void add(int x, int i){
- vector<thread> thrds;
- for (int p = 1; p < parts.size(); p++) thrds.emplace_back(&Partition::add, &parts[p], x, i);
- parts[0].add(x, i);
- for (thread &t: thrds) t.join();
- }
-
- void rmv(int x, int i){
- vector<thread> thrds;
- for (int p = 1; p < parts.size(); p++) thrds.emplace_back(&Partition::rmv, &parts[p], x, i);
- parts[0].rmv(x, i);
- for (thread &t: thrds) t.join();
- }
- */
- void update(int x, int i){
- vector<thread> thrds;
- for (int p = 1; p < parts.size(); p++) thrds.emplace_back(&Partition::update, &parts[p], x, i);
- parts[0].update(x, i);
- for (thread &t: thrds) t.join();
- }
-
- score_t score(){
- score_t res = 0;
- for (int p = 0; p < parts.size(); p++) res += parts[p].score();
- return res;
- }
-};
-
-struct Quadrupartition{
- struct Partition{
- struct Node{
- score_t a = 0, b = 0, c = 0, d = 0;
- score_t ab_c = 0, ab_d = 0, a_cd = 0, b_cd = 0;
- score_t ac_b = 0, a_bd = 0, ac_d = 0, c_bd = 0;
- score_t a_bc = 0, ad_b = 0, ad_c = 0, d_bc = 0;
- score_t ab_cd = 0, ac_bd = 0, ad_bc = 0;
-
- int up = -1, small = -1, large = -1; // -1 for dummy!
- bool dup = false;
- };
-
- array<score_t, 3> normal(Node& w){
- Node& u = nodes[w.small];
- Node& v = nodes[w.large];
-
- w.ab_c = u.ab_c + v.ab_c + u.a * u.b * v.c + u.c * v.a * v.b;
- w.ab_d = u.ab_d + v.ab_d + u.a * u.b * v.d + u.d * v.a * v.b;
- w.a_cd = u.a_cd + v.a_cd + u.c * u.d * v.a + u.a * v.c * v.d;
- w.b_cd = u.b_cd + v.b_cd + u.c * u.d * v.b + u.b * v.c * v.d;
-
- w.ac_b = u.ac_b + v.ac_b + u.a * u.c * v.b + u.b * v.a * v.c;
- w.a_bd = u.a_bd + v.a_bd + u.b * u.d * v.a + u.a * v.b * v.d;
- w.ac_d = u.ac_d + v.ac_d + u.a * u.c * v.d + u.d * v.a * v.c;
- w.c_bd = u.c_bd + v.c_bd + u.b * u.d * v.c + u.c * v.b * v.d;
-
- w.a_bc = u.a_bc + v.a_bc + u.b * u.c * v.a + u.a * v.b * v.c;
- w.ad_b = u.ad_b + v.ad_b + u.a * u.d * v.b + u.b * v.a * v.d;
- w.ad_c = u.ad_c + v.ad_c + u.a * u.d * v.c + u.c * v.a * v.d;
- w.d_bc = u.d_bc + v.d_bc + u.b * u.c * v.d + u.d * v.b * v.c;
-
- score_t ab_cd = w.ab_cd, ac_bd = w.ac_bd, ad_bc = w.ad_bc;
- w.ab_cd = u.a * u.b * v.c * v.d + u.c * u.d * v.a * v.b
- + u.ab_c * v.d + v.ab_c * u.d
- + u.ab_d * v.c + v.ab_d * u.c
- + u.a_cd * v.b + v.a_cd * u.b
- + u.b_cd * v.a + v.b_cd * u.a;
- w.ac_bd = u.a * u.c * v.b * v.d + u.b * u.d * v.a * v.c
- + u.ac_b * v.d + v.ac_b * u.d
- + u.a_bd * v.c + v.a_bd * u.c
- + u.ac_d * v.b + v.ac_d * u.b
- + u.c_bd * v.a + v.c_bd * u.a;
- w.ad_bc = u.a * u.d * v.b * v.c + u.b * u.c * v.a * v.d
- + u.a_bc * v.d + v.a_bc * u.d
- + u.ad_b * v.c + v.ad_b * u.c
- + u.ad_c * v.b + v.ad_c * u.b
- + u.d_bc * v.a + v.d_bc * u.a;
- return {w.ab_cd - ab_cd, w.ac_bd - ac_bd, w.ad_bc - ad_bc};
- }
-
- void special(Node& w){
- Node& u = nodes[w.small];
- Node& v = nodes[w.large];
- w.ab_c = u.ab_c + v.ab_c;
- w.ab_d = u.ab_d + v.ab_d;
- w.a_cd = u.a_cd + v.a_cd;
- w.b_cd = u.b_cd + v.b_cd;
-
- w.ac_b = u.ac_b + v.ac_b;
- w.a_bd = u.a_bd + v.a_bd;
- w.ac_d = u.ac_d + v.ac_d;
- w.c_bd = u.c_bd + v.c_bd;
-
- w.a_bc = u.a_bc + v.a_bc;
- w.ad_b = u.ad_b + v.ad_b;
- w.ad_c = u.ad_c + v.ad_c;
- w.d_bc = u.d_bc + v.d_bc;
- }
-
- vector<vector<int> > leafParent;
- vector<score_t> score1, score2, score3;
- score_t totalScore1 = 0, totalScore2 = 0, totalScore3 = 0, cnt[4] = {};
- vector<Node> nodes;
- vector<int> color;
-
- Partition(const TripartitionInitializer &init, int p): leafParent(init.leafParent[p]), nodes(init.nodes[p].size()), color(init.leafParent[p].size(), -1){
- for (int i = 0; i < nodes.size(); i++){
- nodes[i].up = init.nodes[p][i].up;
- nodes[i].small = init.nodes[p][i].small;
- nodes[i].large = init.nodes[p][i].large;
- nodes[i].dup = init.nodes[p][i].dup;
- }
- }
-
- void update(int x, int i){
- int y = color[i];
- if (x == y) return;
- if (y != -1) cnt[y]--;
- if (x != -1) cnt[x]++;
- for (int u: leafParent[i]){
- if (y != -1) ((y == 0) ? nodes[u].a : (y == 1) ? nodes[u].b : (y == 2) ? nodes[u].c : nodes[u].d)--;
- if (x != -1) ((x == 0) ? nodes[u].a : (x == 1) ? nodes[u].b : (x == 2) ? nodes[u].c : nodes[u].d)++;
- int w = nodes[u].up;
- while (w != -1 && (nodes[w].dup == false || nodes[w].large == u)){
- if (y != -1) ((y == 0) ? nodes[w].a : (y == 1) ? nodes[w].b : (y == 2) ? nodes[w].c : nodes[w].d)--;
- if (x != -1) ((x == 0) ? nodes[w].a : (x == 1) ? nodes[w].b : (x == 2) ? nodes[w].c : nodes[w].d)++;
- if (nodes[w].dup) special(nodes[w]);
- else {
- array<score_t, 3> s = normal(nodes[w]);
- totalScore1 += s[0]; totalScore2 += s[1]; totalScore3 += s[2];
- }
- u = w;
- w = nodes[u].up;
- }
- if (w != -1){
- special(nodes[w]);
- }
- }
- color[i] = x;
- }
-
- array<double, 3> score(){
- //cerr << cnt[0] << " " << cnt[1] << " " << cnt[2] << " " << cnt[3] << "; " << totalScore1 << " " << totalScore2 << " " << totalScore3 << "\n";
- double prod = cnt[0] * cnt[1] * cnt[2] * cnt[3];
- return {totalScore1 / prod, totalScore2 / prod, totalScore3 / prod};
- }
- };
-
- vector<Partition> parts;
-
- Quadrupartition(const TripartitionInitializer &init){
- for (int p = 0; p < init.nodes.size(); p++) parts.emplace_back(init, p);
- }
-
- void update(int x, int i){
- vector<thread> thrds;
- for (int p = 1; p < parts.size(); p++) thrds.emplace_back(&Partition::update, &parts[p], x, i);
- parts[0].update(x, i);
- for (thread &t: thrds) t.join();
- }
-
- array<double, 3> score(){
- array<double, 3> res;
- res[0] = 0;
- res[1] = 0;
- res[2] = 0;
- for (int p = 0; p < parts.size(); p++){
- auto t = parts[p].score();
- res[0] += t[0];
- res[1] += t[1];
- res[2] += t[2];
- }
- return res;
- }
-};
diff --git a/addons/ASTER/sequence-pair.hpp b/addons/ASTER/sequence-pair.hpp
deleted file mode 100644
index 5443d89f199a4e5944849b75d15e2eb0750f14b3..0000000000000000000000000000000000000000
--- a/addons/ASTER/sequence-pair.hpp
+++ /dev/null
@@ -1,159 +0,0 @@
-#include<vector>
-#include<array>
-#include<thread>
-
-using namespace std;
-
-inline score_t scorePos(const array<array<int, 4>, 3> cnt, const score_t R){
- const score_t M = 1 - 2 * R + 2 * R * R;
- const long long rr0 = cnt[0][0], ry0 = cnt[0][1], yr0 = cnt[0][2], yy0 = cnt[0][3];
- const long long rr1 = cnt[1][0], ry1 = cnt[1][1], yr1 = cnt[1][2], yy1 = cnt[1][3];
- const long long rr2 = cnt[2][0], ry2 = cnt[2][1], yr2 = cnt[2][2], yy2 = cnt[2][3];
- const long long rn0 = rr0 + ry0, nr0 = rr0 + yr0, yn0 = yr0 + yy0, ny0 = ry0 + yy0;
- const long long rn1 = rr1 + ry1, nr1 = rr1 + yr1, yn1 = yr1 + yy1, ny1 = ry1 + yy1;
- const long long rn2 = rr2 + ry2, nr2 = rr2 + yr2, yn2 = yr2 + yy2, ny2 = ry2 + yy2;
-
- return (rn0 * (rn0 - 1) * ny1 * ny2 + nr0 * (nr0 - 1) * yn1 * yn2) - M * (rn0 * (rn0 - 1) * yn1 * yn2 + nr0 * (nr0 - 1) * ny1 * ny2)
- + (rn1 * (rn1 - 1) * ny2 * ny0 + nr1 * (nr1 - 1) * yn2 * yn0) - M * (rn1 * (rn1 - 1) * yn2 * yn0 + nr1 * (nr1 - 1) * ny2 * ny0)
- + (rn2 * (rn2 - 1) * ny0 * ny1 + nr2 * (nr2 - 1) * yn0 * yn1) - M * (rn2 * (rn2 - 1) * yn0 * yn1 + nr2 * (nr2 - 1) * ny0 * ny1)
- //+ (yn0 * (yn0 - 1) * nr1 * nr2 + ny0 * (ny0 - 1) * rn1 * rn2) - M * (yn0 * (yn0 - 1) * rn1 * rn2 + ny0 * (ny0 - 1) * nr1 * nr2)
- //+ (yn1 * (yn1 - 1) * nr2 * nr0 + ny1 * (ny1 - 1) * rn2 * rn0) - M * (yn1 * (yn1 - 1) * rn2 * rn0 + ny1 * (ny1 - 1) * nr2 * nr0)
- //+ (yn2 * (yn2 - 1) * nr0 * nr1 + ny2 * (ny2 - 1) * rn0 * rn1) - M * (yn2 * (yn2 - 1) * rn0 * rn1 + ny2 * (ny2 - 1) * nr0 * nr1)
- ;
-}
-
-struct TripartitionInitializer{
- int npos, nThreads = 1;
- vector<score_t> pi;
- vector<vector<int> > seq;
- vector<bool> weight;
-};
-
-struct Tripartition{
- int nThreads, n = 0;
- const int npos;
- vector<array<array<int, 4>, 3> > cnt; // pos * part * letter
- vector<array<int, 4> > total; // pos * letter
- const vector<score_t> pi; // pos * letter
- const vector<vector<int> > seq; // taxon * pos -> letter
- const vector<bool> weight;
- vector<int> color;
- // i, j, k -> taxon; p, q, r -> pos; x, y, z -> part; a, b, c -> letter
-
- Tripartition(const TripartitionInitializer &init): nThreads(init.nThreads), npos(init.npos), seq(init.seq), pi(init.pi), weight(init.weight), cnt(init.npos), total(init.npos),
- color(init.seq.size(), -1){}
- /*
- void resetWork(int start, int end){
- for (int p = start; p < end; p++){
- for (int a = 0; a < 4; a++){
- cnt[p][0][a] = total[p][a];
- cnt[p][1][a] = 0;
- cnt[p][2][a] = 0;
- }
- }
- }
-
- void addTotalWork(int i, int start, int end){
- for (int p = start; p < end; p++){
- int a = seq[i][p];
- if (a != -1) total[p][a]++;
- }
- }
-
- void rmvTotalWork(int i, int start, int end){
- for (int p = start; p < end; p++){
- int a = seq[i][p];
- if (a != -1) total[p][a]--;
- }
- }
-
- void addWork(int x, int i, int start, int end){
- for (int p = start; p < end; p++){
- int a = seq[i][p];
- if (a != -1) cnt[p][x][a]++;
- }
- }
-
- void rmvWork(int x, int i, int start, int end){
- for (int p = start; p < end; p++){
- int a = seq[i][p];
- if (a != -1) cnt[p][x][a]--;
- }
- }
-
- void reset(){
- vector<thread> thrds;
- for (int t = 1; t < nThreads; t++) thrds.emplace_back(&Tripartition::resetWork, this, npos * t / nThreads, npos * (t + 1) / nThreads);
- resetWork(0, npos / nThreads);
- for (thread &t: thrds) t.join();
- }
-
- void addTotal(int i){
- n++;
- vector<thread> thrds;
- for (int t = 1; t < nThreads; t++) thrds.emplace_back(&Tripartition::addTotalWork, this, i, npos * t / nThreads, npos * (t + 1) / nThreads);
- addTotalWork(i, 0, npos / nThreads);
- for (thread &t: thrds) t.join();
- }
-
- void rmvTotal(int i){
- n--;
- vector<thread> thrds;
- for (int t = 1; t < nThreads; t++) thrds.emplace_back(&Tripartition::rmvTotalWork, this, i, npos * t / nThreads, npos * (t + 1) / nThreads);
- rmvTotalWork(i, 0, npos / nThreads);
- for (thread &t: thrds) t.join();
- }
-
- void add(int x, int i){
- vector<thread> thrds;
- for (int t = 1; t < nThreads; t++) thrds.emplace_back(&Tripartition::addWork, this, x, i, npos * t / nThreads, npos * (t + 1) / nThreads);
- addWork(x, i, 0, npos / nThreads);
- for (thread &t: thrds) t.join();
- }
-
- void rmv(int x, int i){
- vector<thread> thrds;
- for (int t = 1; t < nThreads; t++) thrds.emplace_back(&Tripartition::rmvWork, this, x, i, npos * t / nThreads, npos * (t + 1) / nThreads);
- rmvWork(x, i, 0, npos / nThreads);
- for (thread &t: thrds) t.join();
- }
- */
- void updateWork(int x, int y, int i, int start, int end){
- for (int p = start; p < end; p++){
- int a = seq[i][p];
- if (a != -1 && y != -1) cnt[p][y][a]--;
- if (a != -1 && x != -1) cnt[p][x][a]++;
- }
- }
-
- void update(int x, int i){
- int y = color[i];
- if (x == y) return;
- vector<thread> thrds;
- for (int t = 1; t < nThreads; t++) thrds.emplace_back(&Tripartition::updateWork, this, x, y, i, npos * t / nThreads, npos * (t + 1) / nThreads);
- updateWork(x, y, i, 0, npos / nThreads);
- for (thread &t: thrds) t.join();
- color[i] = x;
- }
-
- void scoreWork(score_t &res, int start, int end){
- score_t temp = 0;
- for (int p = start; p < end; p++){
- if (weight[p]) {
- temp += scorePos(cnt[p], pi[p]);
- //tempH += scorePosHelper(cnt[p], pi[p]);
- }
- }
- res = temp; // + tempH * weightHelper[n];
- }
-
- score_t score(){
- vector<score_t> res(nThreads);
- vector<thread> thrds;
- for (int t = 1; t < nThreads; t++) thrds.emplace_back(&Tripartition::scoreWork, this, ref(res[t]), npos * t / nThreads, npos * (t + 1) / nThreads);
- scoreWork(res[0], 0, npos / nThreads);
- for (thread &t: thrds) t.join();
- for (int t = 1; t < nThreads; t++) res[0] += res[t];
- return res[0];
- }
-};
diff --git a/addons/ASTER/sequence.hpp b/addons/ASTER/sequence.hpp
deleted file mode 100644
index c241ef666bfd489babb68a11cbceef0933d169e1..0000000000000000000000000000000000000000
--- a/addons/ASTER/sequence.hpp
+++ /dev/null
@@ -1,145 +0,0 @@
-#include<vector>
-#include<array>
-#include<thread>
-
-using namespace std;
-
-inline score_t scorePos(const array<array<int, 4>, 3> cnt, const array<score_t, 4> pi){
- // AAGG*2*Y^2 + AAYY*2*G*R - YYAG*A*R - AAGY*2*R*Y
- // + AAGG*2*Y^2 + GGYY*2*A*R - YYAG*G*R - GGAY*2*R*Y
- //---------------------------------------------------
- // + AAGG*4*Y^2 - YYAG*R^2
-
- const score_t A = pi[0], C = pi[1], G = pi[2], T = pi[3], R = A + G, Y = C + T;
- const long long a0 = cnt[0][0], c0 = cnt[0][1], g0 = cnt[0][2], t0 = cnt[0][3], r0 = a0 + g0, y0 = c0 + t0;
- const long long a1 = cnt[1][0], c1 = cnt[1][1], g1 = cnt[1][2], t1 = cnt[1][3], r1 = a1 + g1, y1 = c1 + t1;
- const long long a2 = cnt[2][0], c2 = cnt[2][1], g2 = cnt[2][2], t2 = cnt[2][3], r2 = a2 + g2, y2 = c2 + t2;
-
- if (R > Y){
- const score_t aagg = (g0 * (g0 - 1) * a1 * a2 + g1 * (g1 - 1) * a2 * a0 + g2 * (g2 - 1) * a0 * a1) * 2 * Y * Y;
- const score_t aayy = (y0 * (y0 - 1) * a1 * a2 + y1 * (y1 - 1) * a2 * a0 + y2 * (y2 - 1) * a0 * a1) * G * R;
- const score_t ggyy = (y0 * (y0 - 1) * g1 * g2 + y1 * (y1 - 1) * g2 * g0 + y2 * (y2 - 1) * g0 * g1) * A * R;
- const score_t yyag = (a0 * g0 * y1 * y2 + a1 * g1 * y2 * y0 + a2 * g2 * y0 * y1) * R * R;
- const score_t aagy = (g0 * y0 * a1 * a2 + g1 * y1 * a2 * a0 + g2 * y2 * a0 * a1) * 2 * R * Y;
- const score_t ggay = (a0 * y0 * g1 * g2 + a1 * y1 * g2 * g0 + a2 * y2 * g0 * g1) * 2 * R * Y;
- return aagg + aayy + ggyy - yyag - aagy - ggay;
- }
- else {
- const score_t cctt = (t0 * (t0 - 1) * c1 * c2 + t1 * (t1 - 1) * c2 * c0 + t2 * (t2 - 1) * c0 * c1) * 2 * R * R;
- const score_t ccrr = (r0 * (r0 - 1) * c1 * c2 + r1 * (r1 - 1) * c2 * c0 + r2 * (r2 - 1) * c0 * c1) * T * Y;
- const score_t ttrr = (r0 * (r0 - 1) * t1 * t2 + r1 * (r1 - 1) * t2 * t0 + r2 * (r2 - 1) * t0 * t1) * C * Y;
- const score_t rrct = (c0 * t0 * r1 * r2 + c1 * t1 * r2 * r0 + c2 * t2 * r0 * r1) * Y * Y;
- const score_t cctr = (t0 * r0 * c1 * c2 + t1 * r1 * c2 * c0 + t2 * r2 * c0 * c1) * 2 * R * Y;
- const score_t ttcr = (c0 * r0 * t1 * t2 + c1 * r1 * t2 * t0 + c2 * r2 * t0 * t1) * 2 * R * Y;
- return cctt + ccrr + ttrr - rrct - cctr - ttcr;
- }
-}
-
-struct TripartitionInitializer{
- int npos, nThreads = 1;
- vector<array<score_t, 4> > pi;
- vector<vector<int> > seq;
-};
-
-struct Tripartition{
- int nThreads;
- const int npos;
- vector<array<array<int, 4>, 3> > cnt; // pos * part * letter
- vector<array<int, 4> > total; // pos * letter
- const vector<array<score_t, 4> > pi; // pos * letter
- const vector<vector<int> > seq; // taxon * pos -> letter
- // i, j, k -> taxon; p, q, r -> pos; x, y, z -> part; a, b, c -> letter
-
- Tripartition(const TripartitionInitializer &init): nThreads(init.nThreads), npos(init.npos), seq(init.seq), pi(init.pi), cnt(init.npos), total(init.npos){}
-
- void resetWork(int start, int end){
- for (int p = start; p < end; p++){
- for (int a = 0; a < 4; a++){
- cnt[p][0][a] = total[p][a];
- cnt[p][1][a] = 0;
- cnt[p][2][a] = 0;
- }
- }
- }
-
- void addTotalWork(int i, int start, int end){
- for (int p = start; p < end; p++){
- int a = seq[i][p];
- if (a != -1) total[p][a]++;
- }
- }
-
- void rmvTotalWork(int i, int start, int end){
- for (int p = start; p < end; p++){
- int a = seq[i][p];
- if (a != -1) total[p][a]--;
- }
- }
-
- void addWork(int x, int i, int start, int end){
- for (int p = start; p < end; p++){
- int a = seq[i][p];
- if (a != -1) cnt[p][x][a]++;
- }
- }
-
- void rmvWork(int x, int i, int start, int end){
- for (int p = start; p < end; p++){
- int a = seq[i][p];
- if (a != -1) cnt[p][x][a]--;
- }
- }
-
- void scoreWork(score_t &res, int start, int end){
- score_t temp = 0;
- for (int p = start; p < end; p++){
- temp += scorePos(cnt[p], pi[p]);
- }
- res = temp;
- }
-
- void reset(){
- vector<thread> thrds;
- for (int t = 1; t < nThreads; t++) thrds.emplace_back(&Tripartition::resetWork, this, npos * t / nThreads, npos * (t + 1) / nThreads);
- resetWork(0, npos / nThreads);
- for (thread &t: thrds) t.join();
- }
-
- void addTotal(int i){
- vector<thread> thrds;
- for (int t = 1; t < nThreads; t++) thrds.emplace_back(&Tripartition::addTotalWork, this, i, npos * t / nThreads, npos * (t + 1) / nThreads);
- addTotalWork(i, 0, npos / nThreads);
- for (thread &t: thrds) t.join();
- }
-
- void rmvTotal(int i){
- vector<thread> thrds;
- for (int t = 1; t < nThreads; t++) thrds.emplace_back(&Tripartition::rmvTotalWork, this, i, npos * t / nThreads, npos * (t + 1) / nThreads);
- rmvTotalWork(i, 0, npos / nThreads);
- for (thread &t: thrds) t.join();
- }
-
- void add(int x, int i){
- vector<thread> thrds;
- for (int t = 1; t < nThreads; t++) thrds.emplace_back(&Tripartition::addWork, this, x, i, npos * t / nThreads, npos * (t + 1) / nThreads);
- addWork(x, i, 0, npos / nThreads);
- for (thread &t: thrds) t.join();
- }
-
- void rmv(int x, int i){
- vector<thread> thrds;
- for (int t = 1; t < nThreads; t++) thrds.emplace_back(&Tripartition::rmvWork, this, x, i, npos * t / nThreads, npos * (t + 1) / nThreads);
- rmvWork(x, i, 0, npos / nThreads);
- for (thread &t: thrds) t.join();
- }
-
- score_t score(){
- vector<score_t> res(nThreads);
- vector<thread> thrds;
- for (int t = 1; t < nThreads; t++) thrds.emplace_back(&Tripartition::scoreWork, this, ref(res[t]), npos * t / nThreads, npos * (t + 1) / nThreads);
- scoreWork(res[0], 0, npos / nThreads);
- for (thread &t: thrds) t.join();
- for (int t = 1; t < nThreads; t++) res[0] += res[t];
- return res[0];
- }
-};
diff --git a/addons/ASTER/sequencenontrivialpi.hpp b/addons/ASTER/sequencenontrivialpi.hpp
deleted file mode 100644
index a16e280a6db337d1214ad36d7ae1d3fff2de5186..0000000000000000000000000000000000000000
--- a/addons/ASTER/sequencenontrivialpi.hpp
+++ /dev/null
@@ -1,140 +0,0 @@
-#include<vector>
-#include<array>
-#include<thread>
-
-using namespace std;
-
-inline score_t scorePos(const array<array<int, 4>, 3> cnt, const score_t pi){
- const score_t R = pi, Y = 1 - R;
- const long long r0 = cnt[0][0], p0 = cnt[0][1], q0 = cnt[0][2], y0 = cnt[0][3], n0 = r0 + p0 + q0 + y0;
- const long long r1 = cnt[1][0], p1 = cnt[1][1], q1 = cnt[1][2], y1 = cnt[1][3], n1 = r1 + p1 + q1 + y1;
- const long long r2 = cnt[2][0], p2 = cnt[2][1], q2 = cnt[2][2], y2 = cnt[2][3], n2 = r2 + p2 + q2 + y2;
-
- const score_t rrnn = r0 * (r0 - 1) * n1 * n2 + r1 * (r1 - 1) * n2 * n0 + r2 * (r2 - 1) * n0 * n1;
- const score_t yynn = y0 * (y0 - 1) * n1 * n2 + y1 * (y1 - 1) * n2 * n0 + y2 * (y2 - 1) * n0 * n1;
- const score_t rryy = r0 * (r0 - 1) * y1 * y2 + r1 * (r1 - 1) * y2 * y0 + r2 * (r2 - 1) * y0 * y1;
- const score_t ppqq = p0 * (p0 - 1) * q1 * q2 + p1 * (p1 - 1) * q2 * q0 + p2 * (p2 - 1) * q0 * q1;
-
- const score_t rrpq = p0 * q0 * r1 * r2 + p1 * q1 * r2 * r0 + p2 * q2 * r0 * r1;
- const score_t yypq = p0 * q0 * y1 * y2 + p1 * q1 * y2 * y0 + p2 * q2 * y0 * y1;
-
- return ((R > Y) ? 1 : -1) * (R*R * yynn - Y*Y * rrnn + (R - Y)*(2*rryy - ppqq) + (Y*Y - R*R)*(rryy + 2*rrpq + 2*yypq));
-}
-
-struct TripartitionInitializer{
- int npos, nThreads = 1;
- vector<score_t> pi;
- vector<vector<int> > seq;
- vector<bool> weight;
- vector<score_t> weightHelper;
-};
-
-struct Tripartition{
- int nThreads, n = 0;
- const int npos;
- vector<array<array<int, 4>, 3> > cnt; // pos * part * letter
- vector<array<int, 4> > total; // pos * letter
- const vector<score_t> pi; // pos * letter
- const vector<vector<int> > seq; // taxon * pos -> letter
- const vector<bool> weight;
- const vector<score_t> weightHelper;
- // i, j, k -> taxon; p, q, r -> pos; x, y, z -> part; a, b, c -> letter
-
- Tripartition(const TripartitionInitializer &init): nThreads(init.nThreads), npos(init.npos), seq(init.seq), pi(init.pi), weight(init.weight), cnt(init.npos), total(init.npos), weightHelper(init.weightHelper){}
-
- void resetWork(int start, int end){
- for (int p = start; p < end; p++){
- for (int a = 0; a < 4; a++){
- cnt[p][0][a] = total[p][a];
- cnt[p][1][a] = 0;
- cnt[p][2][a] = 0;
- }
- }
- }
-
- void addTotalWork(int i, int start, int end){
- for (int p = start; p < end; p++){
- int a = seq[i][p];
- if (a != -1) total[p][a]++;
- }
- }
-
- void rmvTotalWork(int i, int start, int end){
- for (int p = start; p < end; p++){
- int a = seq[i][p];
- if (a != -1) total[p][a]--;
- }
- }
-
- void addWork(int x, int i, int start, int end){
- for (int p = start; p < end; p++){
- int a = seq[i][p];
- if (a != -1) cnt[p][x][a]++;
- }
- }
-
- void rmvWork(int x, int i, int start, int end){
- for (int p = start; p < end; p++){
- int a = seq[i][p];
- if (a != -1) cnt[p][x][a]--;
- }
- }
-
- void scoreWork(score_t &res, int start, int end){
- score_t temp = 0, tempH = 0;
- for (int p = start; p < end; p++){
- if (weight[p]) {
- temp += scorePos(cnt[p], pi[p]);
- //tempH += scorePosHelper(cnt[p], pi[p]);
- }
- }
- res = temp; // + tempH * weightHelper[n];
- }
-
- void reset(){
- vector<thread> thrds;
- for (int t = 1; t < nThreads; t++) thrds.emplace_back(&Tripartition::resetWork, this, npos * t / nThreads, npos * (t + 1) / nThreads);
- resetWork(0, npos / nThreads);
- for (thread &t: thrds) t.join();
- }
-
- void addTotal(int i){
- n++;
- vector<thread> thrds;
- for (int t = 1; t < nThreads; t++) thrds.emplace_back(&Tripartition::addTotalWork, this, i, npos * t / nThreads, npos * (t + 1) / nThreads);
- addTotalWork(i, 0, npos / nThreads);
- for (thread &t: thrds) t.join();
- }
-
- void rmvTotal(int i){
- n--;
- vector<thread> thrds;
- for (int t = 1; t < nThreads; t++) thrds.emplace_back(&Tripartition::rmvTotalWork, this, i, npos * t / nThreads, npos * (t + 1) / nThreads);
- rmvTotalWork(i, 0, npos / nThreads);
- for (thread &t: thrds) t.join();
- }
-
- void add(int x, int i){
- vector<thread> thrds;
- for (int t = 1; t < nThreads; t++) thrds.emplace_back(&Tripartition::addWork, this, x, i, npos * t / nThreads, npos * (t + 1) / nThreads);
- addWork(x, i, 0, npos / nThreads);
- for (thread &t: thrds) t.join();
- }
-
- void rmv(int x, int i){
- vector<thread> thrds;
- for (int t = 1; t < nThreads; t++) thrds.emplace_back(&Tripartition::rmvWork, this, x, i, npos * t / nThreads, npos * (t + 1) / nThreads);
- rmvWork(x, i, 0, npos / nThreads);
- for (thread &t: thrds) t.join();
- }
-
- score_t score(){
- vector<score_t> res(nThreads);
- vector<thread> thrds;
- for (int t = 1; t < nThreads; t++) thrds.emplace_back(&Tripartition::scoreWork, this, ref(res[t]), npos * t / nThreads, npos * (t + 1) / nThreads);
- scoreWork(res[0], 0, npos / nThreads);
- for (thread &t: thrds) t.join();
- for (int t = 1; t < nThreads; t++) res[0] += res[t];
- return res[0];
- }
-};
diff --git a/addons/java_libraries/FastInfoset-1.2.13.jar b/addons/java_libraries/FastInfoset-1.2.13.jar
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diff --git a/addons/java_libraries/README b/addons/java_libraries/README
new file mode 100644
index 0000000000000000000000000000000000000000..f17e3076cdb91a26940387cc138103c8d243a13e
--- /dev/null
+++ b/addons/java_libraries/README
@@ -0,0 +1,9 @@
+As of version 3.3 the default compilation method was changed to Maven and the .jar files in this repository were removed.
+
+The .jar files are still required in case you want to edit and compile the PanTools code in NetBeans.
+
+NetBeans will check for the files in the pantools/addons/java_libraries/ directory. Follow these steps before opening the project in NetBeans.
+
+cd pantools/addons/
+wget bioinformatics.nl/pangenomics/data/java_libraries.tar.gz
+tar -xvf java_libraries.tar.gz
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@@ -1,93 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- You may freely edit this file. See commented blocks below for -->
-<!-- some examples of how to customize the build. -->
-<!-- (If you delete it and reopen the project it will be recreated.) -->
-<!-- By default, only the Clean and Build commands use this build script. -->
-<!-- Commands such as Run, Debug, and Test only use this build script if -->
-<!-- the Compile on Save feature is turned off for the project. -->
-<!-- You can turn off the Compile on Save (or Deploy on Save) setting -->
-<!-- in the project's Project Properties dialog box.-->
-<project name="pantools" default="default" basedir=".">
- <description>Builds, tests, and runs the project pantools.</description>
- <import file="nbproject/build-impl.xml"/>
- <!--
-
- There exist several targets which are by default empty and which can be
- used for execution of your tasks. These targets are usually executed
- before and after some main targets. They are:
-
- -pre-init: called before initialization of project properties
- -post-init: called after initialization of project properties
- -pre-compile: called before javac compilation
- -post-compile: called after javac compilation
- -pre-compile-single: called before javac compilation of single file
- -post-compile-single: called after javac compilation of single file
- -pre-compile-test: called before javac compilation of JUnit tests
- -post-compile-test: called after javac compilation of JUnit tests
- -pre-compile-test-single: called before javac compilation of single JUnit test
- -post-compile-test-single: called after javac compilation of single JUunit test
- -pre-jar: called before JAR building
- -post-jar: called after JAR building
- -post-clean: called after cleaning build products
-
- (Targets beginning with '-' are not intended to be called on their own.)
-
- Example of inserting an obfuscator after compilation could look like this:
-
- <target name="-post-compile">
- <obfuscate>
- <fileset dir="${build.classes.dir}"/>
- </obfuscate>
- </target>
-
- For list of available properties check the imported
- nbproject/build-impl.xml file.
-
-
- Another way to customize the build is by overriding existing main targets.
- The targets of interest are:
-
- -init-macrodef-javac: defines macro for javac compilation
- -init-macrodef-junit: defines macro for junit execution
- -init-macrodef-debug: defines macro for class debugging
- -init-macrodef-java: defines macro for class execution
- -do-jar: JAR building
- run: execution of project
- -javadoc-build: Javadoc generation
- test-report: JUnit report generation
-
- An example of overriding the target for project execution could look like this:
-
- <target name="run" depends="pantools-impl.jar">
- <exec dir="bin" executable="launcher.exe">
- <arg file="${dist.jar}"/>
- </exec>
- </target>
-
- Notice that the overridden target depends on the jar target and not only on
- the compile target as the regular run target does. Again, for a list of available
- properties which you can use, check the target you are overriding in the
- nbproject/build-impl.xml file.
-
- -->
- <target name="package-for-store" depends="jar">
- <property name="store.jar.name" value="pantools"/>
- <property name="store.dir" value="store"/>
- <property name="store.jar" value="${store.dir}/${store.jar.name}.jar"/>
- <echo message="Packaging ${application.title} into a single JAR at ${store.jar}"/>
- <delete dir="${store.dir}"/>
- <mkdir dir="${store.dir}"/>
- <jar destfile="${store.dir}/temp_final.jar" filesetmanifest="skip" zip64mode="always">
- <zipgroupfileset dir="dist" includes="*.jar"/>
- <zipgroupfileset dir="addons/java_libraries" includes="*.jar"/>
- <manifest>
- <attribute name="Main-Class" value="${main.class}"/>
- </manifest>
- </jar>
- <zip destfile="${store.jar}">
- <zipfileset src="${store.dir}/temp_final.jar"
- excludes="META-INF/*.SF, META-INF/*.DSA, META-INF/*.RSA"/>
- </zip>
- <delete file="${store.dir}/temp_final.jar"/>
-</target>
-</project>
diff --git a/conda.yaml b/conda.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..7a9f365a7c05bac157da004ce702ba3095892c41
--- /dev/null
+++ b/conda.yaml
@@ -0,0 +1,21 @@
+channels:
+ - bioconda
+ - defaults
+ - conda-forge
+dependencies:
+ - openjdk=8.0
+ - maven
+ - python=3.7
+ - kmc=3.0.1
+ - mcl
+ - mafft
+ - iqtree
+ - fasttree
+ - blast
+ - mash=2.3
+ - fastani
+ - busco=5.2.2
+ - r-base=3.4.3
+ - r-ggplot2=2.2.1
+ - r-ape=5.0
+ - graphviz
diff --git a/nbproject/private/.LCKprivate.xml~ b/docs/.gitkeep
similarity index 100%
rename from nbproject/private/.LCKprivate.xml~
rename to docs/.gitkeep
diff --git a/docs/Makefile b/docs/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..d0c3cbf1020d5c292abdedf27627c6abe25e2293
--- /dev/null
+++ b/docs/Makefile
@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS ?=
+SPHINXBUILD ?= sphinx-build
+SOURCEDIR = source
+BUILDDIR = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+ @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+ @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/make.bat b/docs/make.bat
new file mode 100644
index 0000000000000000000000000000000000000000..9534b018135ed7d5caed6298980c55e8b1d2ec82
--- /dev/null
+++ b/docs/make.bat
@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+ set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+ echo.
+ echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+ echo.installed, then set the SPHINXBUILD environment variable to point
+ echo.to the full path of the 'sphinx-build' executable. Alternatively you
+ echo.may add the Sphinx directory to PATH.
+ echo.
+ echo.If you don't have Sphinx installed, grab it from
+ echo.http://sphinx-doc.org/
+ exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd
diff --git a/nbproject/private/config.properties b/docs/source/.gitkeep
old mode 100755
new mode 100644
similarity index 100%
rename from nbproject/private/config.properties
rename to docs/source/.gitkeep
diff --git a/docs/source/_static/css/s5defs-roles.css b/docs/source/_static/css/s5defs-roles.css
new file mode 100644
index 0000000000000000000000000000000000000000..b688171bc3b88110ecd9a4721af30edbd326f129
--- /dev/null
+++ b/docs/source/_static/css/s5defs-roles.css
@@ -0,0 +1,83 @@
+.black {
+ color: black;
+}
+
+.gray {
+ color: gray;
+}
+
+.grey {
+ color: gray;
+}
+
+.silver {
+ color: silver;
+}
+
+.white {
+ color: white;
+}
+
+.maroon {
+ color: maroon;
+}
+
+.red {
+ color: red;
+}
+
+.magenta {
+ color: magenta;
+}
+
+.fuchsia {
+ color: fuchsia;
+}
+
+.pink {
+ color: pink;
+}
+
+.orange {
+ color: orange;
+}
+
+.yellow {
+ color: yellow;
+}
+
+.lime {
+ color: lime;
+}
+
+.green {
+ color: green;
+}
+
+.olive {
+ color: olive;
+}
+
+.teal {
+ color: teal;
+}
+
+.cyan {
+ color: cyan;
+}
+
+.aqua {
+ color: aqua;
+}
+
+.blue {
+ color: blue;
+}
+
+.navy {
+ color: navy;
+}
+
+.purple {
+ color: purple;
+}
\ No newline at end of file
diff --git a/docs/source/characterize.rst b/docs/source/characterize.rst
new file mode 100644
index 0000000000000000000000000000000000000000..2d9c651941a33049de50fac828412658c2082716
--- /dev/null
+++ b/docs/source/characterize.rst
@@ -0,0 +1,772 @@
+Pangenome characterization
+==========================
+
+Functionalities for characterization a pangenome based on genes, *k*-mer
+sequences and functions. In this manual we use several pangenome related
+terms with the following definitions:
+
+- **Core**, an element is present in all genomes
+- **Unique**, an element is present in a single genome
+- **Accessory**, an element is present in some but not all genomes
+
+When phenotype information is used in the analysis, three additional
+categories can be assigned:
+
+- **Shared**, an element present in all genomes of a phenotype
+- **Exclusive**, an element is only present in a certain phenotype
+- **Specific**, an element present in all genomes of a phenotype and is
+ also exclusive
+
+.. _classify table:
+
+.. figure:: figures/classify_table.png
+ :width: 600
+ :align: center
+
+ *The possible classification categories for genes, k mers and functions.
+ Additional copies of an element are assigned to the same category.*
+
+--------------
+
+Pangenome metrics
+-----------------
+
+Generates relevant metrics of the pangenome and the individual genomes
+and sequences.
+
+- On the pangenome level: the number of genomes, sequences,
+ annotations, genes, proteins, homology groups, *k*-mers, and database
+ nodes and edges.
+- On the genome and sequence level: assembly statistics and metrics
+ about functional elements. The assembly statistics consists of genome
+ size, N25-N95, L25-L95, BUSCO scores and GC content. An overview of
+ the functional elements is created by summarizing the functional
+ annotations per genome (and sequence) and reporting the shortest,
+ longest, average length and density per MB for genome features such
+ as genes, exons and CDS.
+
+Required argument
+~~~~~~~~~~~~~~~~~
+
+``--database-path``/``-dp`` Path to the pangenome database.
+
+Optional arguments
+~~~~~~~~~~~~~~~~~~
+
+| ``--skip``/``-sk`` Exclude a selection of genomes
+| ``--reference``/``-ref`` Only include a selection of genomes.
+| ``--annotations-file``/``-af`` A text file with the identifiers of
+ annotations that should be used. The most recent annotation is
+ selected for genomes without an identifier.
+
+Example commands
+~~~~~~~~~~~~~~~~
+
+.. code:: bash
+
+ $ pantools metrics -dp tomato_DB
+ $ pantools metrics -dp tomato_DB --skip 1,2,5
+
+Output
+~~~~~~
+
+Output files are written to the **metrics** directory in the database.
+Note: the percentage a genome or sequence is covered by a genes, repeats
+etc., (currently) does not consider overlap between features!
+
+- **metrics.txt**, overview of the metrics calculated on the pangenome
+ and genome level.
+- **metrics_per_genome.csv**, summary of the metrics that are
+ calculated on a genome level. The output is formatted as table.
+- **metrics_per_sequence.csv**, summary of metrics that are calculated
+ on a sequence (contig/scaffold) level. The output is formatted as
+ table. This file is **not** created when using a panproteome.
+
+--------------
+
+Homology groups
+---------------
+
+The following functions require the protein sequences to be clustered by
+:ref:`group <construct:group>`.
+
+Gene classification
+~~~~~~~~~~~~~~~~~~~
+
+Classification of the pangenome's gene repertoire. Homology groups are
+utilized to identify shared genes between genomes. The default criteria
+for defining the category of a gene is shown in :numref:`classify table`.
+
+To identify soft core and cloud genes, the core and unique thresholds (%)
+can be relaxed by ``--core-threshold`` and ``--unique-threshold``,
+respectively. The ``--phenotype-threshold`` argument can be used to
+lower the threshold for phenotype specific and shared homology groups.
+
+Required arguments
+""""""""""""""""""
+
+``--database-path``/``-dp`` Path to the pangenome database.
+
+Optional arguments
+""""""""""""""""""
+
+| ``--phenotype``/``-ph`` A phenotype name, used to find genes specific
+ to the phenotype.
+| ``--skip``/``-sk`` Exclude a selection of genomes. This automatically
+ lowers the threshold for core genes.
+| ``--reference``/``-ref`` Only include a selection of genomes. This
+ automatically lowers the threshold for core genes.
+| ``--core-threshold``/``-ct`` Threshold (%) for (soft) core genes.
+ Default is 100% of genomes.
+| ``--unique-threshold``/``-ut`` Threshold (%) for unique/cloud genes.
+ Default is a single genome, not a percentage.
+| ``--phenotype-threshold``/``-pt`` Threshold (%) for phenotype
+ specific/shared genes. Default is 100% of genomes with phenotype.
+| ``--mode MLSA`` Finds suitable single-copy groups for a
+ :ref:`phylogeny:mlsa`.
+
+Example command
+"""""""""""""""
+
+.. code:: bash
+
+ $ pantools gene_classification -dp tomato_DB
+ $ pantools gene_classification -dp tomato_DB --unique-threshold 5 --core-threshold 95
+ $ pantools gene_classification -dp tomato_DB --phenotype resistance --skip 2,3 --phenotype-threshold 95
+
+Output
+""""""
+
+Output files are written to the **gene_classification** directory in the
+database.
+
+1. **gene_classification_overview.txt**, statistics of the core,
+ accessory, unique groups of the pangenome and individual genomes.
+2. **classified_groups.csv**, the classified homology groups formatted
+ as the table in the example table above.
+3. **cnv_core_accessory.txt**, core and accessory groups with genomes
+ that have additional copies compared to the lowest number (at least
+ 1) in the group.
+4. **group_size_occurrence.txt**, number of times a group of a certain
+ size occurs in the pangenome. The homology group sizes can be based
+ on the number of proteins or the number of genomes.
+5. **gene_distance_tree.R**, an R script to cluster genomes based on gene
+ distance (absence/presence). For more information, see the
+ :ref:`phylogeny:gene distance tree` manual.
+6. **shared_unshared_gene_count.csv**, six tables with the number of
+ shared and unshared genes between genomes: all genes, distinct genes
+ and informative distinct genes. To get the number of distinct genes,
+ additional copies of a gene within a homology group are ignored.
+ Genes are considered informative when shared by at least two genomes.
+
+Additional files are generated when the ``--phenotype`` argument is
+included.
+
+1. **gene_classification_phenotype_overview.txt**, the number of
+ identified phenotype shared and specific groups.
+2. **phenotype_disrupted.txt**, this file shows which proteins prevented
+ phenotype shared groups to be specific.
+3. **phenotype_cnv**, homology groups where all members of a phenotype
+ have at least one additional copy of a gene compared to one of the
+ other phenotypes.
+4. **phenotype_association.csv**, results of performed Fisher exact
+ tests on homology groups with an unequal proportion of phenotype
+ members.
+
+The following files contain homology group node identifiers.
+
+1. **all_homology_groups.csv**, the node identifiers of all homology
+ groups.
+2. **core_groups.csv**, the node identifiers of the core homology
+ groups.
+3. **single_copy_orthologs.csv**, the node identifiers of single-copy
+ ortholog groups. This is a subset of the core set where each genome
+ is only allowed to have a one copy of a gene.
+4. **accessory_groups.csv**, the node identifiers of accessory homology
+ groups. The groups are ordered (in descending order) by the group size based
+ on the total number of genomes present.
+5. **accessory_combinations.csv**, the node identifiers of accessory
+ homology groups, ordered by the combination of genomes by which they
+ are shared.
+6. **unique_groups.csv**, the node identifiers of unique homology groups
+ ordered by genome.
+7. **phenotype_specific_groups.csv**, the node identifiers of phenotype
+ specific homology groups.
+8. **phenotype_shared_groups.csv**, the node identifiers of phenotype
+ shared homology groups.
+9. **phenotype_exclusive_groups.csv**, the node identifiers of phenotype
+ exclusive homology groups.
+
+When ``--mode MLSA`` is included
+
+1. **mlsa_suggestions.txt**, a list of single copy ortholog genes all
+ having the same gene name. This file cannot be created when using a
+ panproteome.
+
+--------------
+
+Core unique thresholds
+~~~~~~~~~~~~~~~~~~~~~~
+
+Runs a simplified version of the **gene_classification** function to
+test the effect of different ``--core-threshold`` and
+``--unique-threshold`` cut-offs between 1 and 100%.
+
+Required arguments
+""""""""""""""""""
+
+``--database-path``/``-dp`` Path to the pangenome database.
+
+Optional arguments
+""""""""""""""""""
+
+| ``--skip``/``-sk`` Exclude a selection of genomes. This automatically
+ lowers the threshold for core genes.
+| ``--reference``/``-ref`` Only include a selection of genomes. This
+ automatically lowers the threshold for core genes.
+
+Example command
+"""""""""""""""
+
+.. code:: bash
+
+ $ pantools core_unique_thresholds -dp tomato_DB
+ $ pantools core_unique_thresholds -dp tomato_DB --skip 1,2,5-10
+ $ R script tomato_DB/R_scripts/core_unique_thresholds/core_unique_thresholds.R
+
+Output
+""""""
+
+Output files are written to **core_unique_thresholds** directory in the
+database.
+
+- **core_unique_thresholds.csv**, the number of (soft) core
+ unique/cloud homology groups for all tested thresholds.
+- **core_unique_thresholds.R**, the R script plots the number of
+ (soft) core unique/cloud homology groups for all tested thresholds.
+
+.. figure:: figures/core_unique_thresholds.png
+ :width: 600
+ :align: center
+
+ *Example output of*\ **core_unique_thresholds.R**\ *on a pangenome of
+ 197 Pectobacterium genomes demonstrates the effect of loosening the
+ thresholds. The number of (soft) core (orange) homology groups
+ slightly increases when the cut-off for this category is lowered from
+ 100% (200 genomes) to 1% (2) in steps of 1%. Unique/cloud (blue) start
+ at 0.00 which represents a single genome. Using a 0.01 cut-off, groups
+ are unique/cloud having 2 genomes or less. The threshold is further
+ increased to 100% (200) in steps of 1%.*
+
+--------------
+
+Grouping overview
+~~~~~~~~~~~~~~~~~
+
+Reports the content of all (active & inactive) homology groups for the
+different groupings in the pangenome. Include ``--mode fast`` into the
+command to get a quick overview of the available groupings and the
+settings that were used.
+
+Required arguments
+""""""""""""""""""
+
+``--database-path``/``-dp`` Path to the pangenome database.
+
+Optional arguments
+""""""""""""""""""
+
+``--mode fast`` Only show which grouping is active and which groupings
+can be activated.
+
+Example commands
+""""""""""""""""
+
+.. code:: bash
+
+ $ pantools grouping_overview -dp tomato_DB
+ $ pantools grouping_overview -dp tomato_DB --mode fast
+
+Output
+""""""
+
+Output files are written to */database_directory/group/*
+
+- **grouping_overview.txt**, all homology groups in the pangenome. For
+ each homology group, the total number of members and the number of
+ members per per genome is reported.
+- **current_pantools_homology_groups.txt**, overview of the active
+ homology groups. Each line represents one homology group. The line
+ starts with the homology group (database) identifier followed by a
+ colon and the rest are mRNA IDs (from gff/genbank) seperated by a
+ space.
+
+--------------
+
+Pangenome structure
+-------------------
+
+Iterations of random genome combinations according to the models
+proposed by Tettelin et al.\ :sup:`*` in 2005 are used to determine the
+contribution of new accessions with respect to the increase in core,
+accessory, and unique. Each iteration starts with three random genomes
+from which core, accessory and unique homology groups are identified.
+Subsequently, random genomes are added and group reclassified until the
+maximum number of genomes is reached. To simulate the overall
+pangenome-size increase and core-genome decrease, we suggest to use at
+least 10,000 iterations. Additional copies of a gene are ignored in the
+simulation.
+
+Heaps' law (a power law) can be fitted to the number of new genes
+observed when increasing the pangenome by one random genome. The formula
+for the power law model is :math:`n = k * N^{-a}`, where *n* is the
+newly discovered genes, *N* is the total number of genomes, and *k* and
+*a* are the fitting parameters. A pangenome can be considered open when
+*a* < 1 and closed if *a* > 1.
+
+Pangenome size genes
+~~~~~~~~~~~~~~~~~~~~
+
+Pangenome size estimation based on homology groups. This function
+requires the sequences to be already clustered by
+:ref:`group <construct:group>`.
+
+Required argument
+"""""""""""""""""
+
+``--database-path``/``-dp`` Path to the pangenome database.
+
+Optional arguments
+""""""""""""""""""
+| ``--threads``/``-tn`` (**default value**: 1) : The number of parallel
+ working threads.
+| ``--skip``/``-sk`` Exclude a selection of genomes
+| ``--reference``/``-ref`` Only include a selection of genomes.
+| ``--value`` Number of loops (default is 10.000).
+
+Example commands
+""""""""""""""""
+
+.. code:: bash
+
+ $ pantools pangenome_structure_genes -dp tomato_DB
+ $ pantools pangenome_structure_genes -dp tomato_DB --value 1000 --skip 1-3,5
+
+ $ R script pangenome_growth.R
+ $ R script gains_losses_median_or_average.R
+ $ R script gains_losses_median_and_average.R
+ $ R script heaps_law.R
+
+Output
+""""""
+
+Output files are written to */database_directory/pangenome_size/gene/*
+
+- **pangenome_size.txt**, various statistics on the number core,
+ accessory, and unique homology groups for the different pangenome
+ sizes.
+- **gains_losses.txt**, the average group gain and loss between
+ different pangenome sizes. First the average number (core, accessory,
+ and unique) groups for each pangenome size is calculated. The average
+ gain and loss of groups is then found by subtracting the averages of
+ a certain size to the averages of one genome larger (e.g. pangenome
+ size of 5 is compared to 6).
+- **gains_losses_last_genome.txt**, the number of (core, accessory, and
+ unique) groups that are gained or lost when including one of the
+ genomes to a pangenome of the remaining genomes.
+- **pangenome_growth.R**, an R script to plot the number of core,
+ accessory and unique groups for the different genome combinations.
+ Second option is to only plot a core and accessory curve by
+ including unique groups to the accessory.
+- **gains_losses_median_and/or_average.R**, R scripts to plot the
+ average and median group gain and loss between pangenome sizes.
+- **heaps_law.R**, an R script to perform Heaps' law.
+
+.. figure:: figures/size.png
+ :width: 600
+ :align: center
+
+ *Example output of*\ **pangenome_growth.R**\ *(left)
+ and*\ **gains_losses_median_and_average.R**\ *(right) on a
+ pangenome of 204 bacteria.*
+
+Relevant literature
+""""""""""""""""""""
+
+- `Genome analysis of multiple pathogenic isolates of Streptococcus
+ agalactiae: Implications for the microbial "pan-genome"
+ <https://doi.org/10.1073/pnas.0506758102>`_
+- `Comparative genomics: the bacterial pan-genome
+ <https://doi.org/10.1016/j.mib.2008.09.006>`_
+
+--------------
+
+Pangenome size *k*-mers
+~~~~~~~~~~~~~~~~~~~~~~~
+
+The same simulation as **pangenome_size_genes**, but performed on
+*k*-mer sequences instead of homology groups. As the number of *k*-mers is
+significantly higher than the number of homology groups, the runtime is
+much longer and the (default) number of loops is set to only 100.
+
+Required argument
+"""""""""""""""""
+
+``--database-path``/``-dp`` Path to the pangenome database.
+
+Optional arguments
+""""""""""""""""""
+| ``--threads``/``-tn`` (**default value**: 1) : The number of parallel
+ working threads.
+| ``--skip``/``-sk`` Exclude a selection of genomes.
+| ``--reference``/``-ref`` Only include a selection of genomes.
+| ``--value`` Number of loops (default is 100).
+
+Example command
+"""""""""""""""
+
+.. code:: bash
+
+ $ pantools pangenome_size_kmer -dp tomato_db
+ $ pantools pangenome_size_kmer -dp tomato_db --skip 4,5-9 --value 500
+ $ R script core_access_unique.R
+
+Output
+""""""
+
+Output files are written to */database_directory/pangenome_size/kmer/*
+
+- **pangenome_size_kmer.txt**, statistics of the number of *k*-mers with
+ different pangenome sizes.
+- **core_access_unique.R**, an R script to plot the number core,
+ accessory, unique *k*-mers for the different genome combinations.
+- **core_access.R**, an R script to plot the number of core and accessory
+ (including unique) *k*-mers for the different genome combinations.
+
+--------------
+
+K-mer classification
+----------------------
+
+Calculate the number of core, accessory, unique, (and phenotype
+specific) *k*-mer sequences. Because *k*-mer sequences of non-branching
+paths of the DBG graph are collapsed into a single node, *k*-mers are
+first uncompressed before they are counted. When ``--mode compressed``
+is included, sequences are not uncompressed and considered as a single
+*k*-mer. Nucleotide nodes with a 'degenerate' label contain letters
+other than the four non-ambiguous ones (A, T, C, G). and are ignored by
+this function.
+
+Required argument
+~~~~~~~~~~~~~~~~~
+
+``--database-path``/``-dp`` Path to the pangenome database.
+
+Optional arguments
+~~~~~~~~~~~~~~~~~~
+
+| ``--phenotype``/``-ph`` A phenotype name, used to identify phenotype
+ specific *k*-mers.
+| ``--skip``/``-sk`` Exclude a selection of genomes. This automatically
+ lowers the threshold for core *k*-mers.
+| ``--reference``/``-ref`` Only include a selection of genomes. This
+ automatically lowers the threshold for core *k*-mers.
+| ``--core-threshold``/``-ct`` Threshold (%) for (soft) core *k*-mers.
+ Default is 100% of the genomes.
+| ``--unique-threshold``/``-ut`` Threshold (%) for unique/cloud
+ *k*-mers. Default is a single genome, not a percentage.
+| ``--phenotype-threshold``/``-pt`` Threshold (%) for phenotype
+ specific/shared *k*-mers. Default is 100% of genomes with phenotype.
+ ``--mode compressed`` Do not uncompress collapsed non-branching
+ *k*-mers for *k*-mer counting.
+
+Example commands
+~~~~~~~~~~~~~~~~
+
+.. code:: bash
+
+ $ pantools kmer_classification -dp tomato_DB
+ $ pantools kmer_classification -dp tomato_DB --phenotype resistant --skip 2,3,4
+ $ pantools kmer_classification -dp tomato_DB --mode compressed --core-threshold 95 --unique-threshold 5
+
+Output
+~~~~~~
+
+Output files are written to */database_directory/kmer_classification/*
+
+- **kmer_classification_overview.txt**, some general statistics and
+ percentages about the core, accessory unique *k*-mers per genome.
+- **kmer_occurrence.txt**, the occurrence of *k*-mers per genome and
+ total occurrence in the pangenome.
+- **kmer_distance_tree.R**, an R script to cluster genomes with four
+ different *k*-mer distances to choose from. For more information, see
+ The *k*-mers are ordered from high to low by the total number of
+ genomes the *k*-mer is found.
+- **unique_kmers.csv**, the node identifiers of unique *k*-mers ordered
+ by genome.
+- **phenotype_specific_kmers.csv**, the node identifiers of phenotype
+ specific *k*-mers.
+- **phenotype_shared_kmers.csv**, the node identifiers of phenotype
+ shared *k*-mers.
+
+--------------
+
+Functional annotations
+----------------------
+
+The following functions can only be used when any type of functional
+annotation is
+:ref:`added to the database <construct:add functional annotations>`.
+
+Functional classification
+~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Similar to **gene** and **k-mer classification**, this function
+identifies core, accessory, unique functional annotations in the
+pangenome. Only the following functions are considered for this
+analysis: biosynthetic gene clusters from antiSMASH, GO, PFAM, InterPro,
+TIGRFAM.
+
+Required arguments
+""""""""""""""""""
+
+``--database-path``/``-dp`` Path to the pangenome database.
+
+Optional commands
+"""""""""""""""""
+
+| ``--phenotype``/``-ph`` A phenotype name, used to find functions
+ specific to a phenotype.
+| ``--skip``/``-sk`` Exclude a selection of genomes. This automatically
+ lowers the threshold for core genes.
+| ``--reference``/``-ref`` Only include a selection of genomes. This
+ automatically lowers the threshold for core genes.
+| ``--core-threshold``/``-ct`` Threshold (%) For (soft) core functions
+ (default is 100%).
+| ``--unique-threshold``/``-ut`` Threshold (%) For unique/cloud
+ functions (default is a single genome, not a percentage).
+| ``--annotations-file``/``-af`` A text file with the identifiers of
+ annotations that should be used. The most recent annotation is
+ selected for genomes without an identifier.
+
+Example command
+"""""""""""""""
+
+.. code:: bash
+
+ $ pantools functional_classification -dp tomato_DB
+ $ pantools functional_classification -dp tomato_DB -ph flowering_time
+
+Output
+""""""
+
+Output files are written to
+*/database_directory/function/functional_classification/*
+
+- **functional_annotation_overview**, number of core, accessory, and
+ unique functions. Holds the number of phenotype shared and specific
+ functions when a phenotype is included.
+- **core_functions.txt**, functional annotations found in every genome
+ of the pangenome.
+- **accessory_functions.txt**, functional annotations labeled as
+ accessory.
+- **unique_functions.txt**, functional annotations unique to a single
+ genome.
+
+When a ``--phenotype`` is included
+
+- **phenotype_shared_functions.txt**, functional annotations shared by
+ all phenotype members.
+- **phenotype_specific_functions.txt**, functional annotations specific
+ to certain phenotypes.
+
+--------------
+
+Functional annotation overview
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Creates several summary files for each type of functional annotation
+present in the database: GO, PFAM, InterPro, TIGRFAM, COG, Phobius, and
+biosynthetic gene clusters from antiSMASH. In addition to the functions
+that must be added via
+:ref:`add_functional_annotations <construct:add functional annotations>`,
+this function also requires proteins to be clustered by
+:ref:`group <construct:group>`.
+
+Required argument
+"""""""""""""""""
+
+``--database-path``/``-dp`` Path to the pangenome database.
+
+Optional commands
+"""""""""""""""""
+
+| ``--skip``/``-sk`` Exclude a selection of genomes.
+| ``--reference``/``-ref`` Only include a selection of genomes.
+| ``--annotations-file``/``-af`` A text file with the identifiers of
+ annotations that should be used. The most recent annotation is
+ selected for genomes without an identifier.
+
+Example command
+"""""""""""""""
+
+.. code:: bash
+
+ $ pantools function_overview -dp tomato_DB
+ $ pantools function_overview -dp tomato_DB --reference 2-4
+
+Output
+""""""
+
+Output files are written to *function* directory in the database. The
+overview CSV files are tables with on each row a function identifier
+with the frequency of per genome and.
+
+- **functions_per_group_and_mrna.csv**, overview of all homology groups
+ and the associated functions.
+- **function_counts_per_group.csv**,
+- **go_overview.csv**, overview of the GO terms in the pangenome.
+- **pfam_overview.csv**, overview of the PFAM domains in the pangenome.
+- **tigrfam_overview.csv**, overview of the TIGRFAMs in the pangenome.
+- **interpro_overview.csv**, overview of the InterPro domains in the
+ pangenome.
+- **bgc_overview.csv**, overview of the added biosynthetic gene
+ clusters from antiSMASH in the pangenome.
+- **phobius_signalp_overview.csv**, overview of the included Phobius
+ transmembrane topology and signal peptide predictions in the
+ pangenome.
+- **cog_overview.csv**, overview of the functional COG categories in
+ the pangenome.
+- **cog_per_class.R**, an R script to plot the distribution of COG
+ categories over the core, accessory, unique homology groups.
+
+.. figure:: figures/COG_abundance.png
+ :width: 600
+ :align: center
+
+ *Example output of*\ **cog_per_class.R**\ *. The proportion of COGs
+ functional categories assigned to homology groups.*
+
+--------------
+
+GO enrichment
+~~~~~~~~~~~~~
+
+For a given set of mRNA's or homology groups, this function identifies
+over or underrepresented GO terms by using a hypergeometric
+distribution.
+
+The p-value is calculated from the hypergeometric distribution
+
+.. math:: P(X = k) = \frac{\binom{K}{k} \binom{N-K}{n-k}}{\binom{N}{n}}
+
+- Parameter **N** = size of the population (Universe of genes).
+- Parameter **n** = size of the sample (signature gene set)
+- Parameter **K** = successes in population (enrichment gene set)
+- Parameter **k** = successes in sample (intersection of both gene sets)
+- Return the **p-value** of the Hypergeometric Distribution for P(X=k)
+
+**Prepare input for hypergeometric tests**
+
+The size and number of successes of the sample (n, k) and background (N,
+K) is prepared for each genome individually. Per genome, loops over
+every mRNA and checks for connected GO nodes. Each GO node connected to
+the mRNA is used to move up in the GO hierarchy via '*is_a*' relations
+until the **molecular_function**, **biological_process** or
+**cellular_component** node is reached. Each GO term is counted only
+once per mRNA and a mRNA needs at least one GO term to be included in
+the sample and background sets. mRNA nodes which are part of the input
+homology groups are included into the sample set.
+
+**Multiple testing correction**
+
+**Critical p-value using Bonferroni**
+
+For a GO germ to be significant, the p-value should be below 0.05
+divided by number of tests per genome. For example, when 100 tests were
+performed, each p-value must be below 0.05/100 = 0.0005 to be considered
+significant.
+
+**Critical p-value using Benjamini-Hochberg procedure**
+
+1. Individual p-values are put in ascending order.
+2. Ranks are assigned to the p-values. The lowest value has a rank of 1,
+ the second lowest gets rank 2, etc..
+3. The individual p-values Benjamini-Hochberg critical value is
+ calculated using the formula :math:`(i/m)Q`, where i is the individual
+ p-values rank, m = total number of tests and Q is the false discovery rate.
+4. Compare your original p-values to the critical B-H from Step 3; find
+ the largest p value that is smaller than the critical value.
+
+The critical p-value for the first rank for a total of 100 GO terms
+(tests) with a 5% false discovery rate is :math:`(1/100) * 0.05 = 0.0005`. For
+the second and third rank this will be 0.0010 and 0.0015, respectively.
+
+Required software
+"""""""""""""""""
+
+- dot. Although this function still works when dot is not (properly)
+ installed, no visualizations of the GO hierarchy can be created.
+
+Required arguments
+""""""""""""""""""
+
+``--database-path``/``-dp`` Path to the database.
+
+Requires either **one** of the following arguments
+
+``--homology-groups``/``-hm`` A text file with homology group node
+identifiers, seperated by a comma ``--node`` mRNA node identifiers,
+seperated by a comma on the command line
+
+Optional arguments
+""""""""""""""""""
+
+| ``--skip``/``-sk`` Exclude a selection of genomes.
+| ``--reference``/``-ref`` Only include a selection of genomes.
+| ``--value`` The false discovery rate (percentage), default is 5%.
+
+Example command
+"""""""""""""""
+
+.. code:: bash
+
+ $ pantools go_enrichment -dp tomato_DB -hm unique_groups.txt
+ $ pantools go_enrichment -dp tomato_DB -hm pheno_specific.txt --value 1 -ref 1-3,5
+
+Output
+""""""
+
+Output files are stored in
+*/database_directory/function/go_enrichment/*.
+
+- **go_enrichment.csv**, overview of all GO terms, p-values and the
+ significance of enrichment. The output is formatted as a table.
+- **go_enrichment_overview_per_go.txt**, results of the analysis are
+ ordered by GO term.
+- **function_overview_per_mrna.txt**, all functional annotations
+ connected to the input sequences, ordered per mRNA.
+- **function_overview_per_genome.txt**, all functional annotations
+ connected to the input sequences, ordered per genome.
+
+Additional files are generated per individual genome and placed in
+*/results_per_genome/*.
+
+- **go_enrichment.txt**, list of GO terms, p-values and the critical
+ p-values of Benjamin-Hochberg and Bonferroni.
+- **revigo.txt**, a list of GO terms and p-values that can be
+ visualized on http://revigo.irb.hr
+- **bio_process.pdf**, dot visualisation of the Biological Process GO
+ hierarchy.
+- **cell_comp.pdf**, dot visualisation of the Cellular Component GO
+ hierarchy.
+- **mol_function.pdf**, dot visualisation of the Molecular Function GO
+ hierarchy.
+
+.. figure:: figures/bio_process.png
+ :width: 600
+ :align: center
+
+ *Visualization of GO hierarchy by dot*
+
+--------------
diff --git a/docs/source/conf.py b/docs/source/conf.py
new file mode 100644
index 0000000000000000000000000000000000000000..8b6afe8fc8159b3dbd275e153c2a44dd25be3c13
--- /dev/null
+++ b/docs/source/conf.py
@@ -0,0 +1,58 @@
+# Configuration file for the Sphinx documentation builder.
+
+# -- Project information
+
+project = 'PanTools'
+copyright = '2016, the PanTools team'
+author = 'Sandra Smit'
+
+release = '3.4.0'
+version = '3.4.0'
+
+# -- General configuration
+
+extensions = [
+ 'sphinx.ext.duration',
+ 'sphinx.ext.doctest',
+ 'sphinx.ext.autodoc',
+ 'sphinx.ext.autosummary',
+ 'sphinx.ext.intersphinx',
+ 'sphinx.ext.autosectionlabel',
+ 'sphinx.ext.mathjax'
+]
+
+intersphinx_mapping = {
+ 'python': ('https://docs.python.org/3/', None),
+ 'sphinx': ('https://www.sphinx-doc.org/en/master/', None),
+}
+intersphinx_disabled_domains = ['std']
+
+templates_path = ['_templates']
+
+# -- Options for HTML output
+
+html_theme = 'sphinx_rtd_theme'
+
+# -- Options for EPUB output
+
+epub_show_urls = 'footnote'
+
+# Make sure the target is unique
+autosectionlabel_prefix_document = True
+
+# Enable numref
+numfig = True
+
+# Math alignment configuration
+mathjax3_config = {'chtml': {'displayAlign': 'left',
+ 'displayIndent': '2em'}}
+
+# CSS files
+html_css_files = ['css/s5defs-roles.css',]
+
+# Prolog
+rst_prolog = """
+.. include:: <s5defs.txt>
+.. default-role::
+
+"""
\ No newline at end of file
diff --git a/docs/source/construct.rst b/docs/source/construct.rst
new file mode 100644
index 0000000000000000000000000000000000000000..273342125245091449a02ecddd7bfd9b791fa430
--- /dev/null
+++ b/docs/source/construct.rst
@@ -0,0 +1,1157 @@
+Construct pangenome
+===================
+
+Build pangenome
+---------------
+
+Build a pangenome out of a set of genomes.
+
+Required software
+~~~~~~~~~~~~~~~~~
+
+`KMC 2.3 or 3.0 <http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&project=kmc&subpage=about>`_
+
+Required arguments
+~~~~~~~~~~~~~~~~~~
+
+| ``--database-path``/``-dp`` Path to the pangenome database.
+| ``--genomes-file``/``-gf`` A text file containing paths to FASTA files
+ of genomes to be added to the pangenome; each on a separate line.
+
+Optional arguments
+~~~~~~~~~~~~~~~~~~
+
+``--kmer-size``/``-ks`` Size of *k*-mers, allowed to be 6 <= K_SIZE <=
+255. By not giving this argument, the most optimal *k*-mer size is
+calculated automatically.
+
+Example input file
+~~~~~~~~~~~~~~~~~~
+
+.. code:: text
+
+ /always/genome1.fasta
+ /use_the/genome2.fasta
+ /full_path/genome3.fasta
+
+Example command
+~~~~~~~~~~~~~~~
+
+.. code:: bash
+
+ $ pantools build_pangenome -dp tomato_DB -gf tomato_3.txt
+
+Relevant literature
+~~~~~~~~~~~~~~~~~~~
+
+- `PanTools: representation, storage and exploration of pan-genomic data
+ <https://academic.oup.com/bioinformatics/article/32/17/i487/2450785>`_
+
+--------------
+
+Add annotations
+---------------
+
+Construct or expand the annotation layer of an existing pangenome. The
+layer consists of genomic features like genes, mRNAs, proteins, tRNAs
+etc. PanTools is only able to read General Feature Format (**GFF**)
+files.
+
+Multiple annotations can be assigned to a single genome; however, only
+one annotation a time can be included in an analysis. The most recently
+included annotation of a genome is included as default, unless a
+different annotation is specified via ``--annotations-file``, see the
+explanation
+:ref:`below <construct:select specific annotations for analysis>`
+
+Required arguments
+~~~~~~~~~~~~~~~~~~
+
+| ``--database-path``/``-dp`` Path to the pangenome database.
+| ``--annotations-file``/``-af`` A text file with on each line a genome
+ number and the full path to the corresponding annotation file,
+ separated by a space.
+
+Optional arguments
+~~~~~~~~~~~~~~~~~~
+
+``--connect-annotations``/``-ca`` Connect the annotated genomic features
+to nucleotide nodes in the DBG.
+
+Example command
+~~~~~~~~~~~~~~~
+
+.. code:: bash
+
+ $ pantools add_annotations -dp tomato_DB -af annotations.txt
+
+Output
+~~~~~~
+
+The annotated features are incorporated in the graph. Output files are
+written to the database directory.
+
+- **annotation_overview.txt**, a summary of the GFF files incorporated
+ in the pangenome
+- **annotation.log**, a list of misannotated feature identifiers.
+
+Example input file
+~~~~~~~~~~~~~~~~~~
+
+Each line of the file starts with the genome number followed by the full
+path to the annotation file. The genome numbers match the line number of
+the file that you used to construct the pangenome.
+
+.. code:: text
+
+ 1 /always/genome1.gff
+ 2 /use_the/genome2.gff
+ 3 /full_path/genome3.gff
+
+| \ **GFF3 file format**\
+| The GFF format consists of one line per feature, each containing 9
+ columns of data, plus optional track definition lines, that must be
+ tab separated. Please use the proper hierarchy for the feature:
+ **gene** -> **mRNA** -> **CDS**. Where *gene* is the parent of *mRNA*
+ and *mRNA* is the parent of the *CDS* feature. When a *gene* consists
+ of multiple *CDS* features but is missing *mRNA*, only the last *CDS*
+ feature is annotated in the pangenome. The following example from
+ *Saccharomyces cerevisiae* YJM320 (GCA_000975885) displays a correctly
+ formatted gene entry:
+
+.. code:: text
+
+ CP004621.1 Genbank gene 44836 45753 . - . ID=gene99;Name=RPL23A;end_range=45753,.;gbkey=Gene;gene=RPL23A;gene_biotype=protein_coding;locus_tag=H754_YJM320B00023;partial=true;start_range=.,44836
+ CP004621.1 Genbank mRNA 44836 45753 . - . ID=rna99;Parent=gene99;gbkey=mRNA;gene=RPL23A;product=Rpl23ap
+ CP004621.1 Genbank exon 45712 45753 . - . ID=id112;Parent=rna99;gbkey=mRNA;gene=RPL23A;product=Rpl23ap
+ CP004621.1 Genbank exon 44836 45207 . - . ID=id113;Parent=rna99;gbkey=mRNA;gene=RPL23A;product=Rpl23ap
+ CP004621.1 Genbank CDS 45712 45753 . - 0 ID=cds92;Parent=rna99;Dbxref=SGD:S000000183,NCBI_GP:AJQ01854.1;Name=AJQ01854.1;Note=corresponds to s288c YBL087C;gbkey=CDS;gene=RPL23A;product=Rpl23ap;protein_id=AJQ01854.1
+ CP004621.1 Genbank CDS 44836 45207 . - 0 ID=cds92;Parent=rna99;Dbxref=SGD:S000000183,NCBI_GP:AJQ01854.1;Name=AJQ01854.1;Note=corresponds to s288c YBL087C;gbkey=CDS;gene=RPL23A;product=Rpl23ap;protein_id=AJQ01854.1
+
+Select specific annotations for analysis
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Only **one** annotation per genome is considered by any PanTools
+functionality. When multiple annotations are included, the last added
+annotation of a genome is automatically selected unless an
+``--annotations-file`` is included specifying which annotations to use.
+This annotation file contains only annotation identifiers, each on a
+separate line. The most recent annotation is used for genomes where no
+annotation number is specified in the file. Below is an example where
+the third annotation of genome 1 is selected and the second annotation
+of genome 2 and 3.
+
+.. code:: text
+
+ 1_3
+ 2_2
+ 3_2
+
+--------------
+
+Grouping proteins
+-----------------
+
+Group
+~~~~~
+
+Generate homology groups based on similarity of protein sequences. The
+resulting homology groups connect similar sequences in the pangenome
+database. Homology groups contain not only orthologous pairs, but also
+pairs of homologs duplicated after the speciation of the two species,
+so-called in-paralogs. The sizes of the groups are controlled by the
+``--relaxation`` parameter that can be set very strict or more lenient,
+depending on the evolutionary distance of the genomes. When you are
+unsure which relaxation setting is most suitable for your dataset,
+running the :ref:`optimal_grouping <construct:optimal grouping>`
+functionality is recommended.
+
+Be aware that not every sequence within a homology group has to be
+similar to the other sequences. For example, two non-similar protein
+sequences each have a high-similarity hit with the same protein sequence
+but align to a different region, one at the start and one near the end
+of the sequence.
+
+When you want to run **group** another time but with different
+parameters, the currently active grouping must first either be moved or
+removed. This can be achieved with the
+:ref:`move- or remove_homology_groups <construct:move or remove grouping>`
+functions.
+
+| **Method**
+| Here, we explain a simplified version of the original algorithm,
+ please take a look at our publication for an extensive explanation.
+ First, potential similar sequences are identified by counting shared
+ *k*-mer (protein) sequences. Similarity between the selected protein
+ sequences is calculated through (local) Smith-Waterman alignments.
+ When the (normalized) similarity score of two sequences is above a
+ given threshold (controlled by ``--relaxation``), the proteins are
+ connected with each other in the similarity graph. Every similarity
+ component is then passed to the MCL (Markov clustering) algorithm to
+ be possibly broken into several homology groups.
+
+Required software
+~~~~~~~~~~~~~~~~~
+
+`MCL <https://micans.org/mcl/>`_
+
+Required arguments
+~~~~~~~~~~~~~~~~~~
+
+``--database-path``/``-dp`` Path to the pangenome database.
+
+Optional arguments
+~~~~~~~~~~~~~~~~~~
+
+| ``--skip``/``-sk`` Exclude a selection of genomes.
+| ``--reference``/``-ref`` Only include a selection of genomes.
+| ``--threads``/``-tn`` The number of parallel working threads. Default
+ and minimum required threads is 3.
+| ``--longest-transcript`` Only cluster the longest protein-coding
+ transcript of genes.
+| ``--annotations-file``/``-af`` A text file with the identifiers of
+ annotations to be included, each on a separate line. The most recent
+ annotation is selected for genomes without an identifier.
+
+Optional arguments that influence the clustering sensitivity
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+| ``--relaxation``/``-rn`` The relaxation in homology calls. Should be
+ in range [1-8], from strict to relaxed (default 1). **IMPORTANT!**
+ This argument automatically sets the four remaining arguments, stated
+ here below.
+| ``--intersection-rate``/``-ir`` The fraction of *k*-mers that needs to
+ be shared by two intersecting proteins. Should be in range [0.001,
+ 0.1] (default = 0.08).
+| ``--similarity-threshold``/``-st`` The minimum normalized similarity
+ score of two proteins. Should be in range [1-99] (default = 95).
+| ``--mcl-inflation``/``-mi`` The MCL inflation. Should be in range
+ [1-19] (default = 10.8).
+| ``--contrast``/``-cn`` The contrast factor. Should be in range [0-10]
+ (default = 8).
+
+Example commands
+~~~~~~~~~~~~~~~~
+
+.. code:: bash
+
+ $ pantools group -dp tomato_DB
+ $ pantools group -dp tomato_DB -tn 12 -rn 4
+
+Output
+~~~~~~
+
+- **pantools_homology_groups.txt**, overview of the created homology
+ groups. Each line represents one homology group, starting with the
+ homology group (database) identifier followed by a colon (:) and mRNA
+ identifiers (from GFF) that are separated by a space. To ensure all
+ identifiers are unique in this file, the mRNA ids are extended by a
+ hash symbol (#) and a genome number. The following line is example
+ output of an homology group with two genes from genome 1 and 146:
+
+.. code:: text
+
+ 14001754: DLACAPHP_00001_mRNA#1 OPJEMMMF_03822_mRNA#146
+
+Relevant literature
+~~~~~~~~~~~~~~~~~~~
+
+- `Efficient inference of homologs in large eukaryotic pan-proteomes
+ <https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2362-4>`_
+
+--------------
+
+Optimal grouping
+----------------
+
+Finding the most suitable settings for :ref:`group <construct:group>`
+can be difficult and is always dependent on evolutionary distance of the
+genomes in the pangenome. This functionality runs **group** on all eight
+``--relaxation`` settings, from strictest (d1) to the most relaxed (d8).
+To find the optimal setting, complete and **non-duplicated BUSCO** genes
+that are present in all genomes are used to validate each setting.
+
+| **Method**
+| A perfect clustering of the sequences would place each BUSCO in a
+ separate homology group with one representative protein per genome.
+ When BUSCO is run against the pangenome, the proteins corresponding to
+ the BUSCO HMMs have been identified. For each BUSCO, the
+ representative proteins are checked whether these are clustered into a
+ single or multiple groups. These groups are searched to identify
+ sequences other than the current BUSCO. The highest number of
+ correctly clustered BUSCOs present in one group are true positives
+ (**tp**). Any other gene clustered inside this group is considered a
+ false positive (**fp**) The remaining BUSCO genes outside this best
+ group are counted as false negative (**fn**). The summation of tps fps
+ and fns are defined as **TP**, **FP** and **FN**, respectively. From
+ these scores recall, precision and F-score measures are calculated as
+ follows:
+
+.. math::
+
+ Recall &= \frac{TP}{TP + FN}
+
+ Precision &= \frac{TP}{TP + FP}
+
+ F-score &= 2 \frac{Recall * Precision}{Recall + Precision}
+
+.. figure:: figures/true_false_positives.png
+ :width: 600
+ :align: center
+
+ *Proteins of three distinct homology groups are represented as
+ triangles, circles and squares. Green shapes are true positives (tp)
+ which have been assigned to the true group; red shapes are false
+ positives (fp) for the group they have been incorrectly assigned to, and
+ false negatives (fn) for their true group*
+
+| **Choosing the optimal setting**
+| Choosing the correct setting is usually a trade-off between TPs and
+ FNs. The most strict grouping results in a significantly higher number
+ of clusters as the more relaxed settings. With stringent settings,
+ related proteins could get separated; however, a high number of false
+ positives is (usually) prevented (FN > FP). When you would go for a
+ more loose setting, the related proteins are likely to part of the
+ same group, but other sequences could be included as well (FN < FP).
+
+No grouping is active after running this function. Use the generated
+output files to identify a suitable grouping. Activate this grouping
+using :ref:`change_grouping <construct:change grouping>`. An overview of
+the available groupings and used settings is stored in the 'pangenome'
+node (inside the database), or can be created by running
+:ref:`grouping_overview <characterize:grouping overview>`.
+
+Required software
+~~~~~~~~~~~~~~~~~
+
+`MCL <https://micans.org/mcl/>`_
+
+Required arguments
+~~~~~~~~~~~~~~~~~~
+
+| ``--database-path``/``-dp`` Path to the pangenome database.
+| ``--input-file``/``-if`` The output directory created by the
+ :ref:`busco_protein <construct:busco>` function. This directory is
+ found **inside** the pangenome database, in the *busco* directory.
+
+Optional arguments
+~~~~~~~~~~~~~~~~~~
+
+| ``--skip``/``-sk`` Exclude a selection of genomes.
+| ``--reference``/``-ref`` Only include a selection of genomes.
+| ``--threads``/``tn`` Number of threads. The default and minimum
+ required threads is 3.
+| ``--value`` Only consider a selection of relaxation settings (1-8
+ allowed).
+| ``--fast`` Assume the optimal grouping is found when the F1-score
+ drops compared to the previous clustering round.
+| ``--longest-transcript`` Only cluster protein sequences of the largest
+ transcript per gene.
+| ``--annotations-file``/``-af`` A text file with the identifiers of
+ annotations to be included, each on a separate line. The most recent
+ annotation is selected for genomes without an identifier.
+
+Example commands
+~~~~~~~~~~~~~~~~
+
+.. code:: bash
+
+ $ pantools optimal_grouping -dp bacteria_DB -if bacteria_DB/busco/bacteria_odb9
+ $ pantools optimal_grouping -dp bacteria_DB -if bacteria_DB/busco/bacteria_odb9 -tn 12 --fast
+ $ pantools optimal_grouping -dp bacteria_DB -if bacteria_DB/busco/bacteria_odb9 -tn 12 --fast --longest-transcript
+ $ pantools optimal_grouping -dp bacteria_DB -if bacteria_DB/busco/bacteria_odb9 -tn 12 --value 1,2,3,4
+
+ $ Rscript optimal_grouping.R
+
+Output
+~~~~~~
+
+After each clustering round, homology groups are incorporated in the
+graph. A text file with homology group and gene identifiers is stored in
+the **group** directory in the pangenome database. This file is named
+after the used sequence similarity threshold (25-95). Each line
+represents one homology group, starting with the homology group
+(database) identifier followed by a colon (:) and mRNA identifiers (from
+GFF) that are separated by a space. The mRNA identifiers are extended by
+a hash (#) and their genome number. The following line is example output
+of an homology group with two genes from genome 1 and 146:
+
+.. code:: text
+
+ 14001754: DLACAPHP_00001_mRNA#1 OPJEMMMF_03822_mRNA#146
+
+Output files are written to **optimal_grouping** directory inside the
+database.
+
+- **grouping_overview.csv**, a summary of the benchmark statistics. Use
+ this file to find the most suitable grouping for your pangenome.
+- **optimal_grouping.R**, Rscript to plot FN and FP values per
+ grouping.
+- **counts_per_busco.info**, a log file of the scoring. Shows in which
+ homology groups the BUSCO genes were placed for the different
+ groupings.
+
+.. figure:: figures/best_grouping.png
+ :width: 300
+ :align: center
+
+ :italic:`Example output of **optimal_grouping.R**. The number of FN and FP for all eight relaxation settings.`
+
+--------------
+
+Change grouping
+---------------
+
+Only a single homology grouping can be active in the pangenome. Use this
+function to change the active grouping version. Information of the
+available groupings and used settings is stored in the 'pangenome' node
+(inside the database) and can be created by running
+:ref:`grouping_overview <characterize:grouping overview>`.
+
+Required arguments
+~~~~~~~~~~~~~~~~~~
+
+| ``--database-path``/``-dp`` Path to the pangenome database.
+| ``--version`` The version of homology grouping to become active.
+
+Example command
+~~~~~~~~~~~~~~~
+
+.. code:: bash
+
+ $ pantools change_grouping -dp tomato_DB --version 5
+
+--------------
+
+Build panproteome
+-----------------
+
+Build a panproteome out of a set of proteins. By only including protein
+sequences, the usable functionalities are limited to a protein-based
+analysis, please see :doc:`differences pangenome and panproteome <differences>`. No additional proteins can be added to
+the panproteome, it needs to be rebuilt completely.
+
+Required arguments
+~~~~~~~~~~~~~~~~~~
+
+| ``--database-path``/``-dp`` Path to the pangenome database.
+| ``--proteomes-file``/``-pf`` A text file containing paths to FASTA
+ files of proteins to be added to the panproteome; each on a separate
+ line.
+
+Example input file
+~~~~~~~~~~~~~~~~~~
+
+.. code:: text
+
+ /always/proteins1.fasta
+ /use_the/proteins2.fasta
+ /full_path/proteins3.faa
+
+Example command
+~~~~~~~~~~~~~~~
+
+.. code:: bash
+
+ $ pantools build_panproteome -dp proteome_DB -pf proteins.txt
+
+--------------
+
+Add genomes
+-----------
+
+Include additional genomes to an already available pangenome.
+
+Required software
+~~~~~~~~~~~~~~~~~
+
+`KMC 2.3 or 3.0 <http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&project=kmc&subpage=about>`_
+
+Required arguments
+~~~~~~~~~~~~~~~~~~
+
+| ``--database-path``/``-dp`` Path to the pangenome database.
+| ``--genomes-file``/``-gf`` A text file containing paths to FASTA files
+ of genomes to be added to the pangenome; each on a separate line.
+
+Example input file
+~~~~~~~~~~~~~~~~~~
+
+.. code:: text
+
+ /use_the/genome4.fasta
+ /full_path/genome5.fasta
+
+Example command
+~~~~~~~~~~~~~~~
+
+.. code:: bash
+
+ $ pantools add_genomes -dp pangenome_DB -gf extra_genomes.txt
+
+--------------
+
+Add phenotypes
+--------------
+
+Including phenotype data to the pangenome which allows the
+identification of phenotype specific genes, SNPs, functions, etc..
+Altering the data is done by rerunning the command with an updated CSV
+file.
+
+| **Data types**
+| Each phenotype node contains a genome number and can hold the
+ following data types: **String**, **Integer**, **Float** or
+ **Boolean**.
+
+- Values recognized as round number are converted to an **Integer** and
+ to a **Double** when having one or multiple decimals.
+- **Boolean** types are identified by checking if the value matches
+ 'true' or 'false', ignoring capitalization of letters.
+- **String** values remain completely unaltered except for spaces and
+ quotes characters. Spaces are changed into an underscore ('\_')
+ character and quotes are completely removed.
+
+| **Bin numerical values**
+| When using numerical values, two genomes are only considered to share
+ a phenotype if the value is identical. PanTools creates an
+ alternative version for these phenotypes by binning the values. Taking
+ 'Pathogenicity' from the example below we see the integers between 3
+ and 15. Using these two extreme values three bins are created for a
+ new phenotype 'Pathogenicity_binned': 3-6.33, 6.34-11.66 and 11.67-15.
+ The number of bins is controlled through ``--value``. For skewed data,
+ consider making the bins manually and include this as string
+ phenotype.
+
+Required arguments
+~~~~~~~~~~~~~~~~~~
+
+| ``--database-path``/``-dp`` Path to the pangenome database.
+| ``--phenotype``/``-ph`` A CSV file containing the phenotype
+ information.
+
+Optional argument
+~~~~~~~~~~~~~~~~~
+
+| ``--append`` Do not remove existing phenotype nodes but only add new
+ properties to it. If a property already exists, values from the new
+ file will overwrite the old.
+| ``--value`` Number of bins used to group numerical values of a
+ phenotype.
+
+Example input file
+~~~~~~~~~~~~~~~~~~
+
+The input file needs to be in .CSV format, a plain text file where each
+value is separated by a comma. The first **row** should start with
+'Genome,' followed by the phenotype names and/or identifiers. The first
+**column** must start with genome numbers corresponding to the one in
+your pangenome. Phenotypes and metadata must be placed on the same line
+as their genome number. A field can remain empty when the phenotype for
+a genome is missing or unknown. Here below is an example of five genomes
+contains six phenotypes:
+
+.. code:: text
+
+ Genome,Gram,Region,Pathogenicity,Boolean,float,species
+ 1,+,NL,3,True,0.1,Species
+ 2,+,BE,,False,0.1,Species3
+ 3,+,LUX,7,true,0.1,Species3
+ 4,+,NL,9,false,0.1,Species3
+ 5,+,BE,15,TRUE,0.1,Species1
+
+Example command
+~~~~~~~~~~~~~~~
+
+.. code:: bash
+
+ $ pantools add_phenotype -dp tomato_DB --phenotype pheno.csv
+ $ pantools add_phenotype -dp tomato_DB -ph pheno.csv --append
+
+Output
+~~~~~~
+
+Phenotype information is stored in 'phenotype' nodes in the graph. An
+output file is written to the database directory.
+
+- **phenotype_overview.txt**, a summary of the available phenotypes in
+ the pangenome
+
+--------------
+
+BUSCO
+-----
+
+BUSCO attempts to provide a quantitative assessment of the completeness
+in terms of expected gene content of a genome assembly. Proteins are
+placed into categories of Complete and **single-copy** (S), Complete and
+**duplicated** (D), **fragmented** (F), or **missing** (M). This
+function is able to run BUSCO **v3**, **v4** or **v5** against protein
+sequences of the pangenome.
+
+The number of reported duplicated genes in eukaryotes is often to high
+as different protein isoforms are counted multiple times. To adjust the
+imprecise duplication score, include the ``--longest-transcripts``
+argument to the command.
+
+**You don't have a benchmark set?**
+
+- When using BUSCO v3, go to https://busco.ezlab.org, download a odb9
+ set, and untar it with ``tar -xvzf``. Include the entire directory in
+ the command using the ``--input-file`` argument.
+- For BUSCO v4 and v5, you only have to provide the odb10 database name
+ with the ``--input-file`` argument, the database is downloaded
+ automatically. To get a full list of the available datasets, run
+ ``busco --list-datasets``.
+
+Required software
+~~~~~~~~~~~~~~~~~
+
+BUSCO must be set to your $PATH. For v3, test if the
+``which run_BUSCO.py`` command displays the full path so it can accessed
+anywhere. For v4 and v5, test if ``busco`` is executable.
+
+Required arguments
+~~~~~~~~~~~~~~~~~~
+
+| ``--database-path``/``-dp`` Path to the pangenome database.
+| ``--input-file``/``-if`` A BUSCO benchmark dataset.
+
+Optional arguments
+~~~~~~~~~~~~~~~~~~
+
+| ``--skip``/``-sk`` Exclude a selection of genomes.
+| ``--reference``/``-ref`` Only include a selection of genomes.
+| ``--name`` A string with questionable BUSCOs. Completeness (%) is
+ recalculated by excluding these genes.
+| ``--version`` The BUSCO version. Select either 'busco3', 'busco4' or
+ 'busco5' (default).
+| ``--longest-transcript`` Only search against the longest
+ protein-coding transcript of genes.
+| ``--annotations-file``/``-af`` A text file with the identifiers of
+ annotations to be included, each on a separate line. The most recent
+ annotation is selected for genomes without an identifier.
+
+Example commands
+~~~~~~~~~~~~~~~~
+
+.. code:: bash
+
+ $ pantools busco_protein -dp bacteria_DB -if bacteria_odb10
+ $ pantools busco_protein -dp bacteria_DB -if busco_sets/bacteria_odb9/ --version busco3
+ $ pantools busco_protein -dp bacteria_DB -if busco_sets/bacteria_odb9/ --version busco3 --name POG093P01OY,POG093P0009,POG093P022K,POG093P027M,POG093P00Z2,POG093P013J
+ $ pantools busco_protein -dp bacteria_DB -if bacteria_odb10 --version busco4 --longest-transcript
+
+Output
+~~~~~~
+
+The BUSCO scores are stored inside **BUSCO** nodes of the pangenome
+graph. Output files are written to the **busco** directory inside the
+database.
+
+- **busco_scores.txt**, overview of the BUSCO scores per genome.
+ Average and median statistics are calculated per category.
+- **busco_overview.csv**, a table which combines the completeness
+ scores per genome together with the duplicated, fragmented and
+ missing BUSCO genes.
+- **hmm_overview.txt**, a list of BUSCO genes showing the assigned
+ categories per genome.
+
+--------------
+
+Add functional annotations
+--------------------------
+
+PanTools is able to incorporate functional annotations into the
+pangenome by reading output from various functional annotation tools.
+
+Add functions
+~~~~~~~~~~~~~
+
+This function can integrate different functional annotations from a
+variety of annotation files. Currently available functional annotations:
+**Gene Ontology**, **Pfam**, **InterPro**, **TIGRFAM**, **Phobius**,
+**SignalP** and **COG**. The first time this function is executed, the
+Pfam, TIRGRAM, GO, and InterPro databases are integrated into the
+pangenome. Phobius, SignalP and COG annotations do not have separate
+nodes and are directly annotated on 'mRNA' nodes in the pangenome.
+
+Gene names (or identifiers) from the input file are used to identify
+gene nodes in the pangenome. Only genes with an exactly matching
+name/identifier can be connected to functional annotation nodes! Use the
+same FASTA and GFF3 files that were used to construct the pangenome
+database.
+
+Functional databases
+~~~~~~~~~~~~~~~~~~~
+
+Database versions in v3.4.0 repository
+
+.. list-table::
+ :widths: 25 25 50
+ :header-rows: 1
+
+ * - \
+ - Version
+ - Download date (dd-mm-yyyy)
+ * - Gene ontology
+ - 2021-12-15
+ - 20-12-2021
+ * - Pfam
+ - 35.0
+ - 20-12-2021
+ * - TIGRFAM
+ - 15.0
+ - 01-10-2020
+ * - InterPro
+ - 87+
+ - Not included in repository
+
+We regularly check and update the four functional database. To update
+the functional database manually, download the following files and
+replace the old ones in the */pantools/addons/* directory. The
+TIGRFAM.info files are bundled in the TIGRFAMs_15.0_INFO.tar.gz file;
+download the file to addons/tigrfam and uncompress the tarball first.
+The first time running this function .INFO files are combined into a new
+file **COMBINATION_INFO_FILES** and removed afterwards.
+
+.. csv-table::
+ :file: tables/functional_databases.csv
+ :header-rows: 1
+ :delim: ;
+
+Required arguments
+~~~~~~~~~~~~~~~~~~
+
+| ``--database-path``/``-dp`` Path to the pangenome database.
+| ``--input-file``/``-if`` A text file with on each line a genome number
+ and the full path to the corresponding annotation file, separated by a
+ space.
+
+Optional arguments
+~~~~~~~~~~~~~~~~~~
+
+``--annotations-file``/``-af`` A text file with the identifiers of
+annotations to be included, each on a separate line. The most recent
+annotation is selected for genomes without an identifier.
+
+Example command
+~~~~~~~~~~~~~~~
+
+.. code:: bash
+
+ $ pantools add_functions -dp tomato_DB -if f_annotations.txt
+ $ pantools add_functions -dp tomato_DB -if f_annotations.txt -af annotations.txt
+
+Output
+~~~~~~
+
+Functional annotations are incorporated in the graph. A log file is
+written to the **log** directory.
+
+- **add_functional_annotations.log**, a log file with the the number of
+ added functions per type and the identifiers of functions that could
+ not be included.
+
+Example input files
+~~~~~~~~~~~~~~~~~~~
+
+The ``--input-file`` requires to be formatted like an annotation input
+file. Each line of the file starts with the genome number followed by
+the full path to an annotation file.
+
+.. list-table::
+ :widths: 40 60
+ :header-rows: 1
+
+ * - File type
+ - Recognized by pattern in file name
+ * - InterProScan
+ - interpro & .gff
+ * - eggNOG-mapper
+ - eggnog
+ * - Phobius
+ - phobius
+ * - SignalP
+ - signalp
+ * - Custom file
+ - custom
+
+.. code:: text
+
+ 1 /mnt/scratch/interpro_results_genome_1.gff
+ 1 /mnt/scratch/custom_annotation_1.txt
+ 1 /mnt/scratch/phobius_1.txt
+ 2 /mnt/scratch/signalp.txt
+ 2 /mnt/scratch/eggnog_genome_2.annotations
+ 2 /mnt/scratch/transmembrane_annotations.txt phobius
+ 3 /mnt/scratch/ipro_results_genome_3.annot custom
+
+| **Annotation file types**
+| PanTools can recognize functional annotations in different output
+ formats.
+
+Phobius and SignalP are not standard analyses of the InterProScan
+pipeline and require some additional steps during the InterProScan
+installation. Please take a look at
+:ref:`our InterProScan install instruction <install:install interproscan>`
+to verify if the tools are part of the prediction pipeline. Phobius 1.01
+
+.. list-table::
+ :widths: 20 80
+ :header-rows: 1
+
+ * - Function type
+ - Allowed annotation file
+ * - GO
+ - InterProscan .gff & custom annotation file
+ * - Pfam
+ - InterProscan .gff & custom annotation file
+ * - InterPro
+ - InterProscan .gff & custom annotation file
+ * - TIGRFAM
+ - InterProscan .gff & custom annotation file
+ * - Phobius
+ - InterProscan .gff & Phobius 1.01 output
+ * - SignalP
+ - InterProscan .gff, signalP 4.1 output, signalP 5.0 output
+ * - COG
+ - eggNOG-mapper
+
+InterProScan gff file:
+
+.. code:: text
+
+ ##gff-version 3
+ ##interproscan-version 5.52-86.0
+ AT4G21230.1 ProSiteProfiles protein_match 333 620 39.000664 + . date=06-10-2021;Target=mRNA.AT4G21230.1 333 620;Ontology_term="GO:0004672","GO:0005524","GO:0006468";ID=match$42_333_620;signature_desc=Protein kinase domain profile.;Name=PS50011;status=T;Dbxref="InterPro:IPR000719"
+ AT3G08980.5 TIGRFAM protein_match 25 101 3.7E-14 + . date=06-10-2021;Target=mRNA.AT3G08980.5 25 101;Ontology_term="GO:0006508","GO:0008236","GO:0016020";ID=match$66_25_101;signature_desc=sigpep_I_bact: signal peptidase I;Name=TIGR02227;status=T;Dbxref="InterPro:IPR000223"
+ AT2G17780.2 Phobius protein_match 338 354 . + . date=06-10-2021;Target=AT2G17780.2 338 354;ID=match$141_338_354;signature_desc=Region of a membrane-bound protein predicted to be embedded in the membrane.;Name=TRANSMEMBRANE;status=T
+ AT2G17780.2 Phobius protein_match 1 337 . + . date=06-10-2021;Target=AT2G17780.2 1 337;ID=match$142_1_337;signature_desc=Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.;Name=NON_CYTOPLASMIC_DOMAIN;status=T
+ AT3G11780.2 SignalP_EUK protein_match 1 24 . + . date=06-10-2021;Target=mRNA.AT3G11780.2 1 24;ID=match$230_1_24;Name=SignalP-noTM;status=T
+ AT1G04300.2 CDD protein_match 40 114 1.54717E-13 + . date=06-10-2021;Target=mRNA.AT1G04300.2 40 114;Ontology_term="GO:0005515";ID=match$212_40_114;signature_desc=MATH;Name=cd00121;status=T;Dbxref="InterPro:IPR002083"
+
+eggNOG-mapper (tab separated) file:
+
+.. code:: text
+
+ #query_name seed_eggNOG_ortholog seed_ortholog_evalue seed_ortholog_score best_tax_level Preferred_name GOs EC KEGG_ko KEGG_Pathway KEGG_Module KEGG_Reaction KEGG_rclass BRITE KEGG_TC CAZy BiGG_Reaction taxonomic scope eggNOG OGs best eggNOG OG COG Functional cat. eggNOG free text desc.
+ ATKYO-2G54530.1 3702.AT2G35130.2 1.9e-179 636.0 Brassicales GO:0003674,GO:0003676,GO:0003723,GO:0003824,GO:0004518,GO:0004519,GO:0005488,GO:0005575,GO:0005622,GO:0005623,GO:0006139,GO:0006725,GO:0006807,GO:0008150,GO:0008152,GO:0009451,GO:0009987,GO:0016070,GO:0016787,GO:0016788,GO:0034641,GO:0043170,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0043412,GO:0044237,GO:0044238,GO:0044424,GO:0044464,GO:0046483,GO:0071704,GO:0090304,GO:0090305,GO:0097159,GO:1901360,GO:1901363 Viridiplantae 37R67@33090,3GAUT@35493,3HNDD@3699,KOG4197@1,KOG4197@2759 NA|NA|NA E Pentacotripeptide-repeat region of PRORP
+ ATKYO-UG22500.1 3712.Bo02269s010.1 7.5e-35 153.7 Brassicales Viridiplantae 29I9W@1,2RRH4@2759,383W6@33090,3GWQZ@35493,3I1A9@3699 NA|NA|NA
+ ATKYO-1G60060.1 3702.AT1G48090.1 0.0 6241.0 Brassicales ko:K19525 ko00000 Viridiplantae 37IJB@33090,3GAN0@35493,3HQ90@3699,COG5043@1,KOG1809@2759 NA|NA|NA U Vacuolar protein sorting-associated protein
+ ATKYO-3G74720.1 3702.AT3G52120.1 7.2e-245 852.8 Brassicales ko:K13096 ko00000,ko03041 Viridiplantae 37QYY@33090,3G9VU@35493,3HRDK@3699,KOG0965@1,KOG0965@2759 NA|NA|NA L SWAP (Suppressor-of-White-APricot) surp domain-containing protein D111 G-patch domain-containing protein
+ ATKYO-4G41660.1 3702.AT4G16340.1 0.0 3392.1 Brassicales GO:0003674,GO:0005085,GO:0005088,GO:0005089,GO:0005488,GO:0005515,GO:0005575,GO:0005622,GO:0005623,GO:0005634,GO:0005737,GO:0005783,GO:0005829,GO:0005886,GO:0006810,GO:0008064,GO:0008150,GO:0008360,GO:0009605,GO:0009606,GO:0009628,GO:0009629,GO:0009630,GO:0009958,GO:0009966,GO:0009987,GO:0010646,GO:0010928,GO:0012505,GO:0016020,GO:0016043,GO:0016192,GO:0017016,GO:0017048,GO:0019898,GO:0019899,GO:0022603,GO:0022604,GO:0023051,GO:0030832,GO:0031267,GO:0032535,GO:0032956,GO:0032970,GO:0033043,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044422,GO:0044424,GO:0044425,GO:0044432,GO:0044444,GO:0044446,GO:0044464,GO:0048583,GO:0050789,GO:0050793,GO:0050794,GO:0050896,GO:0051020,GO:0051128,GO:0051179,GO:0051234,GO:0051493,GO:0065007,GO:0065008,GO:0065009,GO:0070971,GO:0071840,GO:0071944,GO:0090066,GO:0098772,GO:0110053,GO:1902903 ko:K21852 ko00000,ko04131 Viridiplantae 37QIM@33090,3G8RK@35493,3HSFN@3699,KOG1997@1,KOG1997@2759 NA|NA|NA T Belongs to the DOCK family
+
+A custom input file must consist of two tab or comma separated columns.
+The first column should contain a gene/mRNA id, the second an identifier
+from one of four functional annotation databases: GO, Pfam, InterPro or
+TIGRFAM.
+
+.. code:: text
+
+ AT5G23090.4,GO:0046982
+ AT5G23090.4,IPR009072
+ AT1G27540.2,PF03478
+ AT2G18450.1,TIGR01816
+
+Phobius 1.01 'short' (tab separated) input file:
+
+.. code:: text
+
+ SEQENCE ID TM SP PREDICTION
+ mRNA-YPR204W 0 0 o
+ mRNA-ndhB-2_1 6 Y n5-16c21/22o37-57i64-83o89-113i134-156o168-189i223-246o
+
+Phobius 1.01 'long' (tab separated) input file:
+
+.. code:: text
+
+ ID mRNA-YPR204W
+ FT DOMAIN 1 1032 NON CYTOPLASMIC.
+ //
+ ID mRNA-ndhB-2_1
+ FT SIGNAL 1 21
+ FT DOMAIN 1 4 N-REGION.
+ FT DOMAIN 5 16 H-REGION.
+ FT DOMAIN 17 21 C-REGION.
+ FT DOMAIN 22 36 NON CYTOPLASMIC.
+ FT TRANSMEM 37 57
+ FT DOMAIN 58 63 CYTOPLASMIC.
+ FT TRANSMEM 64 83
+ FT DOMAIN 84 88 NON CYTOPLASMIC.
+ FT TRANSMEM 89 113
+ FT DOMAIN 114 133 CYTOPLASMIC.
+ FT TRANSMEM 134 156
+ FT DOMAIN 157 167 NON CYTOPLASMIC.
+ FT TRANSMEM 168 189
+ FT DOMAIN 190 222 CYTOPLASMIC.
+ FT TRANSMEM 223 246
+ FT DOMAIN 247 253 NON CYTOPLASMIC.
+ //
+
+SignalP 4.1 'short' (tab separated) input file:
+
+.. code:: text
+
+ # name Cmax pos Ymax pos Smax pos Smean D ? Dmaxcut Networks-used
+ mRNA-rpl2-3 0.148 20 0.136 20 0.146 3 0.126 0.131 N 0.450 SignalP-noTM
+ mRNA-cox2 0.107 25 0.132 12 0.270 4 0.162 0.148 N 0.450 SignalP-noTM
+ mRNA-cox2_1 0.850 17 0.776 17 0.785 2 0.717 0.753 Y 0.500 SignalP-TM
+
+SignalP 5.0 'short' (tab separated) input file:
+
+.. code:: text
+
+ # SignalP-5.0 Organism: Eukarya Timestamp: 20211122233246
+ # ID Prediction SP(Sec/SPI) OTHER CS Position
+ AT3G26880.1 SP(Sec/SPI) 0.998803 0.001197 CS pos: 21-22. VYG-KK. Pr: 0.9807
+ mRNA-rpl2-3 OTHER 0.001227 0.998773
+
+Relevant literature
+~~~~~~~~~~~~~~~~~~~
+
+- `Expansion of the Gene Ontology knowledgebase and resources
+ <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210579/>`_
+- `InterPro in 2019: improving coverage, classification and access to
+ protein sequence annotations
+ <https://academic.oup.com/nar/article/47/D1/D351/5162469>`_
+- `TIGRFAMs and Genome Properties in 2013
+ <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531188/>`_
+- `A Combined Transmembrane Topology and Signal Peptide Prediction
+ Method
+ <https://www.sciencedirect.com/science/article/abs/pii/S0022283604002943?via%3Dihub>`_
+- `Expanded microbial genome coverage and improved protein family
+ annotation in the COG database
+ <https://academic.oup.com/nar/article/43/D1/D261/2439462>`_
+
+--------------
+
+Add antiSMASH gene clusters
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Read antiSMASH output and incorporate **Biosynthetic Gene Clusters**
+(BGC) nodes into the pangenome database. A 'bgc' node holds the gene
+cluster product, the cluster address and has a relationship to all gene
+nodes of the cluster. For this function to work, antiSMASH should be
+performed with the same FASTA and GFF3 files used for building the
+pangenome. antiSMASH output will not match the identifiers of the
+pangenome when no GFF file was included.
+
+As of PanTools v3.3.4 the required antiSMASH version is 6.0.0. Gene
+cluster information is parsed from the .JSON file that is generated in
+each run. We try to keep the parser updated with newer versions but
+please contact us when this is no longer the case.
+
+========= ======= ============
+\ Version Version date
+========= ======= ============
+antiSMASH 6.0.0 21-02-2021
+========= ======= ============
+
+Required arguments
+~~~~~~~~~~~~~~~~~~
+
+| ``--database-path``/``-dp`` Path to the pangenome database.
+| ``--input-file``/``-if`` A text file with on each line a genome number
+ and the full path to the corresponding antiSMASH output file,
+ separated by a space.
+
+Optional arguments
+~~~~~~~~~~~~~~~~~~
+
+``--annotations-file``/``-af`` A text file with the identifiers of
+annotations to be included, each on a separate line. The most recent
+annotation is selected for genomes without an identifier.
+
+Example input file
+~~~~~~~~~~~~~~~~~~
+
+The ``--input-file`` requires to be formatted like a regular annotation
+input file. Each line of the file starts with the genome number followed
+by the full path to the **JSON** file.
+
+.. code:: text
+
+ 1 /mnt/scratch/IPO3844/antismash/IPO3844.json
+ 4 /home/user/IPO3845/antismash/IPO3845.json
+
+Example command
+~~~~~~~~~~~~~~~
+
+.. code:: bash
+
+ $ pantools add_antismash -dp tomato_DB -if clusters.txt
+
+--------------
+
+Removing data
+-------------
+
+The following functionalities allow the removal of large sets of nodes
+and relationships from the pangenome. These functions will first ask for
+a confirmation before the nodes are actually removed. Be careful, the
+data is not backed up and removing nodes or properties means it is
+permanently gone.
+
+--------------
+
+Remove nodes
+~~~~~~~~~~~~
+
+Remove a selection of nodes and their relationships from the pangenome.
+For a pangenome database the following nodes cannot be removed:
+*nucleotide*, *pangenome*, *genome*, *sequence*. When using a
+panproteome, *mRNA* nodes cannot be removed.
+
+Required argument
+"""""""""""""""""
+
+``--database-path``/``-dp`` Path to the pangenome database.
+
+**Requires either one of the following arguments**
+
+| ``--node`` one or multiple node identifiers, separated by a comma.
+| ``--label`` a node label, all nodes matching the label are removed.
+
+Optional arguments
+""""""""""""""""""
+
+Both optional arguments can only be used in combination with
+``--label``.
+
+| ``--skip``/``-sk`` Do not remove nodes of the selected genomes.
+| ``--reference``/``-ref`` Only remove nodes of the selected genomes.
+
+Example commands
+""""""""""""""""
+
+.. code:: bash
+
+ $ pantools remove_nodes -dp tomato_DB --node 10348734,10348735,10348736
+ $ pantools remove_nodes -dp tomato_DB --label pfam
+ $ pantools remove_nodes -dp tomato_DB --label interpro --reference 2-6
+
+--------------
+
+Remove phenotypes
+~~~~~~~~~~~~~~~~~
+
+Delete **phenotype** nodes or remove specific phenotype information from
+the nodes. The specific phenotype property needs to be specified with
+``--phenotype``. When this argument is not included, *phenotype* nodes
+are removed.
+
+Required argument
+"""""""""""""""""
+
+``--database-path``/``-dp`` Path to the pangenome database.
+
+Optional arguments
+""""""""""""""""""
+
+| ``--phenotype``/``-ph`` name of the phenotype. All information of the
+ given phenotype is removed from 'phenotype' nodes.
+| ``--skip``/``-sk`` Do not remove nodes of the selected genomes.
+| ``--reference``/``-ref`` Only remove nodes of the selected genomes.
+
+Example commands
+""""""""""""""""
+
+.. code:: bash
+
+ $ pantools remove_phenotype -dp tomato_DB
+ $ pantools remove_phenotype -dp tomato_DB --phenotype color
+ $ pantools remove_phenotype -dp tomato_DB --phenotype color --skip 11,12
+
+--------------
+
+Remove annotations
+~~~~~~~~~~~~~~~~~~
+
+Remove all the genomic features that belong to annotations, such as
+*gene*, *mRNA*, *exon*, *tRNA*, and *feature* nodes. Functional
+annotation nodes are not removed with this function but can be removed
+with :ref:`remove_nodes <construct:remove nodes>`. Removing annotations
+can be done in two ways:
+
+1. Selecting genomes with ``--reference`` or ``--skip``, for which all
+ annotation features will be removed.
+2. Remove specific annotations by providing a text file with identifiers
+ via the ``--annotations-file`` argument.
+
+Required argument
+"""""""""""""""""
+
+``--database-path``/``-dp`` Path to the pangenome database.
+
+**Requires either one of the following arguments**
+
+| ``--skip``/``-sk`` a selection of genomes excluded from the removal of
+ annotations.
+| ``--reference``/``-ref`` a selection of genomes for which all
+ annotations will be removed.
+| ``--annotations-file``/``-af`` A text file with the identifiers of
+ annotations to be removed, each on a separate line.
+
+Example input file
+""""""""""""""""""
+
+The input file should be a single line with annotation identifiers
+separated by a comma. The following example will remove the first
+annotations of genome 1, 2 and 3 and the second annotation of genome 1.
+
+.. code:: text
+
+ 1_1
+ 1_2
+ 2_1
+ 3_1
+
+Example command
+"""""""""""""""
+
+.. code:: bash
+
+ $ pantools remove_annotations --skip 3,4,5
+ $ pantools remove_annotations -af annotations.txt
+
+--------------
+
+Move or remove grouping
+~~~~~~~~~~~~~~~~~~~~~~~
+
+As only one grouping can be active at the time, the currently active
+grouping needs to be removed or inactivated before
+:ref:`group <construct:group>` can be run again.
+
+- **remove_grouping** deletes all 'homology_group' nodes and
+ 'is_similar' relations between 'mRNA' nodes from the database.
+- **move_grouping** relabels 'homology_group' nodes to
+ 'inactive_homology_group'. The moved grouping can be activated again
+ with :ref:`change_grouping <construct:change-grouping>`.
+
+Required argument
+"""""""""""""""""
+
+``--database-path``/``-dp`` Path to the pangenome database.
+
+Optional arguments for **remove_grouping**
+""""""""""""""""""""""""""""""""""""""""""
+
+| ``--version`` Select a specific grouping version to be removed. Two
+ additional options: 'all' to remove all groupings and 'all_inactive' to
+ remove all inactive groupings.
+| ``--fast`` Do not remove the 'is_similar' relationships between mRNA
+ nodes. This does not influence the next grouping.
+
+Example command
+"""""""""""""""
+
+.. code:: bash
+
+ $ pantools move_grouping -dp tomato_DB
+
+ $ pantools remove_grouping -dp tomato_DB
+ $ pantools remove_grouping -dp tomato_DB --version 1
+ $ pantools remove_grouping -dp tomato_DB --version all --fast
+ $ pantools remove_grouping -dp tomato_DB --version all_inactive
diff --git a/docs/source/differences.rst b/docs/source/differences.rst
new file mode 100644
index 0000000000000000000000000000000000000000..0445b539eeec48d0baab38f3e44a22c03845f3a3
--- /dev/null
+++ b/docs/source/differences.rst
@@ -0,0 +1,77 @@
+Differences between pangenome and panproteome
+=============================================
+
+PanTools offers functionalities to build and analyze a pangenome or
+panproteome.
+
+A **pangenome** is constructed from genome and annotation files. First,
+genome sequences are k-merized and compressed into a De Bruijn graph.
+Genes and other annotation features from annotation files are integrated
+into the pangenome as ‘gene’, ‘mRNA’ and ‘CDS’ nodes. Gene start and
+stop positions are annotated in the graph as relationships and connect
+the annotation layer to the nucleotide layer. The protein sequences can
+be clustered into homology groups and connect homologous proteins from
+different genomes.
+
+A **panproteome** is built from protein sequences only, ignoring the
+underlying genome structure. Again, the protein sequences are clustered
+into homology groups which serve as main input for many functionalities.
+
+In addition to the single layer in panproteomes and three layers in
+pangenomes, a functional layer can be included in both databases. This
+layer consists of multiple functional annotation databases (e.g. GO,
+PFAM) and connects proteins with a shared function.
+
+Since there is only a protein layer and functional layer present in
+panproteomes, not all functions can be utilized. See the table below for
+which functions can be used for pangenomes and panproteomes.
+
+.. figure:: figures/layers.png
+ :width: 600
+ :align: center
+
+ *Schematic of genome, annotation, and protein layer of a pangenome
+ database. Figure taken from Efficient inference of homologs in large
+ eukaryotic pan-proteomes*
+
+Available functions
+-------------------
+:doc:`construct`
+
+.. csv-table::
+ :file: tables/differences_construct.csv
+ :header-rows: 1
+ :delim: ;
+
+:doc:`characterize`
+
+.. csv-table::
+ :file: tables/differences_characterize.csv
+ :header-rows: 1
+ :delim: ;
+
+:doc:`explore`
+
+.. csv-table::
+ :file: tables/differences_explore.csv
+ :header-rows: 1
+ :delim: ;
+
+:doc:`phylogeny`
+
+.. csv-table::
+ :file: tables/differences_phylogeny.csv
+ :header-rows: 1
+ :delim: ;
+
+:doc:`mapping`
+
+.. list-table::
+ :header-rows: 1
+
+ * - Function
+ - Pangenome
+ - Panproteome
+ * - Map
+ - :green:`YES`
+ - :red:`NO`
diff --git a/docs/source/explore.rst b/docs/source/explore.rst
new file mode 100644
index 0000000000000000000000000000000000000000..6ecf02035e7d3f588aa7fd38ed636b8c40a4e106
--- /dev/null
+++ b/docs/source/explore.rst
@@ -0,0 +1,588 @@
+Explore the pangenome
+=====================
+
+The functionalities on this page allow to actively explore the
+pangenome.
+
+- Retrieve regions from the pangenome
+- Retrieve sequences and functional annotations from homology groups
+- Search for genes using a gene name, functional annotation or database
+ node identifier
+- Align homology groups or genomic regions
+- GO enrichment analysis
+
+Gene locations
+--------------
+
+Identify and compare gene clusters of neighbouring genes based on a set
+of homology groups. First, identifies the genomic position of genes in
+homology groups, retrieves the order of genes per genome and based on
+this construct the gene clusters. If homology groups with multiple
+genomes were selected, the gene cluster composition is compared between
+genomes. When a ``--phenotype`` is included, gene clusters can be found
+that only consist of groups of a certain phenotype.
+
+For example, 100 groups were predicted as core in a pangenome of 5
+genomes. The gene clusters are first identified per genome, after which
+it compares the gene order of one genome to all the other genomes. The
+result could be 75 groups with genes that are not only homologous but
+also share their gene neighbourhood. Another example, when accessory
+(present 2 in to 4 genomes) groups are given to this function in
+combination with a ``--phenotype`` (assigned to only two genomes), the
+function can return clusters that can only be found in the phenotype
+members.
+
+Required arguments
+~~~~~~~~~~~~~~~~~~
+
+| ``--database-path``/``-dp`` Path to the database.
+| ``--homology-groups``/``-hm`` A text file with homology group node
+ identifiers, seperated by a comma.
+
+Optional arguments
+~~~~~~~~~~~~~~~~~~
+
+| ``--phenotype``/``-ph`` A phenotype name, used to identify gene
+ clusters shared by all phenotype members.
+| ``--value`` The number of allowed nucleotides between two neighbouring
+ genes (default is 1 MB).
+| ``--gap-open``/``-go`` When constructing the clusters, allow a number
+ of genes for each cluster that are not originally part of the input
+ groups (default is 0).
+| ``--core-threshold`` Lower the threshold (%) for a group to be
+ considered (soft) core (default is the total number of genomes found
+ in the groups, not a percentage).
+| ``--skip``/``-sk`` Exclude a selection of genomes.
+| ``--reference``/``-ref`` Only include a selection of genomes.
+| ``--mode ignore-copies`` Duplicated and co-localized genes no longer
+ break up clusters.
+
+Example command
+~~~~~~~~~~~~~~~
+
+.. code:: bash
+
+ $ pantools locate_genes -dp tomato_DB -hm phenotype_groups.csv
+ $ pantools locate_genes -dp tomato_DB -hm unique_groups.csv --value 5000 -go 1
+ $ pantools locate_genes -dp tomato_DB -hm accessory_groups.csv --core-threshold 95 -go 1
+
+Output files
+~~~~~~~~~~~~
+
+Output files are stored in *database_directory/locate_genes/*
+
+- **gene_clusters_by_position.txt**, the identified gene clusters
+ ordered by their position in the genome.
+- **gene_clusters_by_size.txt**, the identified gene clusters ordered
+ from largest to smallest.
+- **compare_gene_clusters**, the composition of found gene clusters is
+ compared to the other genomes. For each cluster, it shows which parts
+ match other clusters and which parts do not. The file is not created
+ when homology groups only contain proteins of a single genome
+ (unique).
+
+When a ``--phenotype`` is included
+
+- **phenotype_clusters**, homology group node identifiers from
+ phenotype shared and specific clusters.
+- **compare_gene_clusters_PHENOTYPE.txt**, the same information as
+ **compare_gene_clusters** but now the gene cluster comparison is only
+ done between phenotype members.
+
+--------------
+
+Find genes
+----------
+
+Find genes by name
+~~~~~~~~~~~~~~~~~~
+
+Find your genes of interest in the pangenome by using the gene name and
+extract the nucleotide and protein sequence. To be able to find a gene,
+every letter of the given input must match a gene name. The search is
+not case sensitive. Performing a search with 'sonic1' as query will not
+be able find 'sonic', but is able to find Sonic1, SONIC1 or sOnIc1.
+Including the ``--mode 1`` argument allows a more relaxed search and
+using 'sonic' will now also find gene name variations as 'sonic1',
+'sonic3' etc..
+
+Be aware, for this function to work it is important that genomes are
+annotated by a method that follows the rules for genetic nomenclature.
+Gene naming can be inconsistent when different tools are used for genome
+annotation, making this functionality ineffective.
+
+This function is the same as
+:ref:`mlsa_find_genes <phylogeny:step 1 search for genes>` but
+uses a different output directory. Several warnings (shown in the other
+manual) can be generated during the search. These warning are less
+relevant for this function as the genes are not required to be single
+copy-orthologous.
+
+Required arguments
+""""""""""""""""""
+
+| ``--database-path``/``-dp`` Path to the database.
+| ``--name`` One or multiple gene names, seperated by a comma.
+
+Optional arguments
+""""""""""""""""""
+
+| ``--skip``/``-sk`` Exclude a selection of genomes.
+| ``--reference``/``-ref`` Exclude a selection of genomes.
+| ``--mode extensive`` Perform a more extensive gene search.
+
+Example command
+"""""""""""""""
+
+.. code:: text
+
+ $ pantools find_genes_by_name -dp tomato_DB --name dnaX,gapA,recA
+ $ pantools find_genes_by_name -dp tomato_DB --name gapA --mode extensive
+
+Output files
+""""""""""""
+
+Output files are stored in */database_directory/find_genes/by_name/*.
+For each gene name that was included, a nucleotide and protein and
+.FASTA file is created with sequences found in all genomes.
+
+- **find_genes_by_name.log**, relevant information about the extracted
+ genes: node identifier, gene location, homology group etc..
+
+--------------
+
+Find genes by annotation
+~~~~~~~~~~~~~~~~~~~~~~~~
+
+Find genes of interest in the pangenome that share a functional
+annotation node and extract the nucleotide and protein sequence.
+
+Required arguments
+""""""""""""""""""
+
+``--database-path``/``-dp`` Path to the database.
+
+Requires either **one** of the following arguments
+
+| ``--node`` One or multiple identifiers of function nodes (GO,
+ InterPro, PFAM, TIGRFAM), seperated by a comma.
+| ``--name`` One or multiple function identifiers (GO, InterPro, PFAM,
+ TIGRFAM), seperated by a comma.
+
+Optional arguments
+""""""""""""""""""
+
+| ``--skip``/``-sk`` Exclude a selection of genomes.
+| ``--reference``/``-ref`` Only include a selection of genomes.
+
+Example command
+"""""""""""""""
+
+.. code:: text
+
+ $ pantools find_genes_by_annotation -dp tomato_DB --node 14928,25809
+ $ pantools find_genes_by_annotation -dp tomato_DB --name PF00005,GO:0000160,IPR000683,TIGR02499
+
+Output files
+""""""""""""
+
+Output files are stored in
+*/database_directory/find_genes/by_annotation/*. For each function
+(node) that was included, a nucleotide and protein and .FASTA file is
+created with sequences from the genes that are connected to the node.
+
+- **find_genes_by_annotation.log**, relevant information about the
+ extracted genes: node identifier, gene location, homology group etc..
+
+--------------
+
+Find genes in region
+~~~~~~~~~~~~~~~~~~~~
+
+Find genes of interest in the pangenome that can be (partially) found
+within a given region (partially). For each found gene, relevant
+information, the nucleotide sequence and protein sequence is extracted.
+
+Required arguments
+""""""""""""""""""
+
+| ``--database-path``/``-dp`` Path to the database.
+| ``--regions-file``/``-rf`` A text file containing genome locations
+ with on each line: a genome number, sequence number, begin and end
+ position, separated by a space.
+
+Optional arguments
+""""""""""""""""""
+
+``--mode partial`` Also retrieve genes that only partially overlap the
+input regions.
+
+Example input file
+""""""""""""""""""
+
+Each line must have a genome number, sequence number, begin and end
+positions that are separated by a space.
+
+.. code:: text
+
+ 195 1 477722 478426
+ 71 10 17346 18056
+ 138 47 159593 160300
+
+Example command
+"""""""""""""""
+
+.. code:: bash
+
+ $ pantools find_genes_in_region -dp tomato_DB -rf regions.txt
+ $ pantools find_genes_in_region -dp tomato_DB -rf regions.txt --mode partial
+
+Output files
+""""""""""""
+
+Output files are stored in */database_directory/find_genes/in_region/*.
+For each region that was included, a nucleotide and protein and .FASTA
+file is created with sequences from the genes that are found within the
+region.
+
+- **find_genes_in_region.log**, relevant information about the
+ extracted genes: node identifier, gene location, homology group etc..
+
+--------------
+
+Functional annotations
+----------------------
+
+The following functions can only be used when any type of functional
+annotation is
+:ref:`added to the database <construct:add functional annotations>`.
+
+Show GO
+~~~~~~~
+
+For a selection of '**GO**' nodes, retrieves connected 'mRNA' nodes,
+child and all parent GO terms that are higher in the GO hierarchy. This
+function follows the 'is_a' relationships of GO each node to their
+parent GO term until the 'biological process', 'molecular function' or
+'cellular location' node is reached. This can be is useful in case
+InterProScan annotations were included, as these only add the most
+specific GO terms of the hierarchy to a sequence.
+
+Required arguments
+""""""""""""""""""
+
+``--database-path``/``-dp`` Path to the database
+
+Requires either **one** of the following arguments
+
+| ``--node`` One or multiple identifiers of 'GO' nodes, seperated by a
+ comma.
+| ``--name`` One or multiple GO term identifiers, seperated by a comma.
+
+Example commands
+""""""""""""""""
+
+.. code:: text
+
+ $ pantools show_go -dp tomato_DB --node 15078,15079
+ $ pantools show_go -dp tomato_DB --name GO:0000001,GO:0000002,GO:0008982
+
+Output file
+"""""""""""
+
+- **show_go.txt**, information of the selected GO node(s): the
+ connected 'mRNA' nodes, the GO layer below, and all layers above.
+
+--------------
+
+Compare GO
+~~~~~~~~~~
+
+Check if and how similar two given GO terms are. For both nodes, follows
+the 'is_a' relationships up to their parent GO terms until the
+'biological process', 'molecular function' or 'cellular location' node
+is reached. After all parent terms are found, the shared GO terms and
+their location in the hierarchy is reported.
+
+Required arguments
+""""""""""""""""""
+
+``--database-path``/``-dp`` Path to the database.
+
+Requires either **one** of the following arguments
+
+| ``--node`` Two node identifiers of 'GO' nodes, seperated by a comma.
+| ``--name`` Two GO identifiers, seperated by a comma.
+
+Example command
+"""""""""""""""
+
+.. code:: text
+
+ $ pantools compare_go -dp tomato_DB --name GO:0032775,GO:0006313
+ $ pantools compare_go -dp tomato_DB --node 741487,741488
+
+Output file
+"""""""""""
+
+Output files are stored in *database_directory/function/*
+
+- **compare_go.txt**, information of the two GO nodes: the connected
+ 'mRNA' nodes, the GO layer below, all layers above and the shared GO
+ terms between the two nodes.
+
+--------------
+
+Homology group information
+--------------------------
+
+Report all available information of one or multiple homology groups.
+
+Required arguments
+~~~~~~~~~~~~~~~~~~
+
+| ``--database-path``/``-dp`` Path to the database.
+| ``--homology-groups``/``-hm`` A text file with homology group node
+ identifiers, seperated by a comma
+
+Optional arguments
+~~~~~~~~~~~~~~~~~~
+
+| ``--label`` Name of function identifiers from GO, PFAM, InterPro or
+ TIGRAM. To find Phobius (P) or SignalP (S) annotations, include:
+ 'secreted' (P/S), 'receptor' (P/S), or 'transmembrane' (P).
+| ``--name`` One or multiple gene names, seperated by a comma.
+| ``--skip``/``-sk`` Exclude a selection of genomes.
+| ``--reference``/``-ref`` Only include a selection of genomes.
+
+Example command
+~~~~~~~~~~~~~~~
+
+.. code:: bash
+
+ $ pantools group_info -dp yeast_DB -hm core_groups.txt
+ $ pantools group_info -dp yeast_DB -hm core_groups.txt --label GO:0032775,GO:0006313 --name budC,estP
+
+Output files
+~~~~~~~~~~~~
+
+Output files are stored in
+*database_directory/alignments/grouping_v?/groups/*. For each homology
+group that was included, a nucleotide and protein and .FASTA file is
+created with sequences found in all genomes.
+
+- **group_info.txt**, relevant information for each homology group:
+ number of copies per genome, gene names, mRNA node identifiers,
+ functions, protein sequence lengths, etc..
+- **group_functions.txt**, full description of the functions found in
+ homology groups
+
+When function identifiers are included via ``--label``
+
+- **groups_with_function.txt**, homology group node identifiers from
+ groups that match one of the input functions.
+
+When gene names are included via ``--name``
+
+- **groups_with_name.txt**, homology group node identifiers from groups
+ that match one of the input gene ames.
+
+--------------
+
+Sequence alignments
+-------------------
+
+The manual for PanTools' sequence alignment functionalities moved to a
+standalone page - :doc:`msa`.
+
+--------------
+
+Matrix files
+------------
+
+Several functions generate tables in a CSV file format. as tables that
+the following functions can work with. For example, ANI scores, *k*-mer
+and gene distance used for constructing the Neighbour Joining
+:ref:`phylogenetic trees <phylogeny:phylogeny>`, and the identity and
+protein sequence similarity tables created by the
+:ref:`alignment functions <msa:sequence alignments>`.
+
+Order matrix
+~~~~~~~~~~~~
+
+Transforms the CSV table to easy to read file by ordering the values in
+ascending order from low to high or descending order when
+``--mode desc`` is included in the command. If phenotype information is
+included in the header, a separate file with the range of found values
+is created for each phenotype. If this information is not present (only
+genome numbers in the header), use
+:ref:`rename_matrix <explore:rename matrix>` to change the headers.
+
+Required argument
+"""""""""""""""""
+
+| ``--database-path``/``-dp`` Path to the database.
+| ``--input-file``/``-af`` A CSV formatted matrix file.
+
+Optional argument
+"""""""""""""""""
+
+| ``--skip``/``-sk`` Skip over the values of a selection of genomes.
+| ``--reference``/``-ref`` Only include the values from a selection of
+ genomes.
+| ``--mode asc`` or ``--mode desc`` Order the matrix in ascending or
+ descending order (ascending is default).
+
+Example command
+"""""""""""""""
+
+.. code:: bash
+
+ $ pantools order_matrix -dp bacteria_DB -if bacteria_DB/ANI/fastANI/ANI_distance_matrix.csv
+ $ pantools order_matrix -dp bacteria_DB -if bacteria_DB/ANI/fastANI/ANI_distance_matrix.csv --mode desc
+
+Output file
+"""""""""""
+
+Output is written to the same directory as the selected input file
+
+- '*old file name*' + '*_ORDERED*', ordered values of the original
+ matrix file.
+
+When phenotype information is present in the header
+
+- '*old file name*' + '*_PHENOTYPE*', range of values per phenotype.
+
+--------------
+
+Rename matrix
+~~~~~~~~~~~~~
+
+Rename the headers (first row and leftmost column) of CSV formatted
+matrix files. If no ``--phenotype`` is included, headers are changed to
+only contain genome numbers.
+
+Required arguments
+""""""""""""""""""
+
+| ``--database-path``/``-dp`` Path to the database.
+| ``--input-file``/``-af`` a matrix file with numerical values.
+
+Optional arguments
+""""""""""""""""""
+
+| ``--phenotype``/``-ph`` A phenotype name, used to include phenotype
+ information into the headers.
+| ``--skip``/``sk`` Exclude a selection of genomes from the new matrix
+ file. ``--reference``/``-ref`` Only include a selection of genomes in
+ the new matrix file.
+| ``--mode no-numbers`` Exclude genome numbers from the headers.
+
+Example command
+"""""""""""""""
+
+.. code:: bash
+
+ $ pantools rename_matrix -dp pecto_DB -phenotype species -if pecto_DB/ANI/fastANI/ANI_distance_matrix.csv
+
+Output file
+"""""""""""
+
+Output is written to the same directory as the selected input file.
+
+- '*old file name*' + '*_RENAMED*', the original matrix file with
+ changed headers.
+
+--------------
+
+Retrieve regions, genomes or features
+-------------------------------------
+
+The two following functions allow users to retrieve genomic regions from
+the pangenome.
+
+Retrieve regions
+~~~~~~~~~~~~~~~~
+
+Retrieve the full genome sequence or genomic regions from the pangenome.
+
+Required arguments
+""""""""""""""""""
+
+| ``--database-path``/``-dp`` Path to the database.
+| ``--regions-file``/``-rf`` A text file containing genome locations
+ with on each line: a genome number, sequence number, begin and end
+ positions separated by a space.
+
+Example command
+"""""""""""""""
+
+.. code:: bash
+
+ $ pantools retrieve_regions -dp pecto_DB -rf regions.txt
+
+Example input
+"""""""""""""
+
+To extract:
+
+- Complete genome - Include a genome number
+- An entire sequence - Include a genome number with sequence number
+- A genomic region - Include a genome number, sequence number, begin
+ and end positions that are separated by a space. Place a minus symbol
+ behind the regions to extract the reverse complement sequence of the
+ region.
+
+.. code:: text
+
+ 1
+ 1 1
+ 1 1 1 10000
+ 1 1 1000 1500 -
+ 195 1 477722 478426
+ 71 10 17346 18056 -
+ 138 47 159593 160300 -
+
+Output file
+"""""""""""
+
+A single FASTA file is created for all given locations and is stored in
+the database directory.
+
+Retrieve features
+~~~~~~~~~~~~~~~~~
+
+To retrieve the sequence of annotated features from the pangenome.
+
+Required arguments
+""""""""""""""""""
+
+| ``--database-path``/``-dp`` Path to the database.
+| ``--feature-type`` or ``-ft`` The feature name; for example 'gene',
+ 'mRNA', 'exon', 'tRNA', etc.
+
+Optional arguments
+""""""""""""""""""
+
+Use one of the following arguments to limit the sequence retrieval to a
+selection of genomes.
+
+| ``--skip``/``-sk`` Exclude a selection of genomes.
+| ``--reference``/``-ref`` Only include a selection of genomes.
+
+Example command
+"""""""""""""""
+
+.. code:: bash
+
+ $ pantools retrieve_features -dp pecto_DB --feature-type gene
+ $ pantools retrieve_features -dp pecto_DB --ft mRNA
+
+Output files
+""""""""""""
+
+For each genome a FASTA file containing the retrieved features will be
+stored in the database directory. For example, genes.1.fasta contains
+all the genes annotated in genome 1.
+
+--------------
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+PanTools version 3.4.0
+======================
+
+PanTools is a toolkit for comparative analysis of large number of
+genomes. It is developed in the Bioinformatics Group of Wageningen
+University, the Netherlands. Please cite the relevant publication(s)
+from the list of publications if you use PanTools in your research.
+
+Licence
+-------
+
+PanTools has been licensed under `GNU GENERAL PUBLIC LICENSE version 3.
+<https://www.gnu.org/licenses/gpl-3.0.en.html>`_
+
+Publications
+------------
+
+- `PanTools: representation, storage and exploration of pan-genomic
+ data.
+ <https://academic.oup.com/bioinformatics/article/32/17/i487/2450785>`_
+- `Efficient inference of homologs in large eukaryotic pan-proteomes
+ <https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2362-4>`_
+- `Pan-genomic read mapping
+ <https://www.biorxiv.org/content/10.1101/813634v1>`_
+- `The Pectobacterium pangenome, with a focus on Pectobacterium
+ brasiliense, shows a robust core and extensive exchange of genes
+ from a shared gene pool
+ <https://doi.org/10.1186/s12864-021-07583-5>`_
+- `Pantools v3: functional annotation, classification, and phylogenomics
+ <https://doi.org/10.1093/bioinformatics/btac506>`_
+
+Functionalities
+---------------
+
+PanTools currently provides these functionalities:
+
+- Construction of a panproteome
+- Adding new genomes to the pangenome
+- Adding structural/functional annotations to the genomes
+- Detecting homology groups based on similarity of proteins
+- Optimization of homology grouping using BUSCO
+- Read mapping
+- Gene classification
+- Phylogenetic methods
+
+Requirements
+------------
+
+- \ **Java Virtual Machine**\ version 1.8 or higher, Add path to the
+ java executable to your OS path environment variable.
+- \ **KMC**\ : A disk-based k-mer counter, After downloading the
+ appropriate version (linux, macos or windows), add path to the *kmc*
+ and *kmc_tools* executables to your OS path environment variable.
+- \ **MCL**\ : The Markov Clustering Algorithm, After downloading and
+ compiling the software, add path to the *mcl* executable to your OS
+ path environment variable.
+
+For installing and configuring all required software, please see our
+:doc:`install` page.
+
+Running the program
+-------------------
+
+Add the path to the java archive of PanTools, located in the
+*pantools/target* subdirectory, to the OS path environment variable.
+Then run PanTools from the command line by:
+
+.. code:: bash
+
+ $ java <JVM options> -jar pantools-3.4.0.jar <subcommand> <arguments>
+
+| **Useful JVM options**
+| - **-server** : To optimize JIT compilations for higher performance
+| - **-Xmn(a number followed by m/g)** : Minimum heap size in mega/giga
+ bytes
+| - **-Xmx(a number followed by m/g)** : Maximum heap size in mega/giga
+ bytes
+
+Contents
+--------
+
+.. toctree::
+ :maxdepth: 1
+
+ install
+ construct
+ characterize
+ phylogeny
+ msa
+ explore
+ mapping
+ query
+ differences
+ Tutorial 1 - Install PanTools <tutorial_part1>
+ Tutorial 2 - Construct pangenome <tutorial_part2>
+ Tutorial 3 - Neo4j browser <tutorial_part3>
+ Tutorial 4 - Characterization <tutorial_part4>
+ Tutorial 5 - Phylogeny <tutorial_part5>
+
+PanTools has its documentation hosted on Read the Docs.
diff --git a/docs/source/install.rst b/docs/source/install.rst
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+Installing and configuring the required software
+================================================
+
+1. :ref:`install:download pantools`
+2. :ref:`install:install neo4j`
+3. :ref:`Install dependencies, either manually or through conda. <install:dependencies>`
+
+For PanTools developers:
+
+4. :ref:`install:installing pre-commit hooks`
+
+Download PanTools
+-----------------
+
+The preferred option is to download the .jar file from
+https://git.wur.nl/bioinformatics/pantools/-/releases and put it in a
+directory named "pantools/target".
+
+Alternatively, follow the installation and compilation instructions from the
+README.md file in the desired version (e.g.
+https://git.wur.nl/bioinformatics/pantools/-/tree/v3.4.0).
+
+Test if PanTools is executable:
+
+.. code:: bash
+
+ $ java -jar /YOUR_FULL_PATH/pantools/target/pantools-3.4.0.jar
+
+If the help page does not appear this (likely) means you don't have a
+properly working Java version 8. Java is included in the PanTools conda
+environment, please consider to first install the environment. To
+manually download Java, follow the instructions at
+https://www.java.com/en/download.
+
+Set PanTools alias
+~~~~~~~~~~~~~~~~~~
+
+To avoid typing long command line arguments every time, we suggest setting an alias to your profile.
+Set an alias in your ~/.bashrc using the following command. Always
+include the **full** path to PanTools' .jar file.
+
+If Java is set to your $PATH.
+
+.. code:: bash
+
+ $ echo "alias pantools='java -Xms20g -Xmx50g -jar /YOUR_FULL_PATH/pantools/target/pantools-3.4.0.jar'" >> ~/.bashrc
+
+If Java is not set to your $PATH, include the **full** path in the
+alias. Replace 'YOUR_PATH' 2x with the correct directory structure.
+
+.. code:: bash
+
+ $ echo "alias pantools='/YOUR_PATH/jdk1.8.0_161/bin/java -Xms20g -Xmx50g -jar /YOUR_PATH/pantools/target/pantools-3.4.0.jar'" >> ~/.bashrc
+
+Source your profile and test if the alias works.
+
+.. code:: bash
+
+ $ source ~/.bashrc
+ pantools version
+
+--------------
+
+Install Neo4j
+-------------
+
+Although Neo4j is not needed for any of the PanTools functionalities, it
+is required to be able to start up a database and use cypher queries. In
+the PanTools versions up to 3.2 we use Neo4j 3.5.3 libraries, whereas
+newer releases use Neo4j 3.5.30. Neo4j version 3.5.30 is compatible with
+all earlier PanTools versions.
+
+Download the Neo4j 3.5.30 community edition from the `Neo4j
+website <https://neo4j.com/download-center/>`_ or download the binaries
+directly from our
+`server <http://www.bioinformatics.nl/pangenomics/tutorial/neo4j-community-3.5.30-unix.tar.gz>`_.
+
+.. code:: bash
+
+ $ wget http://www.bioinformatics.nl/pangenomics/tutorial/neo4j-community-3.5.30-unix.tar.gz
+ $ tar -xvzf neo4j-community-*
+
+ # Edit your ~/.bashrc to include Neo4j to your $PATH
+ $ echo "export PATH=/YOUR_PATH/neo4j-community-3.5.30/bin:\$PATH" >> ~/.bashrc #replace YOUR_PATH with the correct path on your computer
+ $ source ~/.bashrc
+ $ neo4j status # test if Neo4j is executable
+
+Official Neo4j 3.5 manual: https://neo4j.com/docs/operations-manual/3.5/
+
+--------------
+
+Dependencies
+------------
+
+Some of PanTools functionalities require additional software to be
+installed. Installing every dependency will take a considerate amount of
+time, therefore we highly recommend to use Mamba. Mamba efficiently
+manages Conda environments allowing the installation of all required
+tools into a separate environment. Instructions for creating the Mamba
+environment or installing the tools manually are found in the sections
+below.
+
+Install dependencies using Conda
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Instructions on how to install and use conda can be found in the
+\ **conda manual page**\ . Once conda is installed, we suggest to
+install Mamba into the Conda base environment to enable much faster
+dependency solving.
+
+To install every dependency, download \ **pantools.yaml**\ and include
+it in the installation command.
+
+.. code:: bash
+
+ $ wget http://www.bioinformatics.nl/pangenomics/manual/pantools.yaml
+ $ conda install mamba -n base -c conda-forge
+ $ mamba env create -n pantools --file pantools.yaml
+
+ $ conda activate pantools # activate the environment before using PanTools
+ $ conda deactivate # deactivate when you are done
+
+Run the following commands when you do not want to install every
+dependency, but only specific ones for the analysis that you're
+interested in.
+
+.. code:: bash
+
+ $ conda create -n pantools python=3.6 kmc=3.0 mcl # Creates an environment that is able to construct the pangenome and cluster protein sequences
+ $ conda install -n pantools mafft iqtree fasttree blast mash fastani busco=5.2.2 r-ggplot2 r-ape graphviz # include tools you want to install via conda
+
+--------------
+
+Manual installation of dependencies
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+All tools must be set to your $PATH so PanTools is able to use them on
+any location. The instructions below are based on a linux machine.
+
+Install KMC
+"""""""""""
+
+PanTools requires **KMC v2.3** or **3.0** for k-mer counting during the
+constructing of the pangenome graph. KMC v3.0 is fastest, but v2.3
+should also be compatible with PanTools. The KMC3 binaries can be
+downloaded from https://github.com/refresh-bio/KMC/releases.
+
+.. code:: bash
+
+ $ tar -xvzf KMC* #uncompress the KMC binaries
+
+ # Edit your ~/.bashrc to include KMC to your PATH
+ $ echo "export PATH=/YOUR_PATH/KMC/:\$PATH" >> ~/.bashrc #replace YOUR_PATH with the correct path on your computer
+ $ source ~/.bashrc
+ $ kmc # test if KMC is executable
+ $ kmc_tools # test if kmc_tools is executable
+
+--------------
+
+Install MCL
+"""""""""""
+
+The MCL (Markov clustering) algorithm is required for the homology
+grouping of PanTools. The software can be found on
+https://micans.org/mcl under License & software.
+
+.. code:: bash
+
+ $ wget https://micans.org/mcl/src/mcl-14-137.tar.gz
+ $ tar -xvzf mcl-*
+ $ cd mcl-14-137
+ $ ./configure --prefix=/YOUR_PATH/mcl-14-137/shared #replace YOUR_PATH with the correct path on your computer
+ $ make install
+
+ # Edit your ~/.bashrc to include MCL to your PATH
+ $ echo "export PATH=/YOUR_PATH/mcl-14-137/bin/:\$PATH" >> ~/.bashrc #replace YOUR_PATH with the correct path on your computer
+ $ source ~/.bashrc
+ $ mcl -h # test if MCL is executable
+
+--------------
+
+Install BUSCO
+"""""""""""""
+
+**BUSCO v3 to v5** can be run against the pangenome to estimate
+annotation completeness. The versions require a different Python release
+and need to be installed in a different way. We suggest to install BUSCO
+v5, follow the instructions at https://gitlab.com/ezlab/busco/.
+
+--------------
+
+Install FastTree
+""""""""""""""""
+
+**FastTree** is used to infer approximately-maximum-likelihood
+phylogenetic trees from the alignments of nucleotide or protein
+sequences which are extracted from the pangenome. An executable can be
+found on the FastTree website: http://www.microbesonline.org/fasttree/.
+
+.. code:: bash
+
+ $ wget http://www.microbesonline.org/fasttree/FastTree
+ $ chmod +x FastTree
+ $ ./FastTree # test if FastTree is executable
+
+ # Edit your ~/.bashrc to include FastTree to your PATH
+ $ echo "export PATH=/YOUR_PATH:\$PATH" >> ~/.bashrc #replace YOUR_PATH with the correct path on your computer
+ $ source ~/.bashrc
+
+--------------
+
+Install R
+"""""""""
+
+**R** and some additional R packages are required to execute R scripts
+(files with .R extension) that create plots and construct
+Neighbor-Joining phylogenies. In most cases, R is already installed on a
+server. If this is not the case, install it through the instructions on
+the website https://cran.r-project.org/, or compile it by using
+following steps.
+
+.. code:: bash
+
+ mkdir R
+ mkdir R/R_LIBS
+ cd R
+ wget https://cran.r-project.org/src/base/R-4/R-4.0.2.tar.gz #version number might have changed already
+ tar -xvf R-4.0.2.tar.gz
+ cd R-4.0.2/
+ ./configure --prefix=/YOUR_PATH/R/ #replace YOUR_PATH with the correct path on your computer
+ make
+
+ # Edit your ~/.bashrc to include R to your PATH
+ $ echo "export PATH=/YOUR_PATH/R/bin/:\$PATH" >> ~/.bashrc #replace YOUR_PATH with the correct path on your computer
+ $ source ~/.bashrc
+ $ R --help # test if R is executable
+
+When **R_LIB** is set to your $PATH, R scripts know the location of the
+libraries and are able to install additional R packages to the selected
+directory.
+
+.. code:: bash
+
+ $ echo "R_LIBS=/YOUR_PATH/R/R_LIBS/" >> ~/.bashrc
+ $ echo "export R_LIBS" >> ~/.bashrc
+ $ echo $R_LIBS # validate if the path to the R libraries can be found
+
+--------------
+
+Install MAFFT
+"""""""""""""
+
+**MAFFT** is required for all the alignment functionalities, such as the
+alignment of homology groups and inferring the core SNP phylogeny. The
+full manual is available at https://mafft.cbrc.jp/alignment/software/.
+
+.. code:: bash
+
+ $ git clone https://github.com/GSLBiotech/mafft.git
+ $ cd mafft/core
+
+ # Edit the first line of Makefile to change the desired install location, from 'PREFIX = /usr/local' to 'PREFIX = /YOUR_DESIRED_PATH/mafft/'
+ # Make sure the 'ENABLE_MULTITHREAD = -Denablemultithread' line is uncommented, to enable multithreading
+
+ # Edit your ~/.bashrc to include MAFFT to your $PATH
+ $ echo "export PATH=/YOUR_PATH/mafft/bin/:\$PATH" >> ~/.bashrc #replace YOUR_PATH with the correct path on your computer
+ $ source ~/.bashrc
+ $ mafft --help # test if MAFFT is executable
+
+--------------
+
+Install IQ-tree
+"""""""""""""""
+
+Using IQ-tree we infer phylogenetic trees by maximum likelihood.
+Information about the tool can found on their webpage
+https://github.com/ebi-pf-team/interproscan/wiki/HowToDownload
+
+.. code:: bash
+
+ wget https://github.com/Cibiv/IQ-TREE/releases/download/v1.6.12/iqtree-1.6.12-Linux.tar.gz
+ tar -xvf iqtree-1.6.12-Linux
+
+ # Edit your ~/.bashrc to include IQ-tree to your $PATH
+ $ echo "export PATH=/YOUR_PATH/iqtree-1.6.12-Linux/bin/:\$PATH" >> ~/.bashrc #replace YOUR_PATH with the correct path on your computer
+ $ source ~/.bashrc
+ $ iqtree -h # test if IQ-tree is executable
+
+--------------
+
+Install fastANI or MASH
+"""""""""""""""""""""""
+
+To be able to construct a Neighbor-Joining phylogeny using ANI-scores,
+either **fastANI** or **MASH** is required. The manual for **fastANI**
+is available at https://github.com/ParBLiSS/FastANI/. The manual for
+**MASH** can be found at https://mash.readthedocs.io/en/latest/.
+
+.. code:: bash
+
+ $ wget https://github.com/marbl/Mash/releases/download/v2.2/mash-Linux64-v2.2.tar
+ $ tar -xvf mash-Linux64-v2.2.tar
+ $ mv mash-Linux64-v2.2/mash .
+
+ $ wget https://github.com/ParBLiSS/FastANI/releases/download/v1.32/fastANI-Linux64-v1.32.zip #
+ $ unzip fastANI-Linux64-v1.32.zip
+
+ # Edit your ~/.bashrc to include MASH and FastANI to your $PATH
+ $ echo "export PATH=/YOUR_PATH/:\$PATH" >> ~/.bashrc #replace YOUR_PATH with the correct path on your computer
+ $ source ~/.bashrc
+ $ mash -h # test if MASH is executable
+ $ fastANI -h # test if FastANI is executable
+
+--------------
+
+Install BLAST
+"""""""""""""
+
+BLAST is only required by one function, where the sequences are blasted
+against a database to obtain their COG category. Information about BLAST
+can be found at https://www.ncbi.nlm.nih.gov/books/NBK279690/?report=classic.
+
+.. code:: bash
+
+ $ wget https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.10.1+-x64-linux.tar.gz
+ $ tar -xvf ncbi-blast-2.10.1+-x64-linux.tar.gz
+
+ # Edit your ~/.bashrc to include BLAST to your $PATH
+ $ echo "export PATH=/YOUR_PATH/ncbi-blast-2.10.1+/bin/:\$PATH" >> ~/.bashrc #replace YOUR_PATH with the correct path on your computer
+ $ source ~/.bashrc
+ $ blastp -help # test if BLAST is executable
+
+--------------
+
+Install InterProScan
+""""""""""""""""""""
+
+Not required by any function, but the .GFF3 output of **InterProScan**
+can be read to include functional annotations to the database. The
+installation itself can be quite tricky as it uses many different
+third-party binaries and each having their own dependencies. Please
+check https://github.com/ebi-pf-team/interproscan/wiki/HowToDownload and
+take a look at the install requirements as well. Installation of the
+Panther models is not required.
+
+Phobius via InterProScan
+""""""""""""""""""""""""
+
+Phobius predictions can be performed during the InterProScan analysis
+but it is not part of the standard set of predictions. To allow these
+predictions, https://phobius.sbc.su.se/, place the entire directory in
+the InterProScan/bin/ directory and edit the **interproscan.properties**
+configuration file. More information about including Phobius into the
+InterProScan analysis is found at
+https://interproscan-docs.readthedocs.io/en/latest/ActivatingLicensedAnalyses.html.
+
+Install eggNOGmapper
+""""""""""""""""""""
+
+Not required by any function, but the .annotations output of
+**eggNOG-mapper** can be read to include functional annotations to the
+database. Information about this tool can be found on
+http://eggnog-mapper.embl.de/
+
+.. code:: bash
+
+ git clone https://github.com/eggnogdb/eggnog-mapper.git
+
+--------------
+
+Installing pre-commit hooks
+---------------------------
+
+First install the `pre-commit <https://pre-commit.com/>`__ Python
+package by following the `installation
+instructions <https://pre-commit.com/#install>`__.
+
+Then, inside the root directory of the repository, run:
+
+.. code:: bash
+
+ pre-commit install
+
+This step you will need to run only once after cloning the repository.
+The hooks will be installed in your local repository's configuration
+under ``.git/hooks/pre-commit``.
+
+After installation of the hooks they will be triggered at each commit if
+any Java files have changed. Should any of the pre-commit hooks fail,
+git will not allow you to create the commit. The output of the
+pre-commit hooks should tell you what failed, allowing you to fix any
+problems and to re-add the affected files for another commit attempt.
+
+Pre-commit hooks can be run manually as well with:
+
+.. code:: bash
+
+ pre-commit run
+
+--------------
diff --git a/docs/source/mapping.rst b/docs/source/mapping.rst
new file mode 100644
index 0000000000000000000000000000000000000000..8f887e36b239559542fdc19c8776ae5881c90576
--- /dev/null
+++ b/docs/source/mapping.rst
@@ -0,0 +1,113 @@
+Read mapping
+============
+
+Map
+---
+
+Map single or paired-end short reads to one or multiple genomes in the
+pangenome. One SAM or BAM file is generated for each genome included in
+the analysis.
+
+Required arguments
+~~~~~~~~~~~~~~~~~~
+
+| ``--database_path``/``-dp`` Path to the pangenome database.
+| ``-1`` The first short-read archive in FASTQ format, which can be
+ gz/bz2 compressed. This file can be precessed interleaved by -il
+ option.
+| ``--genome-numbers``/``-gn`` A text file containing genome numbers to
+ map reads against in each line.
+
+Optional arguments
+~~~~~~~~~~~~~~~~~~
+
+| ``-2`` The second short-read archive in FASTQ format, which can be
+ gz/bz2 compressed.
+| ``--out-format``/``-of SAM`` ``BAM`` ``none`` Writes the alignment
+ files in BAM or SAM format or don’t write any output files.
+| ``--output-path``/``-op`` (**default value**: Database path determined
+ by *-dp*) : Path to the output files.
+| ``--threads``/``-tn`` (**default value**: 1) : The number of parallel
+ working threads.
+| ``--interleaved``/``-il`` Process the fastq file as an interleaved
+ paired-end archive.
+| ``--raw-abundance-file``/``-raf`` The *mapping_summary.txt* file from
+ a previous mapping run (random-best competitive mode) for a better
+ estimation of coverage in a metagenomic setting.
+| ``--alignment-mode`` or ``-am`` The alignment mode:
+| -1 : Competitive, none-bests
+| -2 : Competitive, random-best
+| -3 : Competitive, all-bests
+| 1 : Normal, none-bests
+| 2 : Normal, random-best (**default**)
+| 3 : Normal, all-bests
+| 0 : Normal, all-hits
+
+Optional arguments that influence the mapping sensitivity
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+| ``--very-fast``/``--fast``/``--sensitive``/``--very-sensitive`` Four
+ settings that automatically set the parameters controlling the
+ sensitivity, ranging from least to most sensitive.
+| ``--min-mapping-identity*``/``-mmi`` (**default value**: 0.5, **valid
+ range**: [0..1)) : The minimum acceptable identity of the alignment.
+| ``--num-kmer-samples``/``-nks`` (**default value**: 15, **valid
+ range**: [1..r-k+1]) : The number of kmers sampled from read.
+| ``--min-hit-length``/``-mhl`` (**default value**: 13, **valid range**:
+ [10..100]) : The minimum acceptable length of alignment after
+ soft-clipping.
+| ``--max-alignment-length``/``-mal`` (**default value**: 1000, **valid
+ range**: [50..5000]) : The maximum acceptable length of alignment.
+| ``--max-fragment-length``/``-mfl`` (**default value**: 2000, **valid
+ range**: [50..5000]) : The maximum acceptable length of fragment.
+| ``--max-num-locations``/``-mnl`` (**default value**: 15, **valid
+ range**: [1..100]) : The maximum number of location of candidate hits
+ to examine.
+| ``--alignment-band``/``-ab`` (**default value**: 5, **valid range**:
+ [1..100]) : The length of bound of banded alignment.
+| ``--clipping-stringency``/``-ci`` (**default value**: 1) : The
+ stringency of soft-clipping.
+| 0 : no soft clipping
+| 1 : low
+| 2 : medium
+| 3 : high
+
+Example input files
+~~~~~~~~~~~~~~~~~~~
+
+FASTQ file
+
+.. code:: text
+
+ @SRR13153715.1 1/1
+ TGGTCATACAGCAAAGCATAATTGTCACCATTACTATGGCAATCAAGCCAGCTATAAAACCTAGCCAAATGTACCATGGCCATTTTATATACTGCTCATACTTTCCAAGTTCTTGGAGATCGAT
+ +
+ EEEEEEEEEEEEEEEAEEEE/EEEEE/AEEEEEEEEEEEEEE/EE/EEE/<EEEEEEE/EEEEEEEEEEEEEAEEEEEAEEEEEAEEAEEEEEEA<AAAEEAEEA<EE/EEEEAEAEA/EEAA/
+
+Genome numbers file
+
+.. code:: text
+
+ 1
+ 2
+ 5
+
+Example commands
+~~~~~~~~~~~~~~~~
+
+.. code:: bash
+
+ $ pantools map -dp arabidopsis_DB -1 ERR031564_1.fastq --reference 1-5
+ $ pantools map -dp arabidopsis_DB -1 ERR031564_1.fastq -gn genome_numbers.txt
+ $ pantools map -dp arabidopsis_DB -1 interleaved_reads.fastq --interleaved -gn genome_numbers.txt
+ $ pantools map -dp arabidopsis_DB -1 ERR031564_1.fastq -2 ERR031564_2.fastq -gn genome_numbers.txt
+
+Output files
+~~~~~~~~~~~~
+
+- **mapping_summary.txt**, number of mapped and unmapped reads per
+ genome
+- One SAM or BAM file is generated for each genome included in the
+ analysis.
+
+--------------
diff --git a/docs/source/msa.rst b/docs/source/msa.rst
new file mode 100644
index 0000000000000000000000000000000000000000..03543f16a8066e9ac4d5fe470a2c189dbf182764
--- /dev/null
+++ b/docs/source/msa.rst
@@ -0,0 +1,195 @@
+Multiple Sequence Alignments
+============================
+
+This page is entirely dedicated to performing Multiple Sequence
+Alignments (MSA) with PanTools.
+
+Sequence alignments
+-------------------
+
+Alignment of homology groups
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Performs multiple sequence alignments with **MAFFT** on sets of sequences.
+These alignments can either be:
+
+- per homology group
+- multiple homology groups
+- regions
+- with all sequences containing a functional domain
+
+The alignment consists of two rounds: After the initial alignment,
+protein sequences are trimmed based on the longest start and end gap of
+the alignment. The number of trimmed amino acids is multiplied by three
+to trim the correct number of nucleotides. If only nucleotide sequences
+are aligned, the nucleotide sequence alignment is used for trimming. The
+trimmed sequences are aligned a second time to identify variable and
+parsimony informative sites. For each round, a ML phylogeny will be
+created with **FastTree**.
+
+| **Select a method**
+| By default, this function will make a MSA per homology group. (It can
+ still be specified with ``--method per_group``.) Using another option
+ from the list above requires use of the ``--method`` argument. For
+ aligning multiple homology groups, please use
+ ``--method multiple_groups`` with the homology groups specified in a
+ csv file on a single line (can be added with ``-hm /path/to/hm.csv``.
+ For aligning regions, please use ``--method regions`` with a regions
+ file that is added with ``-rf /path/to/rf.txt``. For aligning
+ sequences based on a functional domain, please use
+ ``--method functions`` together with a functional domain that is added
+ with ``--name <domain>``.
+
+| **Other options**
+| In case you are only interested in the alignment of the nucleotide or
+ protein sequences, use ``--mode nucleotide`` or ``--mode protein``.
+ When the ``--no-trimming`` argument is included, the variable and
+ parsimony informative sites are identified from the initial alignment
+ and no trimming is performed (thus, only one round of aligning). The
+ option ``--fast`` can be used to skip running FastTree, which is used
+ for generating a tree from the alignment.
+
+| **Identify phenotype shared or specific variation**
+| Shared SNPs or amino acid substitutions can be found among the members
+ of a phenotype when ``--phenotype <phenotype>`` is included. As
+ homology groups can highly differ in size, the threshold for a
+ phenotype shared or specific SNP/substitution is based on the number
+ of sequences (from a certain phenotype) of an homology group instead
+ of the number of genomes in the pangenome. For example, the pangenome
+ holds 500 genomes but the homology group consists of only 100
+ sequences. The threshold can be lowered by including
+ ``--phenotype-threshold <threshold>``, which lowers the original
+ threshold by multiplying it to a given percentage.
+
+| **Sequence identity and similarity**
+| - The percentage **identity** of two sequences is calculated based on
+ the number of exactly matching characters divided by the alignment
+ length minus the positions were both sequences have a gap.
+| - The **similarity** (protein only) is calculated from the number of
+ identical matches, increased by the number of similar amino acids
+ (according to the BLOSUM 62 matrix), divided by the alignment length
+ minus the shared gap positions. The calculated percentage of
+ similarity is dependant on the BLOSUM matrix set by ``--blosum``.
+ Choose a larger BLOSUM number BLOSUM less divergent sequences.
+
+Required software
+"""""""""""""""""
+
+- `MAFFT <https://mafft.cbrc.jp/alignment/software/>`_
+- `FastTree <http://microbesonline.org/fasttree/>`_
+
+Required arguments
+""""""""""""""""""
+
+``--database-path``/``-dp`` Path to the database
+
+Optional arguments
+""""""""""""""""""
+
+| ``--method`` The kind of alignment to make. Can be either
+ ``per_group``, ``multiple_groups``, ``regions`` or ``functions``.
+| ``--homology-groups``/``-hm`` Text file with homology group node
+ identifiers. Default is **all** groups!
+| ``--phenotype``/``-ph`` a phenotype name, used to identify phenotype
+ specific SNPs/substitutions.
+| ``--phenotype-threshold`` Threshold for phenotype specific SNPs (default
+ is 100%).
+| ``--skip`` and ``--reference``/``-ref`` Skip over a selection of
+ genomes.
+| ``--threads-number``/``-tn`` The number of parallel working threads for
+ MAFFT and FastTree (Highly recommended! default is 1).
+| ``--mode nucleotide`` or ``--mode protein`` Choose to only align
+ **nucleotide** or **protein** sequences (default is both).
+| ``--no-trimming`` Align the sequences only once.
+| ``--fast`` Don’t run FastTree.
+| ``--name`` For specifying one or multiple functional domains. (Only used
+ when ``--method functions``.)
+| ``--regions-file``/``-rf`` Regions file for aligning regions. (Only used
+ when ``--method regions``.)
+| ``--blosum`` a BLOSUM matrix number to control MAFFT’s sensitivity and
+ the similarity calculation. Allowed values: 45, 62 (default), 80.
+
+
+Example regions file
+""""""""""""""""""""
+
+Each line must have a genome number, sequence number, begin and end
+positions that are separated by a space. Place a minus symbol behind a
+region to extract the reverse complement sequence.
+
+.. code:: text
+
+ 1 1 1 10000
+ 195 1 477722 478426
+ 71 10 17346 18056 -
+ 138 47 159593 160300 -
+
+Example commands
+""""""""""""""""
+
+.. code:: bash
+
+ $ pantools msa -dp tomato_DB
+ $ pantools msa -dp tomato_DB -hm hmgroups.txt --mode protein
+ $ pantools msa -dp tomato_DB -hm hmgroups.txt --mode nucleotide --no-trimming
+ $ pantools msa -dp tomato_DB -hm hmgroups.txt --phenotype resistance --phenotype-threshold 99
+ $ pantools msa --method multiple_groups -dp tomato_DB
+ $ pantools msa --method multiple_groups -dp tomato_DB -hm hmgroups.txt --mode protein
+ $ pantools msa --method multiple_groups -dp tomato_DB -hm hmgroups.txt --phenotype resistance --phenotype-threshold 95
+ $ pantools msa --method regions -dp tomato_DB -rf regions.txt
+ $ pantools msa --method functions -dp tomato_DB --name PF10137
+
+Output files
+""""""""""""
+
+Output files are stored in *database_directory/alignments/msa\_/grouping_v?/*
+A separate directory is created for each alignment which holds the input
+and output files.
+
+The ‘input’ directory contains the input files for the alignments.
+
+- **nuc/prot(_trimmed).fasta**, original and trimmed input sequences.
+- **trimmed.info**, number of trimmed positions per sequence.
+- **sequences.info**, relevant gene information of sequences in group:
+ gene names, mRNA node id, address, strand orientation.
+
+The alignments and output files are written to the ‘output’ directory.
+
+- **nuc/prot(_trimmed).afa**, the initial and second (trimmed)
+ alignment in CLUSTAL format.
+- **nuc/prot(_trimmed).fasta**, the initial and second (trimmed)
+ alignment in FASTA format.
+- **nuc/prot(_trimmed).newick**, FastTree ML tree inferred from the
+ initial and second (trimmed) alignment.
+- **nuc/prot(_trimmed)_alignment.info**, some statistics about the
+ initial and second (trimmed) alignment: alignment length, number of
+ conserved, variable and parsimony informative sites
+
+Sequence identity and similarity output files.
+
+- **nuc/prot(_trimmed)_identity.csv**, table with the sequence
+ identity scores.
+- **prot(_trimmed)_similarity.csv**, table with similarity of the
+ protein sequences.
+
+Variable and parsimony informative sites output files.
+
+- **informative_nuc/prot(_trimmed)_distance.csv**, table with
+ distances between sequences based on parsimony informative sites in
+ the alignment.
+- **variable_nuc/prot(_trimmed)_distance.csv**, table with distances
+ between sequences based on variable sites in the alignment.
+- **informative_nuc/prot(_trimmed)_sites.csv**, table with the number
+ shared parsimony informative sites between sequences.
+- **variable_nuc/prot(_trimmed)_sites.csv**, table with the number of
+ shared variable sites between sequences.
+
+When a ``--phenotype`` is included.
+
+- **phenotype_specific_changes_nuc/prot_groups.csv**, the node
+ identifiers of homology groups with phenotype specific substitutions.
+- **phenotype_specific_changes_nuc/prot.txt**, the positions of
+ phenotype specific substitutions in the alignments.
+- **phenotype_disrupted_nuc/prot.txt**, shows how many sequences of
+ different phenotypes prevented a SNP/substitution from becoming
+ phenotype specific.
diff --git a/docs/source/phylogeny.rst b/docs/source/phylogeny.rst
new file mode 100644
index 0000000000000000000000000000000000000000..8b0f8731c7750e589f75f4d0d79b2a1138247a0d
--- /dev/null
+++ b/docs/source/phylogeny.rst
@@ -0,0 +1,716 @@
+Phylogeny
+=========
+
+There are six different methods implemented which can create
+phylogenetic trees. The consensus tree method creates a Maximum
+per-Locus Quartet-score Species Tree (MLQST) from a set of gene trees.
+The other five methods use a Neighbour-joining (**NJ**) or Maximum
+Likelihood **(ML**) algorithm to infer the phylogeny.
+
+- :ref:`phylogeny:core phylogeny` **(ML)**
+- :ref:`phylogeny:k-mer distance tree` **(NJ)**
+- :ref:`phylogeny:consensus tree`
+- :ref:`phylogeny:gene distance tree` **(NJ)**
+- :ref:`phylogeny:ani tree` **(NJ)**
+- :ref:`phylogeny:mlsa` **(ML)**
+
+All functions produce tree files in Newick format that can be visualized
+with iTOL or any other phylogenetic tree visualization software.
+
+- :ref:`phylogeny:rename phylogeny`
+- :ref:`phylogeny:reroot phylogeny`
+- :ref:`phylogeny:create tree template`
+
+--------------
+
+Core phylogeny
+--------------
+
+Infer a Maximum likelihood (ML) or Neighbour-Joining (NJ) phylogeny from
+SNPs identified from single copy orthologous genes. This function
+requires single-copy homology groups which are automatically detected if
+:ref:`gene_classification <characterize:gene classification>` was run
+before. The homology groups are aligned in two consecutive rounds with
+:ref:`msa <msa:alignment of homology groups>`.
+
+When using ``--clustering-method ML``, parsimony informative positions
+are extracted from the trimmed alignments and concatenated into single
+continuous sequence per genome. IQ-tree infers the ML tree with minimum
+of 1000 bootstrap iterations.
+
+The ``--clustering-method NJ`` method counts the total and shared number
+of variable sites between two genomes in the alignment and calculates a
+Jaccard distance (0-1):
+
+.. math:: D_J(A,B) = 1 - J(A,B) = \frac{|A \cup B| - |A \cap B|}{|A \cup B|}
+
+Required software
+~~~~~~~~~~~~~~~~~
+
+Please cite the appropriate tool(s) when using the core phylogeny in
+your research.
+
+- `MAFFT <https://mafft.cbrc.jp/alignment/software/>`_
+- `IQ-tree <http://www.iqtree.org>`_ (Only required for ML)
+
+Required arguments
+~~~~~~~~~~~~~~~~~~
+
+``--database-path``/``-dp`` Path to the database.
+
+Optional arguments
+~~~~~~~~~~~~~~~~~~
+
+| ``--homology-groups``/``-hm`` A file with homology group node
+ identifiers of single copy groups. Default is
+ single_copy_orthologs.csv, generated in the previous
+ :ref:`gene_classification <characterize:gene classification>` run.
+| ``--clustering-method ML``/``--clustering-method NJ`` Maximum
+ likelihood (default) or Neighbour joining.
+| ``--mode protein`` Use proteins instead of nucleotide sequences.
+| ``--threads``/``-tn`` Number of threads (default is 1).
+| ``--phenotype``/``-ph`` Include phenotype information in the resulting
+ phylogeny.
+| ``--skip``/``-sk`` Exclude a selection of genomes.
+| ``--reference``/``-ref`` Only include a selection of genomes.
+
+Example commands
+~~~~~~~~~~~~~~~~
+
+::
+
+ $ pantools core_phylogeny -dp tomato_DB -tn 24
+ $ pantools core_phylogeny -dp tomato_DB -tn 24 --clustering-method NJ --mode protein
+ $ pantools core_phylogeny -dp tomato_DB -tn 24 --clustering-method ML --phenotype resistance
+
+Output
+~~~~~~
+
+Output files are written to the **core_snp_tree** directory in the
+database.
+
+- **sites_per_group.csv**, number of parsimony informative and variable
+ sites per homology group.
+
+When ``--clustering-method NJ`` is included
+
+- **core_snp_NJ_tree.R**, Rscript to create NJ tree from distances
+ based on shared sites. Two distances can be selected, based on
+ variable sites and parsimony informative sites.
+- **shared_informative_positions.csv**, table with total number of
+ shared parsimony informative sites between genomes.
+- **shared_variable_positions.csv**, table with total number of shared
+ variable sites between genomes.
+
+When ``--clustering-method ML`` is included
+
+- **informative.fasta**, nucleotides from parsimony informative sites
+ of the alignments, concatenated into a single sequences per genomes.
+- **variable.fasta**, nucleotides from variable sites of the alignment,
+ concatenated into a single sequences per genomes.
+
+A command is generated which can be used to execute IQ-tree and infer
+the phylogeny on **informative.fasta**.
+
+- **informative.fasta.iqtree**, IQ-tree log file.
+- **informative.fasta.treefile**, the ML phylogeny.
+- **informative.fasta.splits.nex**, the splits graph. With ideal data,
+ this file is a tree, whereas data with conflicting phylogenetic
+ signals will result in a tree-like network. This type of tree/network
+ can be visualized with a tool like `SplitsTree
+ <https://uni-tuebingen.de/fakultaeten/mathematisch-naturwissenschaftliche-fakultaet/fachbereiche/informatik/lehrstuehle/algorithms-in-bioinformatics/software/splitstree/>`_
+
+--------------
+
+K-mer distance tree
+---------------------
+
+A NJ phylogeny of *k*-mer distances can be created by executing the
+Rscript generated by
+:ref:`k-mer_classification <characterize:k-mer classification>`.
+
+Three types of distances can be selected to infer the phylogeny. The
+first two distances are Jaccard distances (0-1): one considering only
+distinct *k*-mers and the other using all *k*-mers. The distance from
+distinct *k*-mers ignores additional copies of a *k*-mer.
+
+.. math::
+
+ D_J(A,B) &= 1 - J(A,B) = \frac{|A \cup B| - |A \cap B|}{|A \cup B|}
+
+ D_J(A,B) &= 1 - J(A,B) = \frac{|A \uplus B| - |A \cap B|}{|A \uplus B|}
+
+We observed an exponential increase in the *k*-mer distance as the
+evolutionary distance between two genomes increases. So in the case of
+more distant genomes, the depicted clades are still correct but the
+extreme long branch lengths make the tree hard to decipher. To normalize
+the numbers, we implemented the `MASH distance
+<https://uni-tuebingen.de/fakultaeten/mathematisch-naturwissenschaftliche-fakultaet/fachbereiche/informatik/lehrstuehle/algorithms-in-bioinformatics/software/splitstree/>`_.
+Distance = −1/𝑘 \* ln(J), where k is the *k*-mer length; J is the jaccard
+index (of distinct *k*-mers).
+
+::
+
+ $ Rscript genome_kmer_distance_tree.R
+
+Output file
+~~~~~~~~~~~
+
+The phylogenetic tree **genome_kmer_distance_tree.tree** is written to
+the *kmer_classification* directory in the database.
+
+--------------
+
+Consensus tree
+--------------
+
+Create a consensus tree by combining gene trees from homology groups
+using ASTRAL-Pro. Gene trees are created from all sequences in an
+homology groups, no genomes can be skipped.
+
+Required software
+~~~~~~~~~~~~~~~~~
+
+Please cite MAFFT, FastTree and ASTRAL-Pro when using the consensus tree
+in your research.
+
+- `MAFFT <https://mafft.cbrc.jp/alignment/software/>`_
+- `FastTree <http://microbesonline.org/fasttree/>`_
+- `ASTRAL-Pro <https://github.com/chaoszhang/A-pro>`_
+
+Required arguments
+~~~~~~~~~~~~~~~~~~
+
+``--database-path``/``-dp`` Path to the database.
+
+Optional arguments
+~~~~~~~~~~~~~~~~~~
+
+| ``--threads``/``-tn`` Number of threads (default is 1).
+| ``--homology-groups``/``-hm`` A file with homology group node
+ identifiers. Default is all_homology_groups.csv, generated in the
+ previous :ref:`gene_classification <characterize:gene classification>`
+ run.
+
+Example commands
+~~~~~~~~~~~~~~~~
+
+::
+
+ $ pantools consensus_tree -dp apple_DB -tn 24
+ $ pantools consensus_tree -dp apple_DB -tn 24 -hm apple_DB/gene_classification/group_identifiers/all_homology_groups.csv
+ $ pantools consensus_tree -dp apple_DB -tn 24 -hm apple_DB/gene_classification/group_identifiers/core_homology_groups.csv
+ $ pantools consensus_tree -dp apple_DB -tn 24 -hm apple_DB/gene_classification/group_identifiers/accessory_homology_groups.csv
+
+Output
+~~~~~~
+
+Output files are written to the **consensus_tree** directory in the
+database.
+
+- **all_trees.hmgroups.newick**, all gene trees of homology groups
+ included in the analysis, combined into a single file.
+- **consensus_tree.astral-pro.newick**, the output consensus tree from
+ ASTRAL-Pro.
+
+Relevant literature
+~~~~~~~~~~~~~~~~~~~
+
+- `ASTRAL-Pro: quartet-based species-tree inference despite paralogy.
+ Molecular biology and evolution <https://doi.org/10.1093/molbev/msaa139>`_
+
+--------------
+
+Gene distance tree
+------------------
+
+A NJ phylogeny of gene distances is created by executing the Rscript
+generated by
+:ref:`gene_classification <characterize:gene classification>`.
+
+Shared genes between genomes are identified through homology groups. Two
+Jaccard distance (0-1) can be used to infer a tree: one considering only
+distinct genes and the other using all genes. The distance from distinct
+genes ignores additional gene copies in an homology group.
+
+.. math::
+
+ D_J(A,B) &= 1 - J(A,B) = \frac{|A \cup B| - |A \cap B|}{|A \cup B|}
+
+ D_J(A,B) &= 1 - J(A,B) = \frac{|A \uplus B| - |A \cap B|}{|A \uplus B|}
+
+::
+
+ $ Rscript gene_distance_tree.R
+
+Output file
+~~~~~~~~~~~
+
+The phylogenetic tree **gene_distance_tree.tree** is written to the
+*gene_classification* directory in the database.
+
+--------------
+
+ANI tree
+--------
+
+Average Nucleotide Identity (ANI) is a measure of nucleotide-level
+genomic similarity between the coding regions of two prokaryotic
+genomes. Two very fast ANI estimation tools (**fastANI** and **MASH**)
+are implemented and are able to perform the pairwise comparisons between
+genomes in the pangenome. To convert the ANI score into a distance
+(0-1), the scores are transformed by :math:`1-(ANI/100)`.
+
+Required software
+~~~~~~~~~~~~~~~~~
+
+The required software depends on the tool you want to use. Please cite
+the appropriate tool when using the ANI tree in your research.
+
+- `fastANI <https://github.com/ParBLiSS/FastANI>`_
+- `MASH <https://github.com/marbl/Mash>`_
+
+Required argument
+~~~~~~~~~~~~~~~~~
+
+``--database-path``/``-dp`` Path to the database.
+
+Optional arguments
+~~~~~~~~~~~~~~~~~~
+
+| ``--mode mash``/``--mode fastani`` Software to calculate ANI score
+ (default is MASH)
+| ``--phenotype``/``-ph`` Include phenotype information in the
+ phylogeny.
+| ``--skip``/``-sk`` Exclude a selection of genomes.
+| ``--reference``/``-ref`` Only include a selection of genomes.
+| ``--threads``/``-tn`` Number of threads used by FastANI (default is
+ 1). MASH is single threaded (and currently not parallelized yet).
+
+Example command
+~~~~~~~~~~~~~~~
+
+::
+
+ $ pantools ani -dp pecto_DB
+ $ pantools ani -dp pecto_DB --phenotype species_name --mode fastani
+ $ pantools ani -dp pecto_DB --skip 4,5,6 --mode mash
+
+Output
+~~~~~~
+
+Output files are written to the **ANI** directory in the database.
+
+- **ANI_scores.csv**, a table with ANI scores for all genome pairs.
+- **ANI_distance_matrix.csv**, a table with the ANI distances (1-ANI).
+ This matrix is read by ANI_tree.R.
+- **ANI_tree.R**, Rscript to generate NJ tree from ANI distances
+
+Find closest typestrain
+~~~~~~~~~~~~~~~~~~~~~~~
+
+Compares bacterial strains to the typestrain when this information is
+available in a pangenome database.
+
+1. Add the 'typestrain' phenotype to the pangenome with
+ :ref:`add_phenotypes <construct:add phenotypes>`. You only have to
+ include typestrains names, other genomes can be left empty as shown
+ in the example below, five genomes with three different typestrains.
+2. Run the **ANI** function
+3. The 'typestrain' phenotype is recognized, and
+ **typestrain_comparison.csv** is created. This file contains the
+ highest score of each genome(5) against all the included typestrains
+ and states whether the score is above 95%.
+
+::
+
+ Genome,typestrain
+ 1,Salmonella choleraesuis NCTC 5735
+ 2,Salmonella enteritidisi NCTC 12694
+ 3,
+ 4,Salmonella paratyphi NCTC 5702
+ 5,
+
+Relevant literature
+~~~~~~~~~~~~~~~~~~~
+
+- `High throughput ANI analysis of 90K prokaryotic genomes reveals clear
+ species boundaries <https://doi.org/10.1038/s41467-018-07641-9>`_
+- `Mash: fast genome and metagenome distance estimation using MinHash
+ <https://doi.org/10.1186/s13059-016-0997-x>`_
+
+--------------
+
+MLSA
+----
+
+Within PanTools you can perform a Multilocus sequence analysis
+(**MLSA**) by running three consecutive functions:
+
+1. :ref:`mlsa_find_genes <phylogeny:step 1 search for genes>`
+2. :ref:`mlsa_concatenate <phylogeny:step 2 concatenate genes>`
+3. :ref:`mlsa <phylogeny:step 3 run mlsa>`
+
+Step 1 Search for genes
+~~~~~~~~~~~~~~~~~~~~~~~
+
+Find your genes of interest in the pangenome and extract their
+nucleotide and protein sequence. A regular search is not case sensitive
+but the gene names must exactly match the given input name. For example,
+searching a gene with 'sonic1' as query will not be able find 'sonic',
+but is able to find Sonic1, SONIC1 or sOnIc1. Including the
+``--mode extensive`` argument allows a more relaxed search and using
+'sonic' will now also find gene name variations as 'sonic1', 'sonic3'
+etc.. For this function it is important that genomes are annotated by a
+method that follow the rules for genetic nomenclature, so there are no
+differences in the naming of genes.
+
+To gain insight in which genes are appropriate for this analysis, run
+:ref:`gene_classification <characterize:gene classification>` with the
+``--mode mlsa`` argument. This method creates a list of genes that have
+same gene name, are present in all (selected) genomes and are placed in
+the single-copy homology group. Using genes from this list guarantees a
+successful MLSA.
+
+**Possible generated warnings during gene search**
+
+When a gene is included that is not on the list of suitable genes, it is
+not necessarily unusable but possibly requires manual . This function
+generates a log file with the issues and explains the user what to do.
+
+- Gene is not found in every genome. Consider using
+ ``--mode extensive``. The gene is not suitable with the current
+ genome selection when this argument was already included.
+- The found genes are placed in different homology groups. A directory
+ named the gene name is created where sequences are stored in a
+ separate file per homology group. When one of the groups is single
+ copy orthologous, it is automatically selected. With multiple correct
+ single-copy groups, the first is selected. If no single-copy groups
+ are found, this gene is probably not a suitable candidate based on
+ the high divergence. If you are determined to use the gene, align and
+ infer a gene tree on **all_sequences.fasta** to identify appropriate
+ sequences.
+- At least one gene has an additional copy. The extra copies must be
+ removed from the output file if you want to include this gene in the
+ analysis. Find the copies that stand out by aligning and inferring a
+ gene tree of the homology group.
+
+Required arguments
+""""""""""""""""""
+
+| ``--database-path``/``-dp`` Path to the database.
+| ``--name`` One or multiple gene names, seperated by a comma.
+
+Optional arguments
+""""""""""""""""""
+
+| ``--mode extensive`` Perform a more extensive gene search.
+| ``--skip``/``-sk`` Do not search for genes in this selection of
+ genomes.
+| ``--reference``/``-ref`` Only search for genes in a selection of
+ genomes.
+
+Example command
+"""""""""""""""
+
+.. code:: bash
+
+ $ pantools mlsa_find_genes -dp bacteria_DB --name dnaX,gapA,recA
+ $ pantools mlsa_find_genes -dp bacteria_DB --name gapA --mode extensive
+
+Output
+""""""
+
+Output files are written to the **mlsa/input/** directory in the
+database. For each gene name that was included, a nucleotide and protein
+and FASTA file is created that holding the sequences found in all
+genomes.
+
+- **mlsa_find_genes.log**, when one or multiple warnings are given they
+ are placed in this log file. File is not created when there aren't
+ any warnings.
+
+--------------
+
+Step 2 Concatenate genes
+~~~~~~~~~~~~~~~~~~~~~~~~
+
+Concatenate sequences obtained by
+:ref:`mlsa_find_genes <phylogeny:step 1 search for genes>` into a single
+sequence per genome. The ``--name`` argument is required, but the
+selection of gene names is allowed to be a sub-selection of the earlier
+selection.
+
+1. Proteins are aligned with MAFFT
+2. The longest gap at the start and end of each protein alignment is
+ identified.
+3. Nucleotide sequences are trimmed accordingly
+4. Trimmed nucleotide sequence are concatenated into a single sequence
+ per genome.
+
+Required software
+"""""""""""""""""
+
+- `MAFFT <https://mafft.cbrc.jp/alignment/software/>`_
+
+Required arguments
+""""""""""""""""""
+
+| ``--database-path``/``-dp`` Path to the database.
+| ``--name`` One or multiple gene names, seperated by a comma.
+
+Optional arguments
+""""""""""""""""""
+
+| ``--skip``/``-sk`` Exclude a selection of genomes.
+| ``--reference``/``ref`` Only include a of genomes.
+| ``--threads``/``-tn`` Number of threads for MAFFT (default is 1).
+
+Example command
+"""""""""""""""
+
+.. code:: bash
+
+ $ pantools mlsa_concatenate -dp bacteria_DB --name dnaX,gapA
+ $ pantools mlsa_concatenate -dp bacteria_DB --name dnaX,gapA,recA --skip 1,2,10-25
+
+Output
+""""""
+
+The output file is stored in */database_directory/mlsa/input/*
+
+- **concatenated.fasta**, file holding one concatenated sequence per
+ genome.
+
+--------------
+
+Step 3 Run MLSA
+~~~~~~~~~~~~~~~
+
+Run MAFFT and IQ-tree on the concatenated nucleotide sequences from
+:ref:`mlsa_concatenate <phylogeny:step 2 concatenate genes>`
+to create an unrooted ML tree with 1,000 bootstrappings.
+
+Required software
+"""""""""""""""""
+
+Please cite the MAFFT and IQ-tree when using the MLSA in your research.
+
+- `MAFFT <https://mafft.cbrc.jp/alignment/software/>`_
+- `IQ-tree <http://www.iqtree.org" target="_blank>`_
+
+Required argument
+"""""""""""""""""
+
+``--database-path``/``-dp`` Path to the database.
+
+Optional arguments
+""""""""""""""""""
+
+| ``--threads``/``-tn`` Select number of threads for MAFFT and IQ-tree
+ (default is 1).
+| ``--phenotype``/``-ph`` Add phenotype information/values to the
+ phylogeny. Allows the identification of phenotype specific SNPs in the
+ alignment.
+
+Example commands
+""""""""""""""""
+
+::
+
+ $ pantools mlsa -dp bacteria_DB
+ $ pantools mlsa -dp bacteria_DB -tn 24 -ph species
+
+Output
+""""""
+
+Input and output files are written to the **mlsa/output/** directory in
+the database.
+
+- **mlsa.afa**, the alignment in CLUSTAL format.
+- **mlsa.fasta**, the alignment in FASTA format.
+- **mlsa.fasta.treefile**, the (ML) phylogeny created by IQ-tree in
+ Newick format.
+
+When a ``--phenotype`` is included
+
+- **nuc_phenotype_specific_changes.info**, the positions of phenotype
+ specific substitutions in the alignment.
+
+The *var_inf_positions* directory holds files related to the counting
+variable positions of the alignment.
+
+- **nuc_variable_positions.csv**, a table with the counts of A, T, C,
+ G, or gap for every variable position in the alignment
+- **informative_nuc_distance.csv**, a table with distances calculated
+ from parsimony **informative** positions in the alignment.
+- **informative_nuc_site_counts.csv**, a table with number of shared
+ parsimony informative positions between genomes.
+- **variable_nuc_distance.csv**, a table with distances calculated from
+ **variable** positions in the alignment.
+- **variable_nuc_site_counts.csv**, a table with number of shared
+ positions between genomes.
+
+--------------
+
+Edit Phylogeny
+--------------
+
+Rename phylogeny
+~~~~~~~~~~~~~~~~
+
+Update or the terminal nodes (leaves) of a phylogenic tree. This is
+useful when you already constructed a tree but forgot to include a
+phenotype or to update the tree with a different phenotype. When no
+``--phenotype`` is included, the node values are changed to genome
+numbers.
+
+Required arguments
+""""""""""""""""""
+
+| ``--database-path``/``-dp`` Path to the database.
+| ``--input-file``/``-if`` A phylogenetic tree in **newick** or
+ **nexus** format. The tree must be generated by PanTools.
+
+Optional arguments
+""""""""""""""""""
+
+``--phenotype``/``-ph`` The phenotype used to rename the terminal nodes
+(leaves) of selected tree. ``--mode no-numbers`` Exclude genome numbers
+from the terminal nodes (leaves).
+
+Example command
+"""""""""""""""
+
+.. code:: bash
+
+ $ pantools rename_phylogeny -dp bacteria_DB -if core_snp.tree
+ $ pantools rename_phylogeny -dp bacteria_DB --phenotype species -if bacteria_DB/ANI/fastANI/ani.tree
+
+Output file
+"""""""""""
+
+A new phylogenetic tree is written to the directory of the selected
+input tree:
+
+- When the original file is called '*old_tree.newick*', a new tree is
+ created with filename '*old_tree_RENAMED.newick*'.
+
+--------------
+
+Reroot phylogeny
+~~~~~~~~~~~~~~~~
+
+All phylogenetic trees that come from the PanTools functionalities are
+unrooted. This function is able to create a new rooted tree simply by
+selecting one of the external (terminal) nodes via ``--value``. The
+included number or string should match exactly one node in the phylogeny
+or the program will not execute.
+
+Required software
+"""""""""""""""""
+
+- `ape 5 <http://cran.r-project.org/package=ape>`_
+
+Required arguments
+""""""""""""""""""
+
+| ``--input-file``/``-if`` A phylogenetic tree in **newick** format. The
+ tree must be generated by PanTools.
+| ``--value`` The name of the terminal node that will root the tree.
+
+Example command
+"""""""""""""""
+
+::
+
+ $ pantools reroot_phylogeny -if core_snp.tree --value 1
+ $ pantools reroot_phylogeny -if core_snp.tree --value 1_A.thaliana
+ $ pantools reroot_phylogeny -if kmer.tree --value 1_1
+ $ Rscript reroot.R
+
+Output file
+"""""""""""
+
+A new phylogenetic tree is written to the same location as the provided
+input file
+
+- When the original tree is called '*tree.newick*', the new file is
+ named '*tree_REROOTED.newick*'.
+
+--------------
+
+Create tree template
+~~~~~~~~~~~~~~~~~~~~
+
+Creates 'ring' and 'colored range' ITOL templates based on phenotypes
+for the visualization of phylogenies in iTOL. Phenotypes must already be
+included in the pangenome with the
+:ref:`add_phenotypes <construct:add phenotypes>` functionality. How to
+use the template files in iTOL can be found in one of the
+:ref:`tutorials <tutorial_part5:create itol templates>`.
+
+If you run this function without a ``--phenotype`` argument, templates
+are created for trees that contain only genome numbers as node labels.
+When there is a ``--phenotype`` included, templates are created where
+the leaves are named according to the selected phenotype but are
+coloured by one of the other phenotypes in the pangenome. For example,
+you originally used the 'species name' as a phenotype to construct the
+phylogeny but want them to be coloured by the 'pathogenicity' phenotype.
+
+More information about ITOL templates can be found on
+`their own webpage <https://itol.embl.de/help.cgi>`_.
+
+There is a maximum of 20 possible colors that are used in the following
+order:
+
+.. csv-table::
+ :file: tables/colors.csv
+ :header-rows: 1
+ :delim: ;
+
+.. figure:: figures/color_templates.png
+ :width: 600
+ :align: center
+
+Figures were copied from:
+
+| http://www.cookbook-r.com/Graphs/Colors_(ggplot2)/
+| https://sashamaps.net/docs/resources/20-colors/
+
+Required argument
+"""""""""""""""""
+
+``--database-path``/``-dp`` Path to the database.
+
+Optional argument
+"""""""""""""""""
+
+| ``--phenotype``/``-ph`` Use the names from this phenotype.
+| ``--value 1`` Assign a color to phenotypes shared by only a single
+ genome. If not set, default is a minimum of two genomes.
+
+Example command
+"""""""""""""""
+
+.. code:: bash
+
+ $ pantools create_tree_template -dp bacteria_DB
+ $ pantools create_tree_template -dp bacteria_DB --phenotype flowering --value 1
+ $ pantools create_tree_template -dp bacteria_DB --phenotype root_morph --value 3
+
+Output
+""""""
+
+Output files are written to the **create_tree_template** directory in
+the database.
+
+- When **no** phenotype information is included, a directory
+ 'genome_numbers' is created where the templates are stored.
+- When a ``--phenotype`` is included, a directory (named after the
+ phenotype) is created where the templates are stored.
+
+The template files are named after the phenotypes, therefore the colors
+are based on that phenotype as well.
+
+--------------
diff --git a/docs/source/query.rst b/docs/source/query.rst
new file mode 100644
index 0000000000000000000000000000000000000000..93db3c132cfd0a5a775e3f37eb5fd63dad5825dc
--- /dev/null
+++ b/docs/source/query.rst
@@ -0,0 +1,137 @@
+Querying the pangenome
+======================
+
+Cypher is Neo4j’s graph query language that lets you ask specific
+questions or retrieve data from the graph database. The Cypher query
+language depicts patterns of nodes and relationships and filters those
+patterns based on labels and properties. While using node and
+relationship patterns in databases queries may seem a little daunting, it
+is easy to pick up! This page contains some example queries to help you
+get started. Feel free to email us if you have any question regarding
+Cypher queries.
+
+More information on Neo4j and the Cypher language:
+
+| `Neo4j Cypher Manual v3.5 <https://neo4j.com/docs/developer-manual/3.5/cypher/>`_
+| `Neo4j Cypher Refcard <http://neo4j.com/docs/cypher-refcard/3.5/>`_
+| `Neo4j API <https://neo4j.com/developer/>`_
+
+**Match and return 100 nucleotide nodes**
+
+.. code:: text
+
+ MATCH (n:nucleotide) RETURN n LIMIT 100
+
+**Find all the genome nodes**
+
+.. code:: text
+
+ MATCH (n:genome) RETURN n
+
+Retrieve the pangenome node
+
+.. code:: text
+
+ MATCH (n:pangenome) RETURN n
+
+**Match and return 100 genes**
+
+.. code:: text
+
+ MATCH (g:gene) RETURN g LIMIT 100
+
+**Match and return 100 genes and order them by length**
+
+.. code:: text
+
+ MATCH (g:gene) RETURN g ORDER BY g.length DESC LIMIT 100
+
+**The same query as before but results are now returned in a table**
+
+.. code:: text
+
+ MATCH (g:gene) RETURN g.name, g.address, g.length ORDER BY g.length DESC LIMIT 100
+
+**Return genes which are between 100 and 250 bp. This can also be
+applied to other features such as exons introns or CDS.**
+
+.. code:: text
+
+ MATCH (g:gene) where g.length > 100 AND g.length < 250 RETURN * LIMIT 100
+
+**Find genes located on first genome**
+
+.. code:: text
+
+ MATCH (g:gene) WHERE g.address[0] = 1 RETURN * LIMIT 100
+
+**Find genes located on first genome and first sequence**
+
+.. code:: text
+
+ MATCH (g:gene) WHERE g.address[0] = 1 AND g.address[1] = 1 RETURN * LIMIT 100
+
+**Obtain genes between 100 and 250 nucleotides**
+
+.. code:: text
+
+ MATCH (g:gene) where g.length > 100 AND g.length < 250 RETURN *
+
+**Return pfam identifiers for genes between 100 and 250 nucleotides
+long**
+
+.. code:: text
+
+ match (n:mRNA)--(m:pfam) where n.length > 100 and n.length < 150 return m.id
+
+**Return all genes for a specific contig and count them**
+
+.. code:: text
+
+ MATCH (n:gene) WHERE n.address[0] = 1 and n.address[1] = 1 RETURN count(n)
+
+**Return all genes genes between 1000-1500 nucleotides and order them by
+length**
+
+.. code:: text
+
+ MATCH (n:gene) WHERE n.length > 1000 and n.length < 1500 RETURN n order by n.length DESC
+
+**Returns the homology group matching your gene of interest**
+
+.. code:: text
+
+ MATCH (n:homology_group)--(m:mRNA)--(g:gene) WHERE g.name = 'GENE\_NAME' RETURN *
+
+**Returns the genes of genome 1 that don’t have a homolog in a the other
+genome**
+
+.. code:: text
+
+ MATCH (n:homology_group)--(m:mRNA)--(g:gene) where n.num_members = 1 and g.genome = 1 RETURN g
+
+**Retrieve unique GO identifiers for mRNA’s with a signal peptide**
+
+.. code:: text
+
+ MATCH (m:mRNA)--(g:GO) where m.signalp_signal_peptide = true RETURN DISTINCT m.id, g.id
+
+**Return all sequence nodes for a specific contig**
+
+.. code:: text
+
+ MATCH (n)-[r]->() WHERE exists (r.'a1\_1') and (n:degenerate or n:node) RETURN id(n), n.sequence , r.'a1\_1'
+
+**Return all sequence nodes for a specific contig within the range of
+position 1000 and 2000**
+
+.. code:: text
+
+ MATCH (n)-[r]->() WHERE exists (r.'a1\_1') and (n:degenerate or n:node) and r.'a1'\_1[0] > 1000 and r.'a1\_1'[0] < 2000 RETURN id(n), n.sequence, r.'a1\_1'
+
+**Find SNP bubbles in the graph. For simplification we only use the FF
+relation**
+
+.. code:: text
+
+ MATCH p= (n:nucleotide) -[:FF]-> (a1)-[:FF]->(m:nucleotide) <-[:FF]-(b1) <-[:FF]- (n) return * limit 50
diff --git a/docs/source/s5defs.txt b/docs/source/s5defs.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2ebfb95b7364efe86a5f6f7a47452ecaa38f50b5
--- /dev/null
+++ b/docs/source/s5defs.txt
@@ -0,0 +1,68 @@
+.. Definitions of interpreted text roles (classes) for S5/HTML data.
+.. This data file has been placed in the public domain.
+
+.. Colours
+ =======
+
+.. role:: black
+.. role:: gray
+.. role:: silver
+.. role:: white
+
+.. role:: maroon
+.. role:: red
+.. role:: magenta
+.. role:: fuchsia
+.. role:: pink
+.. role:: orange
+.. role:: yellow
+.. role:: lime
+.. role:: green
+.. role:: olive
+.. role:: teal
+.. role:: cyan
+.. role:: aqua
+.. role:: blue
+.. role:: navy
+.. role:: purple
+
+
+.. Text Sizes
+ ==========
+
+.. role:: huge
+.. role:: big
+.. role:: small
+.. role:: tiny
+
+
+.. Display in Slides (Presentation Mode) Only
+ ==========================================
+
+.. role:: slide
+ :class: slide-display
+
+
+.. Display in Outline Mode Only
+ ============================
+
+.. role:: outline
+
+
+.. Display in Print Only
+ =====================
+
+.. role:: print
+
+
+.. Display in Handout Mode Only
+ ============================
+
+.. role:: handout
+
+
+.. Incremental Display
+ ===================
+
+.. role:: incremental
+.. default-role:: incremental
\ No newline at end of file
diff --git a/docs/source/tables/bacteria_datasets.csv b/docs/source/tables/bacteria_datasets.csv
new file mode 100644
index 0000000000000000000000000000000000000000..9a01ba92e91239618ea39e8ffeed020f856888df
--- /dev/null
+++ b/docs/source/tables/bacteria_datasets.csv
@@ -0,0 +1,7 @@
+Genome;Name;Accession;Length;Sequences;Genes
+1;P. odoriferum Q166;`GCF_002904195.1 <https://www.ncbi.nlm.nih.gov/assembly/GCF_002904195.1>`_;5.09 Mb;66;4510
+2;P. fontis M022;`GCF_000803215.1 <https://www.ncbi.nlm.nih.gov/assembly/GCF_000803215.1>`_;4.15 Mb;107;3723
+3;P. polaris S4.16.03.2B;`GCF_003595035.1 <https://www.ncbi.nlm.nih.gov/assembly/GCF_003595035.1>`_;4.86 Mb;65;4442
+4;P. brasiliense S2;`GCF_000808375.1 <https://www.ncbi.nlm.nih.gov/assembly/GCF_000808375.1>`_;4.84 Mb;37;4367
+5;P. brasiliense Y49;`GCF_000808115.1 <https://www.ncbi.nlm.nih.gov/assembly/GCF_000808115.1>`_;4.70 Mb;31;4231
+6;D. dadantii 3937;`GCF_000147055.1 <https://www.ncbi.nlm.nih.gov/assembly/GCF_000147055.1>`_;4.92 Mb;1;4281
diff --git a/docs/source/tables/chloroplast_datasets.csv b/docs/source/tables/chloroplast_datasets.csv
new file mode 100644
index 0000000000000000000000000000000000000000..f61f59d6f81e7ae4b6ba865cb9777e7b54925699
--- /dev/null
+++ b/docs/source/tables/chloroplast_datasets.csv
@@ -0,0 +1,6 @@
+Genome;Chloroplast genome;Accession;Length;Genes;tRNAs
+1;Cucumis sativus (cucumber);`NC_007144.1 <https://www.ncbi.nlm.nih.gov/nuccore/NC_007144.1/>`_;155,293 bp;85;37
+2;Oryza sativa Indica 93-11 (rice);`NC_008155.1 <https://www.ncbi.nlm.nih.gov/nuccore/NC_008155.1/>`_;134,496 bp;100;40
+3;Solanum lycopersicum (tomato);`NC_007898.3 <https://www.ncbi.nlm.nih.gov/nuccore/NC_007898.3/>`_;155,461 bp;87;45
+4;Solanum tuberosum (potato);`NC_008096.2 <https://www.ncbi.nlm.nih.gov/nuccore/NC_008096.2/>`_;155,296 bp;84;45
+5;Zea mays (maize);`NC_001666.2 <https://www.ncbi.nlm.nih.gov/nuccore/NC_001666.2/>`_;140,384 bp;111;38
diff --git a/docs/source/tables/colors.csv b/docs/source/tables/colors.csv
new file mode 100644
index 0000000000000000000000000000000000000000..6f0e6a6123a6dc74e43cd7dd7b9a8ab4ab7f0ea0
--- /dev/null
+++ b/docs/source/tables/colors.csv
@@ -0,0 +1,21 @@
+;Color (> 8 phenotypes);Hexadecimal color;Color (≤ 8 phenotypes);Hexadecimal color
+1;Pink;#fabebe;Orange;#E69F00
+2;Lime;#bfef45;Sky blue;#56B4E9
+3;Cyan;#42d4f4;Bluish green;#009E73
+4;Apricot;#ffd8b1;Yellow;#F0E442
+5;Mint;#aaffc3;Blue;#0072B2
+6;Beige;#fffac8;Vermilion;#D55E00
+7;Lavender;#e6beff;Reddish purple;#CC79A7
+8;Teal;#469990;Grey;#999999
+9;Red;#e6194B;;
+10;Orange;#f58231;;
+11;Yellow;#ffe119;;
+12;Green;#3cb44b;;
+13;Blue;#4363d8;;
+14;Purple;#911eb4;;
+15;Grey;#a9a9a9;;
+16;Maroon;#800000;;
+17;Olive;#808000;;
+18;Brown;#9A6324;;
+19;Navy;#000075;;
+20;Magenta;#f032e6;;
diff --git a/docs/source/tables/differences_characterize.csv b/docs/source/tables/differences_characterize.csv
new file mode 100644
index 0000000000000000000000000000000000000000..d032a447d2dc849949e346ee02c1079297ffef36
--- /dev/null
+++ b/docs/source/tables/differences_characterize.csv
@@ -0,0 +1,10 @@
+Function;Pangenome;Panproteome
+Statistics;:green:`YES`;:green:`YES`
+Gene classification;:green:`YES`;:green:`YES`
+Core unique thresholds;:green:`YES`;:green:`YES`
+Grouping overview;:green:`YES`;:green:`YES`
+Pangenome size genes;:green:`YES`;:green:`YES`
+Pangenome size k-mers;:green:`YES`;:red:`NO`
+K-mer classification;:green:`YES`;:red:`NO`
+Functional classification;:green:`YES`;:green:`YES`
+Functional annotation overview;:green:`YES`;:green:`YES`
diff --git a/docs/source/tables/differences_construct.csv b/docs/source/tables/differences_construct.csv
new file mode 100644
index 0000000000000000000000000000000000000000..b14aa62a335086a4334a985e45a822acef6ee61e
--- /dev/null
+++ b/docs/source/tables/differences_construct.csv
@@ -0,0 +1,14 @@
+Function;Pangenome;Panproteome
+Build pangenome;:green:`YES`;:red:`NO`
+Build panproteome;:red:`NO`;:green:`YES`
+Add annotations;:green:`YES`;:red:`NO`
+Add genomes;:green:`YES`;:red:`NO`
+Group;:green:`YES`;:green:`YES`
+Optimal grouping;:green:`YES`;:green:`YES`
+Change grouping;:green:`YES`;:green:`YES`
+BUSCO protein;:green:`YES`;:green:`YES`
+Add phenotype;:green:`YES`;:green:`YES`
+Add functional annotations;:green:`YES`;:green:`YES`
+Add antiSMASH;:green:`YES`;:red:`NO`
+Remove nodes;:green:`YES`;:green:`YES`
+Move or remove grouping;:green:`YES`;:green:`YES`
diff --git a/docs/source/tables/differences_explore.csv b/docs/source/tables/differences_explore.csv
new file mode 100644
index 0000000000000000000000000000000000000000..a8e1fbca276c288d01d20b364cb71a16936ef06d
--- /dev/null
+++ b/docs/source/tables/differences_explore.csv
@@ -0,0 +1,16 @@
+Function;Pangenome;Panproteome
+Locate genes;:green:`YES`;:red:`NO`
+mRNAs connected to function;:green:`YES`;:red:`NO`
+Find gene;:green:`YES`;:red:`NO`
+GO enrichment;:green:`YES`;:green:`YES`
+Show GO;:green:`YES`;:green:`YES`
+Compare GO;:green:`YES`;:green:`YES`
+Compare BGC;:green:`YES`;:red:`NO`
+Alignment of homology group;:green:`YES`;:green:`YES`
+Alignment of multiple homology groups;:green:`YES`;:green:`YES`
+Alignment of genomic regions;:green:`YES`;:red:`NO`
+Order matrix;:green:`YES`;:green:`YES`
+Rename matrix;:green:`YES`;:green:`YES`
+Retrieve genomes;:green:`YES`;:red:`NO`
+Retrieve regions;:green:`YES`;:red:`NO`
+Retrieve features;:green:`YES`;:red:`NO`
diff --git a/docs/source/tables/differences_phylogeny.csv b/docs/source/tables/differences_phylogeny.csv
new file mode 100644
index 0000000000000000000000000000000000000000..92af8249db0bbdd006d1046d17b5195c8ebfe452
--- /dev/null
+++ b/docs/source/tables/differences_phylogeny.csv
@@ -0,0 +1,8 @@
+Function;Pangenome;Panproteome
+Core SNP tree;:green:`YES`;:green:`YES`
+K-mer distance tree;:green:`YES`;:red:`NO`
+Gene distance tree;:green:`YES`;:green:`YES`
+ANI tree;:green:`YES`;:red:`NO`
+MLSA;:green:`YES`;:red:`NO`
+Rename phylogeny;:green:`YES`;:green:`YES`
+Create tree template;:green:`YES`;:green:`YES`
diff --git a/docs/source/tables/functional_databases.csv b/docs/source/tables/functional_databases.csv
new file mode 100644
index 0000000000000000000000000000000000000000..914b352a75e0aaf35b57c9bf2be7e0260c1792cc
--- /dev/null
+++ b/docs/source/tables/functional_databases.csv
@@ -0,0 +1,9 @@
+File;Database type;Required directory;Download link
+go.basic.obo;GO;addons;http://purl.obolibrary.org/obo/go/go-basic.obo
+gene_ontology.txt;Pfam;addons;ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases//Pfam35.0/database_files/gene_ontology.txt.gz
+Pfam-A.clans.tsv;Pfam;addons;ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases//Pfam35.0/Pfam-A.clans.tsv.gz
+interpro.xml;InterPro;addons;https://ftp.ebi.ac.uk/pub/databases/interpro/current_release/interpro.xml.gz
+TIGRFAMS_GO_LINK;TIGRFAM;addons/tigrfam;https://ftp.ncbi.nlm.nih.gov/hmm/TIGRFAMs/release_15.0/TIGRFAMS_GO_LINK
+TIGRFAMS_ROLE_LINK;TIGRFAM;addons/tigrfam;https://ftp.ncbi.nlm.nih.gov/hmm/TIGRFAMs/release_15.0/TIGRFAMS_ROLE_LINK
+TIGR_ROLE_NAMES;TIGRFAM;addons/tigrfam;https://ftp.ncbi.nlm.nih.gov/hmm/TIGRFAMs/release_15.0/TIGR_ROLE_NAMES
+TIGR00001.INFO to TIGR04571.INFO;TIGRFAM;addons/tigrfam;https://ftp.ncbi.nlm.nih.gov/hmm/TIGRFAMs/release_15.0/TIGRFAMs_15.0_INFO.tar.gz
diff --git a/docs/source/tutorial.rst b/docs/source/tutorial.rst
new file mode 100644
index 0000000000000000000000000000000000000000..1291edccac881c1f58988e05514725b00b048e0f
--- /dev/null
+++ b/docs/source/tutorial.rst
@@ -0,0 +1,8 @@
+Tutorial
+========
+
+#. :doc:`../install`
+#. :doc:`Construct pangenome <tutorial_part2>`
+#. :doc:`Neo4j browser <tutorial_part3>`
+#. :doc:`Characterization & exploration <tutorial_part4>`
+#. :doc:`Phylogeny <tutorial_part5>`
diff --git a/docs/source/tutorial_part1.rst b/docs/source/tutorial_part1.rst
new file mode 100644
index 0000000000000000000000000000000000000000..348eba590de2e3ff04ff667d6614b5e90ef3ab80
--- /dev/null
+++ b/docs/source/tutorial_part1.rst
@@ -0,0 +1,5 @@
+Part 1. Install PanTools
+========================
+
+For instructions on how to install PanTools,
+see :doc:`install`.
\ No newline at end of file
diff --git a/docs/source/tutorial_part2.rst b/docs/source/tutorial_part2.rst
new file mode 100644
index 0000000000000000000000000000000000000000..dd34aad4fec0d11d1c104b3d3b8fd9b9620cc729
--- /dev/null
+++ b/docs/source/tutorial_part2.rst
@@ -0,0 +1,190 @@
+Part 2. Build your own pangenome using PanTools
+===============================================
+
+To demonstrate the main functionalities of PanTools we use a small
+chloroplasts dataset to avoid long construction times.
+
+.. csv-table::
+ :file: tables/chloroplast_datasets.csv
+ :header-rows: 1
+ :delim: ;
+
+Download the chloroplast fasta and gff files
+`here <http://bioinformatics.nl/pangenomics/tutorial/chloroplasts.tar.gz>`_
+or via wget.
+
+.. code:: bash
+
+ $ wget http://bioinformatics.nl/pangenomics/tutorial/chloroplasts.tar.gz
+ $ tar -xvzf chloroplasts.tar.gz #unpack the archive
+
+We assume a PanTools alias was set during the
+:ref:`installation <install:set pantools alias>`. This allows PanTools
+to be executed with ``pantools`` rather than
+``pantools/target/pantools-3.4.0.jar``. If you don’t have an alias, either
+set one or replace the pantools command with the full path to the .jar
+file in the tutorials.
+
+--------------
+
+BUILD, ANNOTATE and GROUP
+-------------------------
+
+We start with building a pangenome using four of the five chloroplast
+genomes. For this you need a text file which directs PanTools to the
+FASTA files. Call your text file **genome_locations.txt** and include
+the following lines:
+
+.. code:: text
+
+ YOUR_PATH/C_sativus.fasta
+ YOUR_PATH/O_sativa.fasta
+ YOUR_PATH/S_lycopersicum.fasta
+ YOUR_PATH/S_tuberosum.fasta
+
+Make sure that ‘*YOUR_PATH*’ is the full path to the input files! Then
+run PanTools with the :ref:`build_pangenome <construct:build pangenome>`
+function and include the text file
+
+.. code:: bash
+
+ $ pantools build_pangenome -dp chloroplast_DB -gf genome_locations.txt
+
+Did the program run without any error messages? Congratulations, you’ve
+built your first pangenome! If not? Make sure your Java version is up to
+date and kmc is executable. The text file should only contain full paths
+to FASTA files, no additional spaces or empty lines.
+
+Adding additional genomes
+~~~~~~~~~~~~~~~~~~~~~~~~~
+PanTools has the ability to add additional genomes to an already
+existing pangenome. To test the function of PanTools, prepare a text
+file containing the path to the Maize chloroplast genome. Call your
+text file **fifth_genome_location.txt** and include the following
+line to the file:
+
+.. code:: text
+
+ YOUR_PATH/Z_mays.fasta
+
+Run PanTools on the new text file and use the
+:ref:`add_genomes <construct:add genomes>` function
+
+.. code:: bash
+
+ $ pantools add_genomes -dp chloroplast_DB -gf fifth_genome_location.txt
+
+Adding annotations
+To include gene annotations to the pangenome, prepare a text file
+containing paths to the GFF files. Call your text file
+**annotation_locations.txt** and include the following lines into the
+file:
+
+.. code:: text
+
+ 1 YOUR_PATH/C_sativus.gff3
+ 2 YOUR_PATH/O_sativa.gff3
+ 3 YOUR_PATH/S_lycopersicum.gff3
+ 4 YOUR_PATH/S_tuberosum.gff3
+ 5 YOUR_PATH/Z_mays.gff3
+
+Run PanTools using the
+:ref:`add_annotations <construct:add annotations>` function and include
+the new text file
+
+.. code:: bash
+
+ $ pantools add_annotations -dp chloroplast_DB -af annotation_locations.txt -ca
+
+PanTools attached the annotations to our nucleotide nodes so now we can
+cluster them.
+
+Homology grouping
+~~~~~~~~~~~~~~~~~
+
+PanTools can infer homology between the protein sequences of a
+pangenome and cluster them into homology groups. Multiple parameters
+can be set to influence the sensitivity but for now we use the
+:ref:`group <construct:grouping proteins>` functionality with default
+settings.
+
+.. code:: bash
+
+ $ pantools group -dp chloroplast_DB
+
+--------------
+
+Adding phenotypes (requires PanTools v3)
+----------------------------------------
+
+Phenotype values can be Integers, Double, String or Boolean values.
+Create a text file **phenotypes.txt**.
+
+.. code:: text
+
+ Genome,Solanum
+ 1,false
+ 2,false
+ 3,true
+ 4,true
+ 5,false
+
+And use :ref:`add_phenotypes <construct:add phenotypes>` to add the
+information to the pangenome.
+
+.. code:: bash
+
+ $ pantools add_phenotypes -dp chloroplast_DB -ph phenotypes.txt
+
+--------------
+
+RETRIEVE functions
+------------------
+
+Now that the construction is complete, lets quickly validate if the
+construction was successful and the database can be used. To retrieve
+some genomic regions, prepare a text file containing genomic
+coordinates. Create the file **regions.txt** and include the following
+for each region: genome number, contig number, start and stop position
+and separate them by a single space
+
+.. code:: text
+
+ 1 1 200 500
+ 2 1 300 700
+ 3 1 1 10000
+ 3 1 1 10000 -
+ 4 1 9999 15000
+ 5 1 100000 110000
+
+Now run the :ref:`retrieve_regions <explore:retrieve regions>` function
+and include the new text file
+
+.. code:: bash
+
+ $ pantools retrieve_regions -dp chloroplast_DB --regions-file regions.txt
+
+Take a look at the extracted regions that are written to the
+**chloroplast_DB/retrieval/regions/** directory.
+
+To retrieve entire genomes, prepare a text file **genome_numbers.txt**
+and include each genome number on a separate line in the file
+
+.. code:: text
+
+ 1
+ 3
+ 5
+
+Use the **retrieve_regions** function again but include the new text
+file
+
+.. code:: bash
+
+ $ pantools retrieve_regions -dp chloroplast_DB -rf genome_numbers.txt
+
+Genome files are written to same directory as before. Take a look at one
+of the three genomes you have just retrieved.
+
+In :doc:`part 3 <tutorial_part3>` of the tutorial we explore the
+pangenome you just built using the Neo4j browser and the Cypher language.
diff --git a/docs/source/tutorial_part3.rst b/docs/source/tutorial_part3.rst
new file mode 100644
index 0000000000000000000000000000000000000000..a2261a7d9285a94facf4a6c2a0f9ac35bcf40f7f
--- /dev/null
+++ b/docs/source/tutorial_part3.rst
@@ -0,0 +1,291 @@
+Part 3. Explore the pangenome using the Neo4j browser
+=====================================================
+
+Did you skip :doc:`part 2 <tutorial_part2>` of the tutorial or were you
+unable to build the chloroplast pangenome? Download the pre-constructed
+pangenome
+`here <http://bioinformatics.nl/pangenomics/tutorial/chloroplast_DB.tar.gz>`_
+or via wget.
+
+.. code:: bash
+
+ $ wget http://bioinformatics.nl/pangenomics/tutorial/chloroplast_DB.tar.gz
+ $ tar -xvzf chloroplast_DB.tar.gz
+
+--------------
+
+Configuring Neo4j
+-----------------
+
+Set the full path to the chloroplast pangenome database by opening
+neo4j.conf ('*neo4j-community-3.5.30/conf/neo4j.conf*') and include the
+following line in the config file. Please make sure there is always only
+a single uncommented line with 'dbms.directories.data'.
+
+.. code:: text
+
+ #dbms.directories.data=/YOUR_PATH/any_other_database
+ dbms.directories.data=/YOUR_PATH/chloroplast_DB
+
+| **Allowing non-local connections**
+| To be able to run Neo4j on a server and have access to it from
+ anywhere, some additional lines in the config file must be changed.
+
+- **Uncomment** the four following lines in
+ neo4j-community-3.5.30/conf/neo4j.conf.
+- Replace 7686, 7474, and 7473 by three different numbers that are not
+ in use by other people on your server. In this way, everyone can have
+ their own database running at the same time.
+
+.. code:: text
+
+ #dbms.connectors.default_listen_address=0.0.0.0
+ #dbms.connector.bolt.listen_address=:7687
+ #dbms.connector.http.listen_address=:7474
+ #dbms.connector.https.listen_address=:7473
+
+Lets start up the Neo4j server!
+
+.. code:: bash
+
+ $ neo4j start
+
+Start Firefox (or a web browser of your own preference) and let it run
+on the background.
+
+.. code:: bash
+
+ $ firefox &
+
+In case you did not change the config to allow non-local connections,
+browse to *http://localhost:7474*. Whenever you did change the config
+file, go to *server_address:7474*, where 7474 should be replaced with the
+number you chose earlier.
+
+If the database startup was successful, a login terminal will appear in
+the webpage. Use '*neo4j*' both as username and password. After logging
+in, you are requested to set a new password.
+
+--------------
+
+Exploring nodes and edges in Neo4j
+----------------------------------
+
+Go through the following steps to become proficient in using the Neo4j
+browser and the underlying PanTools data structure. If you have any
+difficulty trouble finding a node, relationship or any type of
+information, download and use `this visual
+guide <http://www.bioinformatics.nl/pangenomics/tutorial/neo4j_browser.tar.gz>`_.
+
+1. Click on the database icon on the left. A menu with all node types
+ and relationship types will appear.
+2. Click on the '*gene*' button in the node label section. This
+ automatically generated a query. Execute the query.
+3. The **LIMIT** clause prevents large numbers of nodes popping up to
+ avoid your web browser from crashing. Set LIMIT to 10 and execute the
+ query.
+4. Hover over the nodes, click on them and take a look at the values
+ stored in the nodes. All these features (except ID) were extracted
+ from the GFF annotation files. ID is an unique number automatically
+ assigned to nodes and relationships by Neo4j.
+5. Double-click on the **matK** gene node, all nodes with a connection
+ to this gene node will appear. The nodes have distinct colors as
+ these are different node types, such as **mRNA**, **CDS**,
+ **nucleotide**. Take a look at the node properties to observe that
+ most values and information is specific to a certain node type.
+6. Double-click on the *matK* mRNA node, a **homology_group** node
+ should appear. These type of nodes connect homologous genes in the
+ graph. However, you can see this gene did not cluster with any other
+ gene.
+7. Hover over the **start** relation of the *matK* gene node. As you
+ can see information is not only stored in nodes, but also in
+ relationships! A relationship always has a certain direction, in
+ this case the relation starts at the gene node and points to a
+ nucleotide node. Offset marks the location within the node.
+8. Double-click on the **nucleotide** node at the end of the 'start'
+ relationship. An in- and outgoing relation appear that connect to
+ other nucleotide nodes. Hover over both the relations and compare
+ them. The relations holds the genomic coordinates and shows this
+ path only occurs in contig/sequence 1 of genome 1.
+9. Follow the outgoing **FF**-relationship to the next nucleotide node
+ and expand this node by double-clicking. Three nodes will pop up
+ this time. If you hover over the relations you see the coordinates
+ belong to other genomes as well. You may also notice the
+ relationships between nucleotide nodes is always a two letter
+ combination of F (forward) and R (reverse) which state if a sequence
+ is reverse complemented or not. The first letter corresponds to the
+ sequence of the node at the start of the relation where the second
+ letters refers to the sequence of the end node.
+10. Finally, execute the following query to call the database scheme to
+ see how all node types are connected to each other: *CALL
+ db.schema()*. The schema will be useful when designing your own
+ queries!
+
+--------------
+
+Query the pangenome database using CYPHER
+-----------------------------------------
+
+Cypher is a declarative, SQL-inspired language and uses ASCII-Art to
+represent patterns. Nodes are represented by circles and relationships
+by arrows.
+
+- The **MATCH** clause allows you to specify the patterns Neo4j will
+ search for in the database.
+- With **WHERE** you can add constraints to the patterns described.
+- In the **RETURN** clause you define which parts of the pattern to
+ display.
+
+Cypher queries
+~~~~~~~~~~~~~~
+
+**Match and return 100 nucleotide nodes**
+
+.. code:: text
+
+ MATCH (n:nucleotide) RETURN n LIMIT 100
+
+**Find all the genome nodes**
+
+.. code:: text
+
+ MATCH (n:genome) RETURN n
+
+**Find the pangenome node**
+
+.. code:: text
+
+ MATCH (n:pangenome) RETURN n
+
+**Match and return 100 genes**
+
+.. code:: text
+
+ MATCH (g:gene) RETURN g LIMIT 100
+
+**Match and return 100 genes and order them by length**
+
+.. code:: text
+
+ MATCH (g:gene) RETURN g ORDER BY g.length DESC LIMIT 100
+
+**The same query as before but results are now returned in a table**
+
+.. code:: text
+
+ MATCH (g:gene) RETURN g.name, g.address, g.length ORDER BY g.length DESC LIMIT 100
+
+**Return genes which are longer as 100 but shorter than 250 bp** (this
+can also be applied to other features such as exons introns or CDS)
+
+.. code:: text
+
+ MATCH (g:gene) where g.length > 100 AND g.length < 250 RETURN * LIMIT 100
+
+**Find genes located on first genome**
+
+.. code:: text
+
+ MATCH (g:gene) WHERE g.address[0] = 1 RETURN * LIMIT 100
+
+**Find genes located on first genome and first sequence**
+
+.. code:: text
+
+ MATCH (g:gene) WHERE g.address[0] = 1 AND g.address[1] = 1 RETURN * LIMIT 100
+
+--------------
+
+Homology group queries
+~~~~~~~~~~~~~~~~~~~~~~
+
+**Return 100 homology groups**
+
+.. code:: text
+
+ MATCH (h:homology_group) RETURN h LIMIT 100
+
+**Match homology groups which contain two members**
+
+.. code:: text
+
+ MATCH (h:homology_group) WHERE h.num_members = 2 RETURN h
+
+**Match homology groups and 'walk' to the genes and corresponding start
+and end node**
+
+.. code:: text
+
+ MATCH (h:homology_group)-->(f:feature)<--(g:gene)-->(n:nucleotide) WHERE h.num_members = 2 RETURN * LIMIT 25
+
+Turn off autocomplete by clicking on the button on the bottom right. The
+graph falls apart because relations were not assigned to variables.
+
+**The same query as before but now the relations do have variables**
+
+.. code:: text
+
+ MATCH (h:homology_group)-[r1]-> (f:feature) <-[r2]-(g:gene)-[r3]-> (n:nucleotide) WHERE h.num_members = 2 RETURN * LIMIT 25
+
+When you turn off autocomplete again only the '*is_similar_to*' relation
+disappears since we did not call it
+
+**Find homology group that belong to the rpoC1 gene**
+
+.. code:: text
+
+ MATCH (n:homology_group)--(m:mRNA)--(g:gene) WHERE g.name = 'rpoC1' RETURN *
+
+**Find genes on genome 1 which don't show homology**
+
+.. code:: text
+
+ MATCH (n:homology_group)--(m:mRNA)--(g:gene) WHERE n.num_members = 1 and g.genome = 1 RETURN *
+
+--------------
+
+Structural variant detection
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+**Find SNP bubbles (for simplification we only use the FF relation)**
+
+.. code:: text
+
+ MATCH p= (n:nucleotide) -[:FF]-> (a1)-[:FF]->(m:nucleotide) <-[:FF]-(b1) <-[:FF]- (n) return * limit 50
+
+**The same query but returning the results in a table**
+
+.. code:: text
+
+ MATCH (n:nucleotide) -[:FF]-> (a1)-[:FF]->(m:nucleotide) <-[:FF]-(b1) <-[:FF]- (n) return a1.length,b1.length, a1.sequence, b1.sequence limit 50
+
+Functions such as **count()**, **sum()** and **stDev()** can be used in
+a query.
+
+**The same SNP query but count the hits instead of displaying them**
+
+.. code:: text
+
+ MATCH p= (n:nucleotide) -[:FF]-> (a1)-[:FF]->(m:nucleotide) <-[:FF]-(b1) <-[:FF]- (n) return count(p)
+
+--------------
+
+Hopefully you know have some feeling with the Neo4j browser and cypher
+and you're inspired to create your own queries!
+
+When you're done working in the browser, close the database (by using
+the command line again).
+
+.. code:: text
+
+ $ neo4j stop
+
+| More information on Neo4j and the cypher language:
+| `Neo4j Cypher Manual v3.5 <https://neo4j.com/docs/developer-manual/3.5/cypher/>`_
+| `Neo4j Cypher Refcard <http://neo4j.com/docs/cypher-refcard/3.5/>`_
+| `Neo4j API <https://neo4j.com/developer/>`_
+
+--------------
+
+In :doc:`part 4 <tutorial_part4>` of the tutorial we explore some of the
+functionalities to analyze the pangenome.
diff --git a/docs/source/tutorial_part4.rst b/docs/source/tutorial_part4.rst
new file mode 100644
index 0000000000000000000000000000000000000000..b8fcb0e212d7a4e5d3fc4757faeb5c4dedeab971
--- /dev/null
+++ b/docs/source/tutorial_part4.rst
@@ -0,0 +1,466 @@
+Part 4. Characterization
+========================
+
+Part 4 preparation
+------------------
+
+PanTools v3 is required to follow this part of the tutorial. In
+addition, MAFFT and R (and a few packages) need to be installed and set
+to your $PATH. Everything should already be correctly installed if you
+use the conda environment. Validate if the tools are executable by using
+the following commands.
+
+.. code:: bash
+
+ $ Rscript --help
+ $ mafft -h
+
+We assume a PanTools alias was set during the
+:ref:`installation <install:set pantools alias>`. This allows PanTools
+to be executed with ``pantools`` rather than
+``pantools/target/pantools-3.4.0.jar``. If you don’t have an alias, either
+set one or replace the pantools command with the full path to the .jar
+file in the tutorials.
+
+Input data
+----------
+
+.. csv-table::
+ :file: tables/bacteria_datasets.csv
+ :header-rows: 1
+ :delim: ;
+
+To demonstrate how to use the PanTools functionalities we use a small
+dataset of six bacteria to avoid long runtimes. Download a
+pre-constructed pangenome or test your new skills and construct a
+pangenome yourself using the fasta and gff files.
+
+Option 1: Download separate genome and annotation files
+
+.. code:: bash
+
+ $ wget http://bioinformatics.nl/pangenomics/tutorial/pecto_dickeya_input.tar.gz
+ $ tar -xvzf pecto_dickeya_input.tar.gz
+ $ gzip -d pecto_dickeya_input/annotations/*
+ $ gzip -d pecto_dickeya_input/genomes/*
+ $ gzip -d pecto_dickeya_input/functions/*
+
+ $ pantools build_pangenome -dp pecto_dickeya_DB -gf pecto_dickeya_input/genomes.txt
+ $ pantools add_annotations -dp pecto_dickeya_DB -af pecto_dickeya_input/annotations.txt -ca
+ $ pantools group -dp pecto_dickeya_DB -rn 4 -tn 10
+
+Option 2: Download the pre-constructed pangenome
+
+.. code:: bash
+
+ $ wget http://bioinformatics.nl/pangenomics/tutorial/pecto_dickeya_DB.tar.gz
+ $ tar -xvzf pecto_dickeya_DB.tar.gz
+
+--------------
+
+Adding phenotype/metadata to the pangenome
+------------------------------------------
+
+Before starting with the analysis, we will add some phenotype data to
+the pangenome. Phenotypes allow you to find similarities for a group of
+genomes sharing a phenotype as well as identifying variation between
+different phenotypes. Below is a textfile with data for three
+phenotypes. The third phenotype, *low_temperature*, is in this case a
+made up example! It states whether the strain is capable of growing on
+(extreme) low temperatures. The phenotype file can be found inside the
+database directory or create a new file using the text from the box
+below. Add the phenotype information to the pangenome using
+:ref:`add_phenotype <construct:add phenotypes>`.
+
+.. code:: text
+
+ Genome, species, strain_name, low_temperature
+ 1,P. odoriferum,P. odoriferum Q166, false
+ 2,P. fontis, P. fontis M022, true
+ 3,P. polaris,P. polaris S4.16.03.2B, false
+ 4,P. brasiliense, P. brasiliense S2, true
+ 5,P. brasiliense, P. brasiliense Y49, false
+ 6,D. dadantii, D. dadantii 3937,?
+
+.. code:: bash
+
+ $ pantools add_phenotype -dp pecto_dickeya_DB -ph pecto_dickeya_input/phenotypes.txt
+
+--------------
+
+Metrics and general statistics
+------------------------------
+
+After building or uncompressing the pangenome, run the
+:ref:`metrics <characterize:metrics>` functionality to produce various
+statistics that should verify an errorless construction.
+
+.. code:: bash
+
+ $ pantools metrics -dp pecto_dickeya_DB
+
+Open **metrics_per_genome.csv** with a spreadsheet tool (Excel,
+Libreoffice, Google sheets) and make sure the columns are split on
+commas. You may easily notice the many empty columns in this table as
+these type of annotations or features are not included in the database
+(yet). Functional annotations are incorporated later in this tutorial.
+Columns for features like exon and intron will remain empty as bacterial
+coding sequences are not interrupted.
+
+--------------
+
+Gene classification
+-------------------
+
+With the :ref:`gene_classification <characterize:gene classification>`
+functionality you are able to organize the gene repertoire into the
+core, accessory or unique part of the pangenome.
+
+- **Core**, a gene is present in all genomes
+- **Unique**, a gene is present in a single genome
+- **Accessory**, a gene is present in some but not all genomes
+
+.. code:: bash
+
+ $ pantools gene_classification -dp pecto_dickeya_DB
+
+.. figure:: figures/classify_table.png
+ :width: 600
+ :align: center
+
+Take a look in **gene_classification_overview.txt**. Here you can find
+the number of classified homology groups and genes on a pangenome level
+but also for individual genomes.
+
+Open **additional_copies.csv** with a spreadsheet tool. This file can be
+useful to identify duplicated genes in relation to other genomes.
+
+The default criteria to call a group core is presence in all genomes
+where unique is only allowed to be present in one genome. These two
+categories are highly influenced by annotation quality, especially in
+large pangenomes. Luckily, the threshold for core and unique groups can
+easily be adjusted. Let’s consider genes to be core when present in only
+five of the six genomes by setting the ``--core-threshold`` argument.
+
+.. code:: bash
+
+ $ pantools gene_classification -dp pecto_dickeya_DB --core-threshold 85
+
+Look in **gene_classification_overview.txt** again to observe the
+increase of core groups/genes at the cost of accessory groups.
+
+For this pangenome, the *Dickeya* genome is considered an outgroup to
+the five *Pectobacterium* genomes. While this outgroup is needed to root
+and analyze phylogenetic trees (tutorial part 5), it affects the number
+classified groups for the all other genomes. Use ``--reference`` or
+``--skip`` to exclude the *Dickeya* genome.
+
+.. code:: bash
+
+ $ pantools gene_classification -dp pecto_dickeya_DB --reference 1,2,3,4,5
+ $ pantools gene_classification -dp pecto_dickeya_DB --skip 6
+
+Take a look in **gene_classification_overview.txt** one more time to
+examine the effect of excluding this genome. The total number of groups
+in the analysis is lower now but the number of core and unique genes
+have increased for the five remaining genomes.
+
+When phenotype information is used in the analysis, three additional
+categories can be assigned to a group:
+
+- **Shared**, a gene present in all genomes of a phenotype
+- **Exclusive**, a gene is only present in a certain phenotype
+- **Specific**, a gene present in all genomes of a phenotype and is
+ also exclusive
+
+Include a ``--phenotype`` argument to find genes that are exclusive for
+a certain species.
+
+.. code:: bash
+
+ $ pantools gene_classification -dp pecto_dickeya_DB --phenotype species
+
+Open **gene_classification_phenotype_overview.txt** to see the number of
+classified groups for the species phenotype.
+
+Open **phenotype_disrupted.csv** in a spreadsheet tool. This file
+explains exactly why a homology groups is labeled as phenotype shared
+and not specific.
+
+Open **phenotype_additional_copies.csv** in a spreadsheet tool.
+Similarly to *phenotype_additional.csv* this file shows groups where all
+genomes of a certain phenotype have additional gene copies to (at least
+one of) the other phenotypes.
+
+Each time you run the
+:ref:`gene_classification <characterize:gene classification>` function,
+multiple files are created that contain node identifiers of a certain
+homology group category. These files can be given to other PanTools
+functions for a downstream analysis, for example, sequence alignment,
+phylogeny, or GO enrichment. We will use one of the files later in this
+tutorial.
+
+--------------
+
+Pangenome structure
+-------------------
+
+With the previous functionality we identified the core, accessory and
+unique parts of the pangenome. Now we will use the
+:ref:`pangenome_size_genes <characterize:pangenome size>` function to
+observe how these numbers are reached by simulating the growth of the
+pangenome. Simulating the growth helps explaining if a pangenome should
+be considered open or closed. An pangenome is called open as long as a
+significant number of new (unique) genes are added to the total gene
+repertoire. The openness of a pangenome is usually tested using Heap’s
+law. Heaps’ law (a power law) can be fitted to the number of new genes
+observed when increasing the pangenome by one random genome. The formula
+for the power law model is n = k x N-a, where n is the newly discovered
+genes, N is the total number of genomes, and k and a are the fitting
+parameters. A pangenome can be considered open when a < 1 and closed if
+a > 1.
+
+The outcome of the function can again be controlled through command line
+arguments. Genomes can be excluded from the analysis with ``--skip``.
+You can set the number of iterations with ``--value``. Because
+iterations can be assigned to different threads, including multiple
+threads with ``--threads`` is recommended.
+
+.. code:: bash
+
+ $ pantools pangenome_structure_genes -dp pecto_dickeya_DB -tn 4
+
+The current test set of six bacterial genomes is not representative of a
+full-sized pangenome. Therefore we prepared the results for the
+structure simulation on a set of 197 *Pectobacterium* genomes. The
+runtime of the analysis using 10.000 loops and 24 threads was 1 minute
+and 54 seconds. Download the files here, unpack the archive and take a
+look at the files.
+
+.. code:: bash
+
+ $ wget wget http://bioinformatics.nl/pangenomics/tutorial/pectobacterium_structure.tar.gz
+ $ tar -xvf pectobacterium_structure.tar.gz
+
+Normally you still have to run the R scripts to create the output figures
+and determine the openness of the pangenome.
+
+.. code:: bash
+
+ cd pectobacterium_structure
+ $ Rscript pangenome_growth.R
+ $ Rscript gains_losses_median_and_average.R
+ $ Rscript heaps_law.R
+
+Take a look at the plot. In **core_accessory_unique_size.png**, the
+number of classified groups are plotted for any of the genome
+combination that occured during the simulation. For the
+**core_accessory_size.png** plots, the number of unique groups is
+combined with accessory groups.
+
+The **gains_losses.png** files display the average and mean group gain
+and loss between different pangenome sizes. The line of the core starts
+below zero, meaning for every random genome added, the core genome
+decreases by a number of *X* genes.
+
+.. raw:: html
+
+ <details>
+ <summary>
+ The alpha value of heaps' law is written to
+ <b><i>heaps_law_alpha.txt</i></b>. Click here to reveal the result.
+ </summary>
+ <p>
+ <br>
+ With an alpha of 0.53 the <i>Pectobacterium</i> pangenome has an
+ open structure, which is typical for many bacterial species due
+ their extensive exchange of genetic information. Performing this
+ analysis on a set of closely related animal or plant genomes usually
+ results in a closed pangenome, indicating a limited gene pool.
+ </p>
+ </details>
+
+--------------
+
+Functional annotations
+----------------------
+
+PanTools is able to incorporate functional annotations into the
+pangenome by reading output of various functional annotation tools. In
+this tutorial we only include annotations from InterProScan. Please see
+the :ref:`add_functions <construct:add functional annotations>` manual
+to check which other tools are available. To include the annotations,
+create a file **functions.txt** using text from the box below and add it
+to the command line argument.
+
+.. code:: text
+
+ 1 YOUR_PATH/GCF_002904195.1.gff3
+ 2 YOUR_PATH/GCF_000803215.1.gff3
+ 3 YOUR_PATH/GCF_003595035.1.gff3
+ 4 YOUR_PATH/GCF_000808375.1.gff3
+ 5 YOUR_PATH/GCF_000808115.1.gff3
+ 6 YOUR_PATH/GCA_000147055.1.gff3
+
+.. code:: bash
+
+ $ pantools add_functions -dp pecto_dickeya_DB -if functions.txt
+
+PanTools will ask you to download the InterPro database. Follow the
+steps and execute the program again.
+
+The complete GO, PFAM, Interpro and TIGRFAM, databases are now
+integrated in the graph database after. Genes with a predicted function
+have gained a relationship to that function node. Retrieving a set of
+genes that share a function is now possible through a simple cypher
+query. If you would run **metrics** again, statistics for these type
+functional annotations are calculated. To create a summary table for
+each type of functional annotation, run
+:ref:`function_overview <characterize:functional annotation overview>`.
+
+.. code:: bash
+
+ $ pantools function_overview -dp pecto_dickeya_DB
+
+In **function_overview_per_group.csv** you can navigate to a homology
+group or gene to see the connected functions. You can also search in the
+opposite direction, use one of the created overview files for a type of
+functional annotation and quickly navigate to a function of interest to
+find which genes are connected.
+
+GO enrichment
+~~~~~~~~~~~~~
+
+We go back to the output files from gene classification that only
+contain node identifiers. We can retrieve group functions by providing
+one the files to
+:ref:`group_info <explore:homology group information>` with the
+``--homology-groups`` argument. However, interpreting groups by
+assessing each one individually is not very practical. A common
+approach to discover interesting genes from a large set is
+GO-enrichment. This statistical method enables the identification of
+genes sharing a function that are significantly over or
+under-represented in a given gene set compared to the rest of the
+genome. Let’s perform a :ref:`characterize:go enrichment`
+on homology groups of the core genome.
+
+.. code:: text
+
+ Phenotype: P._brasiliense, 2 genomes, threshold of 2 genomes
+ 1278537,1282642,1283856,1283861,1283862,1283869,1283906,1283921,1283934,1283941,1283945,1283946
+
+.. code:: bash
+
+ $ pantools group_info -dp pecto_dickeya_DB -hm brasiliense_groups.csv
+ $ pantools go_enrichment -dp pecto_dickeya_DB -hm brasiliense_groups.csv
+
+Open **go_enrichment.csv** with a spreadsheet tool. This file holds GO
+terms found in at least one of the genomes, the p-value of the
+statistical test and whether it is actually enriched after the multiple
+testing correction. as this is different for each genome a function
+might enriched in one genome but not in another.
+
+A directory with seperate output files is created for each genome, open
+**go_enrichment.csv** for the genome 4 or 5 in a spreedsheet. Also take
+a look at the PDF files that visualize part of the Gene ontology
+hierarchy.
+
+Classifying functional annotations
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Similarly to classifying gene content, functional annotations can be
+categorized using
+:ref:`functional_classification <characterize:functional classification>`.
+This tool provides an easy way to identify functions shared by a group
+of genomes of a certain phenotype but can also be used to identify
+core or unique functions. The functionality uses the same set of
+arguments as **gene_classification**. You can go through the same
+steps again to see the effect of changing the arguments.
+
+.. code:: bash
+
+ $ pantools functional_classification -dp pecto_dickeya_DB
+ $ pantools functional_classification -dp pecto_dickeya_DB -ct 85
+ $ pantools functional_classification -dp pecto_dickeya_DB --skip 6
+ $ pantools functional_classification -dp pecto_dickeya_DB -ph species
+
+--------------
+
+Sequence alignment
+------------------
+
+In the final part of this tutorial we will test the alignment function
+by aligning homology groups. PanTools is able to align genomic regions,
+genes and proteins to identify SNPs or amino acid changes with
+:doc:`msa <msa>`.
+
+Start with the alignment of protein sequences from the 12 *P.
+brasiliense* specific homology groups.
+
+.. code:: bash
+
+ $ pantools msa -dp pecto_dickeya_DB -hm brasiliense_groups.csv --mode protein --method per_group
+
+Go to the **pecto_dickeya_DB/alignments/grouping_v1/groups/** directory
+and select one of homology groups and check if you can find the
+following files
+
+- The alignments are written to **prot_trimmed.fasta** and
+ **prot_trimmed.afa**.
+- A gene tree is written to **prot_trimmed.newick**
+- **prot_trimmed_variable_positions.csv** located in the
+ **var_inf_positions** subdirectory. This matrix holds every variable
+ position of the alignment; the rows are the position in the alignment
+ and the columns are the 20 amino acids and gaps.
+- The identity and similarity (for proteins) is calculated between
+ sequences and written to tables in the **similarity_identity**
+ subdirectory.
+
+Run the function again but include the ``--no_trimming`` argument.
+
+.. code:: bash
+
+ $ pantools msa -dp pecto_dickeya_DB -hm brasiliense_groups.csv --mode protein --method per_group --no-trimming
+
+The output files are generated right after the first alignment without
+trimming the sequences first. The file names differ from the trimmed
+alignments by the ’*_trimmed*’ substring.
+
+Run the function again but exclude the ``--mode protein`` and
+``--no_trimming`` arguments. When no additional arguments are included
+to the command, both nucleotide and protein sequences are aligned two
+consecutive times.
+
+.. code:: bash
+
+ $ pantools msa -dp pecto_dickeya_DB -hm brasiliense_groups.csv --method per_group
+
+Again, the same type of files are generated but the output files from
+nucleotide sequence can be recognized by the ‘*nuc\_*’ substrings. The
+matrix in **nuc_trimmed_variable_positions.csv** now only has columns
+for the four nucleotides and gaps.
+
+Finally, run the function one more time but include a phenotype. This
+allows you to identify phenotype specific SNPs or amino acid changes.
+
+.. code:: bash
+
+ $ pantools msa -dp pecto_dickeya_DB -hm brasiliense_groups.csv --no-trimming -ph low_temperature
+
+Open the **nuc**- or **prot_trimmed_phenotype_specific_changes.info**
+file inside one of the homology group output directories.
+
+--------------
+
+Besides the functionalities in this tutorial, PanTools has more useful
+functions that may aid you in retrieving more specific information from
+the pangenome.
+
+- Identify shared k-mers between genomes with
+ :ref:`kmer_classification <characterize:k-mer classification>`.
+- Find co-localized genes in a set of homology groups:
+ :ref:`locate_genes <explore:gene locations>`.
+- Mapping short reads against the pangenome with :doc:`map <mapping>`.
+
+In :doc:`part 5 <tutorial_part5>` of the tutorial we explore some of the
+phylogenetic methods implemented in PanTools.
diff --git a/docs/source/tutorial_part5.rst b/docs/source/tutorial_part5.rst
new file mode 100644
index 0000000000000000000000000000000000000000..2e929b01a1fc1663213bfdaf590b14d7b15e7110
--- /dev/null
+++ b/docs/source/tutorial_part5.rst
@@ -0,0 +1,274 @@
+Part 5. Phylogeny
+=================
+
+Part 5 preparation
+------------------
+
+Pantools v3 is required to follow this part of the tutorial. In
+addition, MAFFT, FastTree, IQ-tree, R (and the ape R package) need to be
+installed and set to your $PATH. Validate if the tools are executable by
+using the following commands.
+
+.. code:: bash
+
+ pantools version
+ Rscript --help
+ mafft -h
+ iqtree -h
+ fasttree -h
+
+If you did not follow part 4 of the tutorial, download the
+pre-constructed pangenome
+`here <http://bioinformatics.nl/pangenomics/tutorial/pecto_dickeya_DB.tar.gz>`_.
+
+.. code:: bash
+
+ $ wget http://bioinformatics.nl/pangenomics/tutorial/pecto_dickeya_DB.tar.gz
+ $ tar -xvzf pecto_dickeya_DB.tar.gz
+
+--------------
+
+Adding phenotype/metadata to the pangenome
+------------------------------------------
+
+Before we construct the trees, we will add some phenotype data to the
+pangenome. Once the we have a phylogeny, the information can be included
+or be used to color parts of the tree. Below is a textfile with data for
+three phenotypes. The third phenotype, *low_temperature*, is in this
+case a made up example! It states whether the strain is capable of
+growing on (extreme) low temperatures. The phenotype file can be found
+inside the database directory, add the information to the pangenome by
+using :ref:`add_phenotype <construct:add phenotypes>`.
+
+.. code:: text
+
+ Genome, species, strain_name, low_temperature
+ 1,P. odoriferum,P. odoriferum Q166, false
+ 2,P. fontis, P. fontis M022, true
+ 3,P. polaris,P. polaris S4.16.03.2B, false
+ 4,P. brasiliense, P. brasiliense S2, true
+ 5,P. brasiliense, P. brasiliense Y49, false
+ 6,D. dadantii, D. dadantii 3937,?
+
+.. code:: bash
+
+ $ pantools add_phenotype -dp pecto_dickeya_DB/ -ph pecto_dickeya_DB/phenotypes.txt
+
+--------------
+
+Constructing a phylogeny
+------------------------
+
+In this tutorial we will construct three phylogenies, each based on a
+different type of variation: SNPs, genes and k-mers. Take a look at the
+phylogeny manuals to get an understanding how the three methods work and
+how they differ from each other.
+
+1. :ref:`phylogeny:core snp tree>`
+2. :ref:`phylogeny:gene distance tree>`
+3. :ref:`phylogeny:k-mer distance tree>`
+
+Core SNP phylogeny
+------------------
+
+The core SNP phylogeny will run various Maximum Likelihood models on
+parsimony informative sites of single-copy orthologous sequences. A site
+is parsimony-informative when there are at least two types of
+nucleotides that occur with a minimum frequency of two. The informative
+sites are automatically identified by aligning the sequences; however,
+it does not know which sequences are single-copy orthologous. You can
+identify these conserved sequences by running
+:ref:`gene_classification <characterize:gene classification>`.
+
+.. code:: bash
+
+ $ pantools gene_classification -dp pecto_dickeya_DB/ -ph species
+
+Open **gene_classification_overview.txt** and take a look at statistics.
+As you can see there are 2134 single-copy ortholog groups. Normally, all
+of these groups are aligned to identify SNPs but for this tutorial we’ll
+make a selection of only a few groups to accelerate the steps. You can
+do this in two different ways:
+
+Option 1: Open **single_copy_orthologs.csv** and remove all node
+identifiers after the first 20 homology groups and save the file.
+
+.. code:: bash
+
+ $ pantools core_snp_tree -dp pecto_dickeya_DB/ --mode ML -tn 4
+
+Option 2: Open **single_copy_orthologs.csv** and select the first 20
+homology_group node identifiers. Place them in a new file sco_groups.txt
+and include this file to the function.
+
+.. code:: bash
+
+ $ pantools core_snp_tree -dp pecto_dickeya_DB/ --mode ML -tn 4 -hm sco_groups.txt
+
+The sequences of the homology groups are being aligned two consecutive
+times. After the initial alignment, input sequences are trimmed based on
+the longest start and end gap of the alignment. The parsimony
+informative positions are taken from the second alignment and
+concatenated into a sequence. When opening **informative.fasta** you can
+find 6 sequences, the length of the sequences being the number of
+parsimony-informative sites.
+
+.. code:: bash
+
+ $ iqtree -nt 4 -s pecto_dickeya_DB/alignments/grouping_v1/core_snp_tree/informative.fasta -redo -bb 1000
+
+IQ-tree generates several files, the tree that we later on in the
+tutorial will continue with is called **informative.fasta.treefile**.
+When examining the **informative.fasta.iqtree** file you can find the
+best fit model of the data. This file also shows the number of sites
+that were used, as sites with gaps (which IQ-tree does not allow) were
+changed into singleton or constant sites.
+
+Gene distance tree
+~~~~~~~~~~~~~~~~~~
+
+To create a phylogeny based on gene distances (absence/presence), we can
+simply execute the Rscript that was created by
+:ref:`gene_classification <characterize:gene classification>`.
+
+.. code:: bash
+
+ $ Rscript pecto_dickeya_DB/gene_classification/gene_distance_tree.R
+
+The resulting tree is called **gene_distance.tree**.
+
+K-mer distance tree
+~~~~~~~~~~~~~~~~~~~
+
+To obtain a k-mer distance phylogeny, the k-mers must first be counted
+with the :ref:`kmer_classification <characterize:k-mer classification>`
+function. Afterwards, the tree can be constructed by executing the
+Rscript.
+
+.. code:: bash
+
+ $ pantools kmer_classification -dp pecto_dickeya_DB/
+ $ Rscript pecto_dickeya_DB/kmer_classification/genome_kmer_distance_tree.R
+
+The resulting tree is written to **genome_kmer_distance.tree**.
+
+--------------
+
+Renaming tree nodes
+-------------------
+
+So far, we used three different types of distances (SNPs, genes,
+k-mers), and two different methods (ML, NJ) to create three phylogenetic
+trees. First, lets take a look at the text files. The
+**informative.fasta.treefile** only contain genome numbers, bootstrap
+values and branch lengths but is lacking the metadata. Examining
+**gene_distance.tree** file also shows this information but the species
+names as well, because we included this as a phenotype during
+:ref:`gene_classification <characterize:gene classification>`.
+
+Let’s include the strain identifiers to the core snp tree to make the
+final figure more informative. Use the
+:ref:`rename_phylogeny <phylogeny:rename phylogeny>` function to rename
+the tree nodes.
+
+::
+
+ $ pantools rename_phylogeny -dp pecto_dickeya_DB --phenotype strain_name -if pecto_dickeya_DB/alignments/grouping_v1/core_snp_tree/informative.fasta.treefile
+
+Take a look at **informative.fasta_RENAMED.treefile**, strain
+identifiers have been added to the tree.
+
+--------------
+
+Visualizing the tree in iTOL
+----------------------------
+
+Go to https://itol.embl.de and click on “Upload a tree” under the
+**ANNOTATE** box. On this page you can paste the tree directly into the
+**tree text:** textbox or can click the button to upload the .newick
+file.
+
+.. figure:: figures/tutorial_phylogeny1.png
+ :width: 600
+ :align: center
+
+Basic controls ITOL
+-------------------
+
+- The default way of visualizing a tree is the rectangular view.
+ Depending on the number of genomes, the circular view can be easier
+ to interpret. You can the view by clicking on the “Display Mode”
+ buttons.
+- Increase the font size and branch width to improve readability
+- When visualizing a Maximum likelihood (ML) tree, bootstrap values can
+ be displayed by clicking the “Display” button next to
+ **Bootstrap/metadata** in the Advanced tab of the Control window.
+ This enables you to visualize the values as text or symbol on the
+ branch. or by coloring the branch or adjusting the width.
+
+.. figure:: figures/tutorial_phylogeny2.png
+ :width: 600
+ :align: center
+
+- When you have a known outgroup or one of the genomes is a clear
+ outlier in the tree, you should reroot the tree. Hover over the name,
+ click it so a pop-up menu appears. Click “tree structure” followed by
+ “Reroot the tree here”.
+
+.. figure:: figures/tutorial_phylogeny3.png
+ :width: 600
+ :align: center
+
+- Clicking on the name of a node in the tree allows you to color the
+ name, branch, or background of that specific node.
+- When you’re happy the way your tree looks, go to the Export tab of
+ the Control window. Select the desired output format, click on the
+ “Full image” button and export the file to a figure.
+- Refresh the webpage to go back to the default view of your tree.
+
+Create iTOL templates
+---------------------
+
+In iTOL it is possible to add colors to the tree by coloring the
+terminal nodes or adding an outer ring. The PanTools function
+:ref:`create_tree_template <phylogeny:create tree template>` is able to
+create templates that allows for easy coloring (with maximum of 20
+possible colors). If the function is run without any additional
+argument, templates are created for trees that only contain genome
+numbers (e.g. k-mer distance tree). Here we want to color the (renamed)
+core SNP tree with the ‘low_temperature’ phenotype. Therefore, the
+``--phenotype`` strain_name must be included to the function.
+
+::
+
+ $ pantools create_tree_template -dp pecto_dickeya_DB # Run this command when the tree contains genome numbers only
+ $ pantools create_tree_template -dp pecto_dickeya_DB -ph strain_name
+
+Copy the two low_temperature.txt files from the label/strain_name/ and
+ring/strain_name/ directories to your personal computer. Click and move
+the ring template file into the tree visualization webpage.
+
+.. figure:: figures/tutorial_phylogeny4.png
+ :width: 600
+ :align: center
+
+The resulting tree should look this when: the tree is rooted with the
+*Dickeya* genome, bootstrap values are displayed as text and the ring
+color template was included.
+
+.. figure:: figures/tutorial_phylogeny_color.png
+ :width: 600
+ :align: center
+
+Tree coloring is especially useful for large datasets. An example is
+shown in the figure below, where members of the same species share a
+color.
+
+.. figure:: figures/tutorial_phylogeny_tree.png
+ :width: 600
+ :align: center
+
+--------------
+
+..
+ In [**part 6**](tutorial_part6.md){target=\_blank} of the tutorial we go through a couple of use cases with the pangenomic read mapping functionality implemented in PanTools.
diff --git a/docs/source/tutorial_part6.rst b/docs/source/tutorial_part6.rst
new file mode 100644
index 0000000000000000000000000000000000000000..8c5dda85ab5cf5643b1a17eb68a29a1f7e000d2c
--- /dev/null
+++ b/docs/source/tutorial_part6.rst
@@ -0,0 +1,4 @@
+Part 6. Read mapping
+====================
+
+Soon!
diff --git a/manifest.mf b/manifest.mf
deleted file mode 100755
index 328e8e5bc3b7f1f7bad2bc0751a933e00c801983..0000000000000000000000000000000000000000
--- a/manifest.mf
+++ /dev/null
@@ -1,3 +0,0 @@
-Manifest-Version: 1.0
-X-COMMENT: Main-Class will be added automatically by build
-
diff --git a/nbproject/build-impl.xml b/nbproject/build-impl.xml
deleted file mode 100755
index 35b73745b7c4d61bec828891cf95d7579197d235..0000000000000000000000000000000000000000
--- a/nbproject/build-impl.xml
+++ /dev/null
@@ -1,1799 +0,0 @@
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- <attribute default="${javac.modulepath}" name="modulepath"/>
- <attribute default="${javac.upgrademodulepath}" name="upgrademodulepath"/>
- <attribute default="${javac.processorpath}" name="processorpath"/>
- <attribute default="${build.generated.sources.dir}/ap-source-output" name="apgeneratedsrcdir"/>
- <attribute default="${includes}" name="includes"/>
- <attribute default="${excludes}" name="excludes"/>
- <attribute default="${javac.debug}" name="debug"/>
- <attribute default="${empty.dir}" name="sourcepath"/>
- <attribute default="${empty.dir}" name="gensrcdir"/>
- <element name="customize" optional="true"/>
- <sequential>
- <property location="${build.dir}/empty" name="empty.dir"/>
- <mkdir dir="${empty.dir}"/>
- <javac debug="@{debug}" deprecation="${javac.deprecation}" destdir="@{destdir}" encoding="${source.encoding}" excludes="@{excludes}" executable="${platform.javac}" fork="yes" includeantruntime="false" includes="@{includes}" source="${javac.source}" sourcepath="@{sourcepath}" srcdir="@{srcdir}" target="${javac.target}" tempdir="${java.io.tmpdir}">
- <src>
- <dirset dir="@{gensrcdir}" erroronmissingdir="false">
- <include name="*"/>
- </dirset>
- </src>
- <classpath>
- <path path="@{classpath}"/>
- </classpath>
- <compilerarg line="${endorsed.classpath.cmd.line.arg}"/>
- <compilerarg line="${javac.profile.cmd.line.arg}"/>
- <compilerarg line="${javac.compilerargs}"/>
- <customize/>
- </javac>
- </sequential>
- </macrodef>
- </target>
- <target depends="-init-macrodef-javac-with-module,-init-macrodef-javac-with-processors,-init-macrodef-javac-without-processors" name="-init-macrodef-javac">
- <macrodef name="depend" uri="http://www.netbeans.org/ns/j2se-project/3">
- <attribute default="${src.dir}" name="srcdir"/>
- <attribute default="${build.classes.dir}" name="destdir"/>
- <attribute default="${javac.classpath}" name="classpath"/>
- <sequential>
- <depend cache="${build.dir}/depcache" destdir="@{destdir}" excludes="${excludes}" includes="${includes}" srcdir="@{srcdir}">
- <classpath>
- <path path="@{classpath}"/>
- </classpath>
- </depend>
- </sequential>
- </macrodef>
- <macrodef name="force-recompile" uri="http://www.netbeans.org/ns/j2se-project/3">
- <attribute default="${build.classes.dir}" name="destdir"/>
- <sequential>
- <fail unless="javac.includes">Must set javac.includes</fail>
- <pathconvert pathsep="${line.separator}" property="javac.includes.binary">
- <path>
- <filelist dir="@{destdir}" files="${javac.includes}"/>
- </path>
- <globmapper from="*.java" to="*.class"/>
- </pathconvert>
- <tempfile deleteonexit="true" property="javac.includesfile.binary"/>
- <echo file="${javac.includesfile.binary}" message="${javac.includes.binary}"/>
- <delete>
- <files includesfile="${javac.includesfile.binary}"/>
- </delete>
- <delete>
- <fileset file="${javac.includesfile.binary}"/>
- </delete>
- </sequential>
- </macrodef>
- </target>
- <target if="${junit.available}" name="-init-macrodef-junit-init">
- <condition else="false" property="nb.junit.batch" value="true">
- <and>
- <istrue value="${junit.available}"/>
- <not>
- <isset property="test.method"/>
- </not>
- </and>
- </condition>
- <condition else="false" property="nb.junit.single" value="true">
- <and>
- <istrue value="${junit.available}"/>
- <isset property="test.method"/>
- </and>
- </condition>
- </target>
- <target name="-init-test-properties">
- <property name="test.binaryincludes" value="<nothing>"/>
- <property name="test.binarytestincludes" value=""/>
- <property name="test.binaryexcludes" value=""/>
- </target>
- <target depends="-init-modules-supported" if="modules.supported.internal" name="-init-macrodef-junit-prototype-with-module">
- <macrodef name="junit-prototype" uri="http://www.netbeans.org/ns/j2se-project/3">
- <attribute default="${includes}" name="includes"/>
- <attribute default="${excludes}" name="excludes"/>
- <element name="customizePrototype" optional="true"/>
- <sequential>
- <property name="junit.forkmode" value="perTest"/>
- <junit dir="${work.dir}" errorproperty="tests.failed" failureproperty="tests.failed" fork="true" forkmode="${junit.forkmode}" jvm="${platform.java}" showoutput="true" tempdir="${build.dir}">
- <syspropertyset>
- <propertyref prefix="test-sys-prop."/>
- <mapper from="test-sys-prop.*" to="*" type="glob"/>
- </syspropertyset>
- <classpath>
- <path path="${run.test.classpath}"/>
- </classpath>
- <modulepath>
- <path path="${run.test.modulepath}"/>
- </modulepath>
- <formatter type="brief" usefile="false"/>
- <formatter type="xml"/>
- <jvmarg line="${endorsed.classpath.cmd.line.arg}"/>
- <jvmarg value="-ea"/>
- <jvmarg line="${run.test.jvmargs}"/>
- <customizePrototype/>
- </junit>
- </sequential>
- </macrodef>
- </target>
- <target depends="-init-modules-supported" name="-init-macrodef-junit-prototype-without-module" unless="modules.supported.internal">
- <macrodef name="junit-prototype" uri="http://www.netbeans.org/ns/j2se-project/3">
- <attribute default="${includes}" name="includes"/>
- <attribute default="${excludes}" name="excludes"/>
- <element name="customizePrototype" optional="true"/>
- <sequential>
- <property name="junit.forkmode" value="perTest"/>
- <junit dir="${work.dir}" errorproperty="tests.failed" failureproperty="tests.failed" fork="true" forkmode="${junit.forkmode}" jvm="${platform.java}" showoutput="true" tempdir="${build.dir}">
- <syspropertyset>
- <propertyref prefix="test-sys-prop."/>
- <mapper from="test-sys-prop.*" to="*" type="glob"/>
- </syspropertyset>
- <classpath>
- <path path="${run.test.classpath}"/>
- </classpath>
- <formatter type="brief" usefile="false"/>
- <formatter type="xml"/>
- <jvmarg line="${endorsed.classpath.cmd.line.arg}"/>
- <jvmarg value="-ea"/>
- <customizePrototype/>
- </junit>
- </sequential>
- </macrodef>
- </target>
- <target depends="-init-test-properties,-init-macrodef-junit-prototype-with-module,-init-macrodef-junit-prototype-without-module" if="${nb.junit.single}" name="-init-macrodef-junit-single" unless="${nb.junit.batch}">
- <macrodef name="junit" uri="http://www.netbeans.org/ns/j2se-project/3">
- <attribute default="${includes}" name="includes"/>
- <attribute default="${excludes}" name="excludes"/>
- <attribute default="**" name="testincludes"/>
- <attribute default="" name="testmethods"/>
- <element name="customize" optional="true"/>
- <sequential>
- <j2seproject3:junit-prototype>
- <customizePrototype>
- <test methods="@{testmethods}" name="@{testincludes}" todir="${build.test.results.dir}"/>
- <customize/>
- </customizePrototype>
- </j2seproject3:junit-prototype>
- </sequential>
- </macrodef>
- </target>
- <target depends="-init-test-properties,-init-macrodef-junit-prototype-with-module,-init-macrodef-junit-prototype-without-module" if="${nb.junit.batch}" name="-init-macrodef-junit-batch" unless="${nb.junit.single}">
- <macrodef name="junit" uri="http://www.netbeans.org/ns/j2se-project/3">
- <attribute default="${includes}" name="includes"/>
- <attribute default="${excludes}" name="excludes"/>
- <attribute default="**" name="testincludes"/>
- <attribute default="" name="testmethods"/>
- <element name="customize" optional="true"/>
- <sequential>
- <j2seproject3:junit-prototype>
- <customizePrototype>
- <batchtest todir="${build.test.results.dir}">
- <fileset dir="${test.src.dir}" excludes="@{excludes},${excludes}" includes="@{includes}">
- <filename name="@{testincludes}"/>
- </fileset>
- <fileset dir="${build.test.classes.dir}" excludes="@{excludes},${excludes},${test.binaryexcludes}" includes="${test.binaryincludes}">
- <filename name="${test.binarytestincludes}"/>
- </fileset>
- </batchtest>
- <customize/>
- </customizePrototype>
- </j2seproject3:junit-prototype>
- </sequential>
- </macrodef>
- </target>
- <target depends="-init-macrodef-junit-init,-init-macrodef-junit-single, -init-macrodef-junit-batch" if="${junit.available}" name="-init-macrodef-junit"/>
- <target if="${testng.available}" name="-init-macrodef-testng">
- <macrodef name="testng" uri="http://www.netbeans.org/ns/j2se-project/3">
- <attribute default="${includes}" name="includes"/>
- <attribute default="${excludes}" name="excludes"/>
- <attribute default="**" name="testincludes"/>
- <attribute default="" name="testmethods"/>
- <element name="customize" optional="true"/>
- <sequential>
- <condition else="" property="testng.methods.arg" value="@{testincludes}.@{testmethods}">
- <isset property="test.method"/>
- </condition>
- <union id="test.set">
- <fileset dir="${test.src.dir}" excludes="@{excludes},**/*.xml,${excludes}" includes="@{includes}">
- <filename name="@{testincludes}"/>
- </fileset>
- </union>
- <taskdef classname="org.testng.TestNGAntTask" classpath="${run.test.classpath}" name="testng"/>
- <testng classfilesetref="test.set" failureProperty="tests.failed" jvm="${platform.java}" listeners="org.testng.reporters.VerboseReporter" methods="${testng.methods.arg}" mode="${testng.mode}" outputdir="${build.test.results.dir}" suitename="pantools" testname="TestNG tests" workingDir="${work.dir}">
- <xmlfileset dir="${build.test.classes.dir}" includes="@{testincludes}"/>
- <propertyset>
- <propertyref prefix="test-sys-prop."/>
- <mapper from="test-sys-prop.*" to="*" type="glob"/>
- </propertyset>
- <classpath>
- <path path="${run.test.classpath}"/>
- </classpath>
- <jvmarg line="${endorsed.classpath.cmd.line.arg}"/>
- <customize/>
- </testng>
- </sequential>
- </macrodef>
- </target>
- <target name="-init-macrodef-test-impl">
- <macrodef name="test-impl" uri="http://www.netbeans.org/ns/j2se-project/3">
- <attribute default="${includes}" name="includes"/>
- <attribute default="${excludes}" name="excludes"/>
- <attribute default="**" name="testincludes"/>
- <attribute default="" name="testmethods"/>
- <element implicit="true" name="customize" optional="true"/>
- <sequential>
- <echo>No tests executed.</echo>
- </sequential>
- </macrodef>
- </target>
- <target depends="-init-macrodef-junit" if="${junit.available}" name="-init-macrodef-junit-impl">
- <macrodef name="test-impl" uri="http://www.netbeans.org/ns/j2se-project/3">
- <attribute default="${includes}" name="includes"/>
- <attribute default="${excludes}" name="excludes"/>
- <attribute default="**" name="testincludes"/>
- <attribute default="" name="testmethods"/>
- <element implicit="true" name="customize" optional="true"/>
- <sequential>
- <j2seproject3:junit excludes="@{excludes}" includes="@{includes}" testincludes="@{testincludes}" testmethods="@{testmethods}">
- <customize/>
- </j2seproject3:junit>
- </sequential>
- </macrodef>
- </target>
- <target depends="-init-macrodef-testng" if="${testng.available}" name="-init-macrodef-testng-impl">
- <macrodef name="test-impl" uri="http://www.netbeans.org/ns/j2se-project/3">
- <attribute default="${includes}" name="includes"/>
- <attribute default="${excludes}" name="excludes"/>
- <attribute default="**" name="testincludes"/>
- <attribute default="" name="testmethods"/>
- <element implicit="true" name="customize" optional="true"/>
- <sequential>
- <j2seproject3:testng excludes="@{excludes}" includes="@{includes}" testincludes="@{testincludes}" testmethods="@{testmethods}">
- <customize/>
- </j2seproject3:testng>
- </sequential>
- </macrodef>
- </target>
- <target depends="-init-macrodef-test-impl,-init-macrodef-junit-impl,-init-macrodef-testng-impl" name="-init-macrodef-test">
- <macrodef name="test" uri="http://www.netbeans.org/ns/j2se-project/3">
- <attribute default="${includes}" name="includes"/>
- <attribute default="${excludes}" name="excludes"/>
- <attribute default="**" name="testincludes"/>
- <attribute default="" name="testmethods"/>
- <sequential>
- <j2seproject3:test-impl excludes="@{excludes}" includes="@{includes}" testincludes="@{testincludes}" testmethods="@{testmethods}">
- <customize>
- <jvmarg line="${run.jvmargs}"/>
- <jvmarg line="${run.jvmargs.ide}"/>
- </customize>
- </j2seproject3:test-impl>
- </sequential>
- </macrodef>
- </target>
- <target depends="-init-macrodef-junit" if="${junit.available}" name="-init-macrodef-junit-debug-impl">
- <macrodef name="test-debug-impl" uri="http://www.netbeans.org/ns/j2se-project/3">
- <attribute default="${includes}" name="includes"/>
- <attribute default="${excludes}" name="excludes"/>
- <attribute default="**" name="testincludes"/>
- <attribute default="" name="testmethods"/>
- <element name="customizeDebuggee" optional="true"/>
- <sequential>
- <j2seproject3:junit excludes="@{excludes}" includes="@{includes}" testincludes="@{testincludes}" testmethods="@{testmethods}">
- <customize>
- <jvmarg value="-agentlib:jdwp=transport=${debug-transport},address=${jpda.address}"/>
- <customizeDebuggee/>
- </customize>
- </j2seproject3:junit>
- </sequential>
- </macrodef>
- </target>
- <target if="${testng.available}" name="-init-macrodef-testng-debug">
- <macrodef name="testng-debug" uri="http://www.netbeans.org/ns/j2se-project/3">
- <attribute default="${main.class}" name="testClass"/>
- <attribute default="" name="testMethod"/>
- <element name="customize2" optional="true"/>
- <sequential>
- <condition else="-testclass @{testClass}" property="test.class.or.method" value="-methods @{testClass}.@{testMethod}">
- <isset property="test.method"/>
- </condition>
- <condition else="-suitename pantools -testname @{testClass} ${test.class.or.method}" property="testng.cmd.args" value="@{testClass}">
- <matches pattern=".*\.xml" string="@{testClass}"/>
- </condition>
- <delete dir="${build.test.results.dir}" quiet="true"/>
- <mkdir dir="${build.test.results.dir}"/>
- <j2seproject3:debug classname="org.testng.TestNG" classpath="${debug.test.classpath}">
- <customizeDebuggee>
- <customize2/>
- <jvmarg value="-ea"/>
- <arg line="${testng.debug.mode}"/>
- <arg line="-d ${build.test.results.dir}"/>
- <arg line="-listener org.testng.reporters.VerboseReporter"/>
- <arg line="${testng.cmd.args}"/>
- </customizeDebuggee>
- </j2seproject3:debug>
- </sequential>
- </macrodef>
- </target>
- <target depends="-init-macrodef-testng-debug" if="${testng.available}" name="-init-macrodef-testng-debug-impl">
- <macrodef name="testng-debug-impl" uri="http://www.netbeans.org/ns/j2se-project/3">
- <attribute default="${main.class}" name="testClass"/>
- <attribute default="" name="testMethod"/>
- <element implicit="true" name="customize2" optional="true"/>
- <sequential>
- <j2seproject3:testng-debug testClass="@{testClass}" testMethod="@{testMethod}">
- <customize2/>
- </j2seproject3:testng-debug>
- </sequential>
- </macrodef>
- </target>
- <target depends="-init-macrodef-junit-debug-impl" if="${junit.available}" name="-init-macrodef-test-debug-junit">
- <macrodef name="test-debug" uri="http://www.netbeans.org/ns/j2se-project/3">
- <attribute default="${includes}" name="includes"/>
- <attribute default="${excludes}" name="excludes"/>
- <attribute default="**" name="testincludes"/>
- <attribute default="" name="testmethods"/>
- <attribute default="${main.class}" name="testClass"/>
- <attribute default="" name="testMethod"/>
- <sequential>
- <j2seproject3:test-debug-impl excludes="@{excludes}" includes="@{includes}" testincludes="@{testincludes}" testmethods="@{testmethods}">
- <customizeDebuggee>
- <jvmarg line="${run.jvmargs}"/>
- <jvmarg line="${run.jvmargs.ide}"/>
- </customizeDebuggee>
- </j2seproject3:test-debug-impl>
- </sequential>
- </macrodef>
- </target>
- <target depends="-init-macrodef-testng-debug-impl" if="${testng.available}" name="-init-macrodef-test-debug-testng">
- <macrodef name="test-debug" uri="http://www.netbeans.org/ns/j2se-project/3">
- <attribute default="${includes}" name="includes"/>
- <attribute default="${excludes}" name="excludes"/>
- <attribute default="**" name="testincludes"/>
- <attribute default="" name="testmethods"/>
- <attribute default="${main.class}" name="testClass"/>
- <attribute default="" name="testMethod"/>
- <sequential>
- <j2seproject3:testng-debug-impl testClass="@{testClass}" testMethod="@{testMethod}">
- <customize2>
- <syspropertyset>
- <propertyref prefix="test-sys-prop."/>
- <mapper from="test-sys-prop.*" to="*" type="glob"/>
- </syspropertyset>
- </customize2>
- </j2seproject3:testng-debug-impl>
- </sequential>
- </macrodef>
- </target>
- <target depends="-init-macrodef-test-debug-junit,-init-macrodef-test-debug-testng" name="-init-macrodef-test-debug"/>
- <!--
- pre NB7.2 profiling section; consider it deprecated
- -->
- <target depends="-profile-pre-init, init, -profile-post-init, -profile-init-macrodef-profile, -profile-init-check" if="profiler.info.jvmargs.agent" name="profile-init"/>
- <target if="profiler.info.jvmargs.agent" name="-profile-pre-init">
- <!-- Empty placeholder for easier customization. -->
- <!-- You can override this target in the ../build.xml file. -->
- </target>
- <target if="profiler.info.jvmargs.agent" name="-profile-post-init">
- <!-- Empty placeholder for easier customization. -->
- <!-- You can override this target in the ../build.xml file. -->
- </target>
- <target if="profiler.info.jvmargs.agent" name="-profile-init-macrodef-profile">
- <macrodef name="resolve">
- <attribute name="name"/>
- <attribute name="value"/>
- <sequential>
- <property name="@{name}" value="${env.@{value}}"/>
- </sequential>
- </macrodef>
- <macrodef name="profile">
- <attribute default="${main.class}" name="classname"/>
- <element name="customize" optional="true"/>
- <sequential>
- <property environment="env"/>
- <resolve name="profiler.current.path" value="${profiler.info.pathvar}"/>
- <java classname="@{classname}" dir="${profiler.info.dir}" failonerror="${java.failonerror}" fork="true" jvm="${profiler.info.jvm}">
- <jvmarg line="${endorsed.classpath.cmd.line.arg}"/>
- <jvmarg value="${profiler.info.jvmargs.agent}"/>
- <jvmarg line="${profiler.info.jvmargs}"/>
- <env key="${profiler.info.pathvar}" path="${profiler.info.agentpath}:${profiler.current.path}"/>
- <arg line="${application.args}"/>
- <classpath>
- <path path="${run.classpath}"/>
- </classpath>
- <syspropertyset>
- <propertyref prefix="run-sys-prop."/>
- <mapper from="run-sys-prop.*" to="*" type="glob"/>
- </syspropertyset>
- <customize/>
- </java>
- </sequential>
- </macrodef>
- </target>
- <target depends="-profile-pre-init, init, -profile-post-init, -profile-init-macrodef-profile" if="profiler.info.jvmargs.agent" name="-profile-init-check">
- <fail unless="profiler.info.jvm">Must set JVM to use for profiling in profiler.info.jvm</fail>
- <fail unless="profiler.info.jvmargs.agent">Must set profiler agent JVM arguments in profiler.info.jvmargs.agent</fail>
- </target>
- <!--
- end of pre NB7.2 profiling section
- -->
- <target depends="-init-debug-args" name="-init-macrodef-nbjpda">
- <macrodef name="nbjpdastart" uri="http://www.netbeans.org/ns/j2se-project/1">
- <attribute default="${main.class}" name="name"/>
- <attribute default="${debug.modulepath}" name="modulepath"/>
- <attribute default="${debug.classpath}" name="classpath"/>
- <attribute default="" name="stopclassname"/>
- <sequential>
- <nbjpdastart addressproperty="jpda.address" name="@{name}" stopclassname="@{stopclassname}" transport="${debug-transport}">
- <modulepath>
- <path path="@{modulepath}"/>
- </modulepath>
- <classpath>
- <path path="@{classpath}"/>
- </classpath>
- <bootclasspath>
- <path path="${platform.bootcp}"/>
- </bootclasspath>
- </nbjpdastart>
- </sequential>
- </macrodef>
- <macrodef name="nbjpdareload" uri="http://www.netbeans.org/ns/j2se-project/1">
- <attribute default="${build.classes.dir}" name="dir"/>
- <sequential>
- <nbjpdareload>
- <fileset dir="@{dir}" includes="${fix.classes}">
- <include name="${fix.includes}*.class"/>
- </fileset>
- </nbjpdareload>
- </sequential>
- </macrodef>
- </target>
- <target name="-init-debug-args">
- <condition else="dt_socket" property="debug-transport-by-os" value="dt_shmem">
- <os family="windows"/>
- </condition>
- <condition else="${debug-transport-by-os}" property="debug-transport" value="${debug.transport}">
- <isset property="debug.transport"/>
- </condition>
- </target>
- <target depends="-init-debug-args" name="-init-macrodef-debug">
- <macrodef name="debug" uri="http://www.netbeans.org/ns/j2se-project/3">
- <attribute default="${module.name}" name="modulename"/>
- <attribute default="${main.class}" name="classname"/>
- <attribute default="${debug.modulepath}" name="modulepath"/>
- <attribute default="${debug.classpath}" name="classpath"/>
- <element name="customizeDebuggee" optional="true"/>
- <sequential>
- <j2seproject1:java classname="@{classname}" classpath="@{classpath}" modulename="@{modulename}" modulepath="@{modulepath}">
- <customize>
- <jvmarg value="-agentlib:jdwp=transport=${debug-transport},address=${jpda.address}"/>
- <customizeDebuggee/>
- </customize>
- </j2seproject1:java>
- </sequential>
- </macrodef>
- </target>
- <target depends="-init-source-module-properties" if="named.module.internal" name="-init-macrodef-java-with-module">
- <macrodef name="java" uri="http://www.netbeans.org/ns/j2se-project/1">
- <attribute default="${module.name}" name="modulename"/>
- <attribute default="${main.class}" name="classname"/>
- <attribute default="${run.modulepath}" name="modulepath"/>
- <attribute default="${run.upgrademodulepath}" name="upgrademodulepath"/>
- <attribute default="${run.classpath}" name="classpath"/>
- <attribute default="jvm" name="jvm"/>
- <element name="customize" optional="true"/>
- <sequential>
- <java classname="@{classname}" dir="${work.dir}" failonerror="${java.failonerror}" fork="true" jvm="${platform.java}" module="@{modulename}">
- <classpath>
- <path path="@{classpath}"/>
- </classpath>
- <modulepath>
- <pathelement path="@{modulepath}"/>
- <pathelement location="${module.build.classes.dir}"/>
- </modulepath>
- <upgrademodulepath>
- <path path="@{upgrademodulepath}"/>
- </upgrademodulepath>
- <jvmarg value="-Dfile.encoding=${runtime.encoding}"/>
- <redirector errorencoding="${runtime.encoding}" inputencoding="${runtime.encoding}" outputencoding="${runtime.encoding}"/>
- <jvmarg line="${run.jvmargs}"/>
- <jvmarg line="${run.jvmargs.ide}"/>
- <syspropertyset>
- <propertyref prefix="run-sys-prop."/>
- <mapper from="run-sys-prop.*" to="*" type="glob"/>
- </syspropertyset>
- <customize/>
- </java>
- </sequential>
- </macrodef>
- </target>
- <target depends="-init-source-module-properties" if="unnamed.module.internal" name="-init-macrodef-java-with-unnamed-module">
- <macrodef name="java" uri="http://www.netbeans.org/ns/j2se-project/1">
- <attribute default="" name="modulename"/>
- <attribute default="${main.class}" name="classname"/>
- <attribute default="${run.modulepath}" name="modulepath"/>
- <attribute default="${run.upgrademodulepath}" name="upgrademodulepath"/>
- <attribute default="${run.classpath}" name="classpath"/>
- <attribute default="jvm" name="jvm"/>
- <element name="customize" optional="true"/>
- <sequential>
- <java classname="@{classname}" dir="${work.dir}" failonerror="${java.failonerror}" fork="true" jvm="${platform.java}">
- <classpath>
- <path path="@{classpath}"/>
- </classpath>
- <modulepath>
- <path path="@{modulepath}"/>
- </modulepath>
- <upgrademodulepath>
- <path path="@{upgrademodulepath}"/>
- </upgrademodulepath>
- <jvmarg value="-Dfile.encoding=${runtime.encoding}"/>
- <redirector errorencoding="${runtime.encoding}" inputencoding="${runtime.encoding}" outputencoding="${runtime.encoding}"/>
- <jvmarg line="${run.jvmargs}"/>
- <jvmarg line="${run.jvmargs.ide}"/>
- <syspropertyset>
- <propertyref prefix="run-sys-prop."/>
- <mapper from="run-sys-prop.*" to="*" type="glob"/>
- </syspropertyset>
- <customize/>
- </java>
- </sequential>
- </macrodef>
- </target>
- <target depends="-init-source-module-properties" name="-init-macrodef-java-without-module" unless="modules.supported.internal">
- <macrodef name="java" uri="http://www.netbeans.org/ns/j2se-project/1">
- <attribute default="" name="modulename"/>
- <attribute default="${main.class}" name="classname"/>
- <attribute default="" name="modulepath"/>
- <attribute default="${run.classpath}" name="classpath"/>
- <attribute default="jvm" name="jvm"/>
- <element name="customize" optional="true"/>
- <sequential>
- <java classname="@{classname}" dir="${work.dir}" failonerror="${java.failonerror}" fork="true" jvm="${platform.java}">
- <jvmarg line="${endorsed.classpath.cmd.line.arg}"/>
- <jvmarg value="-Dfile.encoding=${runtime.encoding}"/>
- <redirector errorencoding="${runtime.encoding}" inputencoding="${runtime.encoding}" outputencoding="${runtime.encoding}"/>
- <jvmarg line="${run.jvmargs}"/>
- <jvmarg line="${run.jvmargs.ide}"/>
- <classpath>
- <path path="@{classpath}"/>
- </classpath>
- <syspropertyset>
- <propertyref prefix="run-sys-prop."/>
- <mapper from="run-sys-prop.*" to="*" type="glob"/>
- </syspropertyset>
- <customize/>
- </java>
- </sequential>
- </macrodef>
- </target>
- <target depends="-init-macrodef-java-with-module, -init-macrodef-java-with-unnamed-module, -init-macrodef-java-without-module" name="-init-macrodef-java"/>
- <target name="-init-macrodef-copylibs">
- <macrodef name="copylibs" uri="http://www.netbeans.org/ns/j2se-project/3">
- <attribute default="${manifest.file}" name="manifest"/>
- <element name="customize" optional="true"/>
- <sequential>
- <property location="${build.classes.dir}" name="build.classes.dir.resolved"/>
- <pathconvert property="run.classpath.without.build.classes.dir">
- <path path="${run.classpath}"/>
- <map from="${build.classes.dir.resolved}" to=""/>
- </pathconvert>
- <pathconvert pathsep=" " property="jar.classpath">
- <path path="${run.classpath.without.build.classes.dir}"/>
- <chainedmapper>
- <flattenmapper/>
- <filtermapper>
- <replacestring from=" " to="%20"/>
- </filtermapper>
- <globmapper from="*" to="lib/*"/>
- </chainedmapper>
- </pathconvert>
- <taskdef classname="org.netbeans.modules.java.j2seproject.copylibstask.CopyLibs" classpath="${libs.CopyLibs.classpath}" name="copylibs"/>
- <copylibs compress="${jar.compress}" excludeFromCopy="${copylibs.excludes}" index="${jar.index}" indexMetaInf="${jar.index.metainf}" jarfile="${dist.jar}" manifest="@{manifest}" manifestencoding="UTF-8" rebase="${copylibs.rebase}" runtimeclasspath="${run.classpath.without.build.classes.dir}">
- <fileset dir="${build.classes.dir}" excludes="${dist.archive.excludes}"/>
- <manifest>
- <attribute name="Class-Path" value="${jar.classpath}"/>
- <customize/>
- </manifest>
- </copylibs>
- </sequential>
- </macrodef>
- </target>
- <target name="-init-presetdef-jar">
- <presetdef name="jar" uri="http://www.netbeans.org/ns/j2se-project/1">
- <jar compress="${jar.compress}" index="${jar.index}" jarfile="${dist.jar}" manifestencoding="UTF-8">
- <j2seproject1:fileset dir="${build.classes.dir}" excludes="${dist.archive.excludes}"/>
- </jar>
- </presetdef>
- </target>
- <target name="-init-ap-cmdline-properties">
- <property name="annotation.processing.enabled" value="true"/>
- <property name="annotation.processing.processors.list" value=""/>
- <property name="annotation.processing.processor.options" value=""/>
- <property name="annotation.processing.run.all.processors" value="true"/>
- <property name="javac.processorpath" value="${javac.classpath}"/>
- <property name="javac.test.processorpath" value="${javac.test.classpath}"/>
- <condition property="ap.supported.internal" value="true">
- <not>
- <matches pattern="1\.[0-5](\..*)?" string="${javac.source}"/>
- </not>
- </condition>
- </target>
- <target depends="-init-ap-cmdline-properties" if="ap.supported.internal" name="-init-ap-cmdline-supported">
- <condition else="" property="ap.processors.internal" value="-processor ${annotation.processing.processors.list}">
- <isfalse value="${annotation.processing.run.all.processors}"/>
- </condition>
- <condition else="" property="ap.proc.none.internal" value="-proc:none">
- <isfalse value="${annotation.processing.enabled}"/>
- </condition>
- </target>
- <target depends="-init-ap-cmdline-properties,-init-ap-cmdline-supported" name="-init-ap-cmdline">
- <property name="ap.cmd.line.internal" value=""/>
- </target>
- <target depends="-pre-init,-init-private,-init-user,-init-project,-do-init,-post-init,-init-check,-init-macrodef-property,-init-macrodef-javac,-init-macrodef-test,-init-macrodef-test-debug,-init-macrodef-nbjpda,-init-macrodef-debug,-init-macrodef-java,-init-presetdef-jar,-init-ap-cmdline" name="init"/>
- <!--
- ===================
- COMPILATION SECTION
- ===================
- -->
- <target name="-deps-jar-init" unless="built-jar.properties">
- <property location="${build.dir}/built-jar.properties" name="built-jar.properties"/>
- <delete file="${built-jar.properties}" quiet="true"/>
- </target>
- <target if="already.built.jar.${basedir}" name="-warn-already-built-jar">
- <echo level="warn" message="Cycle detected: pantools was already built"/>
- </target>
- <target depends="init,-deps-jar-init" name="deps-jar" unless="no.deps">
- <mkdir dir="${build.dir}"/>
- <touch file="${built-jar.properties}" verbose="false"/>
- <property file="${built-jar.properties}" prefix="already.built.jar."/>
- <antcall target="-warn-already-built-jar"/>
- <propertyfile file="${built-jar.properties}">
- <entry key="${basedir}" value=""/>
- </propertyfile>
- </target>
- <target depends="init,-check-automatic-build,-clean-after-automatic-build" name="-verify-automatic-build"/>
- <target depends="init" name="-check-automatic-build">
- <available file="${build.classes.dir}/.netbeans_automatic_build" property="netbeans.automatic.build"/>
- </target>
- <target depends="init" if="netbeans.automatic.build" name="-clean-after-automatic-build">
- <antcall target="clean">
- <param name="no.dependencies" value="true"/>
- </antcall>
- </target>
- <target depends="init,deps-jar" name="-pre-pre-compile">
- <mkdir dir="${build.classes.dir}"/>
- </target>
- <target name="-pre-compile">
- <!-- Empty placeholder for easier customization. -->
- <!-- You can override this target in the ../build.xml file. -->
- </target>
- <target if="do.depend.true" name="-compile-depend">
- <pathconvert property="build.generated.subdirs">
- <dirset dir="${build.generated.sources.dir}" erroronmissingdir="false">
- <include name="*"/>
- </dirset>
- </pathconvert>
- <j2seproject3:depend srcdir="${src.dir}:${build.generated.subdirs}"/>
- </target>
- <target depends="init,deps-jar,-pre-pre-compile,-pre-compile, -copy-persistence-xml,-compile-depend" if="have.sources" name="-do-compile">
- <j2seproject3:javac gensrcdir="${build.generated.sources.dir}"/>
- <copy todir="${build.classes.dir}">
- <fileset dir="${src.dir}" excludes="${build.classes.excludes},${excludes}" includes="${includes}"/>
- </copy>
- </target>
- <target if="has.persistence.xml" name="-copy-persistence-xml">
- <mkdir dir="${build.classes.dir}/META-INF"/>
- <copy todir="${build.classes.dir}/META-INF">
- <fileset dir="${meta.inf.dir}" includes="persistence.xml orm.xml"/>
- </copy>
- </target>
- <target name="-post-compile">
- <!-- Empty placeholder for easier customization. -->
- <!-- You can override this target in the ../build.xml file. -->
- </target>
- <target depends="init,deps-jar,-verify-automatic-build,-pre-pre-compile,-pre-compile,-do-compile,-post-compile" description="Compile project." name="compile"/>
- <target name="-pre-compile-single">
- <!-- Empty placeholder for easier customization. -->
- <!-- You can override this target in the ../build.xml file. -->
- </target>
- <target depends="init,deps-jar,-pre-pre-compile" name="-do-compile-single">
- <fail unless="javac.includes">Must select some files in the IDE or set javac.includes</fail>
- <j2seproject3:force-recompile/>
- <j2seproject3:javac excludes="" gensrcdir="${build.generated.sources.dir}" includes="${javac.includes}, module-info.java" sourcepath="${src.dir}"/>
- </target>
- <target name="-post-compile-single">
- <!-- Empty placeholder for easier customization. -->
- <!-- You can override this target in the ../build.xml file. -->
- </target>
- <target depends="init,deps-jar,-verify-automatic-build,-pre-pre-compile,-pre-compile-single,-do-compile-single,-post-compile-single" name="compile-single"/>
- <!--
- ====================
- JAR BUILDING SECTION
- ====================
- -->
- <target depends="init" name="-pre-pre-jar">
- <dirname file="${dist.jar}" property="dist.jar.dir"/>
- <mkdir dir="${dist.jar.dir}"/>
- </target>
- <target name="-pre-jar">
- <!-- Empty placeholder for easier customization. -->
- <!-- You can override this target in the ../build.xml file. -->
- </target>
- <target depends="init,compile" name="-check-module-main-class">
- <pathconvert property="main.class.file">
- <string value="${main.class}"/>
- <unpackagemapper from="*" to="*.class"/>
- </pathconvert>
- <condition property="do.module.main.class">
- <and>
- <isset property="main.class.available"/>
- <available file="${build.classes.dir}/module-info.class"/>
- <available file="${build.classes.dir}/${main.class.file}"/>
- <isset property="libs.CopyLibs.classpath"/>
- <available classname="org.netbeans.modules.java.j2seproject.moduletask.ModuleMainClass" classpath="${libs.CopyLibs.classpath}"/>
- </and>
- </condition>
- </target>
- <target depends="-check-module-main-class" if="do.module.main.class" name="-set-module-main-class">
- <taskdef classname="org.netbeans.modules.java.j2seproject.moduletask.ModuleMainClass" classpath="${libs.CopyLibs.classpath}" name="modulemainclass"/>
- <modulemainclass failonerror="false" mainclass="${main.class}" moduleinfo="${build.classes.dir}/module-info.class"/>
- </target>
- <target depends="init" if="do.archive" name="-do-jar-create-manifest" unless="manifest.available">
- <tempfile deleteonexit="true" destdir="${build.dir}" property="tmp.manifest.file"/>
- <touch file="${tmp.manifest.file}" verbose="false"/>
- </target>
- <target depends="init" if="do.archive+manifest.available" name="-do-jar-copy-manifest">
- <tempfile deleteonexit="true" destdir="${build.dir}" property="tmp.manifest.file"/>
- <copy encoding="${manifest.encoding}" file="${manifest.file}" outputencoding="UTF-8" tofile="${tmp.manifest.file}"/>
- </target>
- <target depends="init,-do-jar-create-manifest,-do-jar-copy-manifest" if="do.archive+main.class.available" name="-do-jar-set-mainclass">
- <manifest encoding="UTF-8" file="${tmp.manifest.file}" mode="update">
- <attribute name="Main-Class" value="${main.class}"/>
- </manifest>
- </target>
- <target depends="init,-do-jar-create-manifest,-do-jar-copy-manifest" if="do.archive+profile.available" name="-do-jar-set-profile">
- <manifest encoding="UTF-8" file="${tmp.manifest.file}" mode="update">
- <attribute name="Profile" value="${javac.profile}"/>
- </manifest>
- </target>
- <target depends="init,-do-jar-create-manifest,-do-jar-copy-manifest" if="do.archive+splashscreen.available" name="-do-jar-set-splashscreen">
- <basename file="${application.splash}" property="splashscreen.basename"/>
- <mkdir dir="${build.classes.dir}/META-INF"/>
- <copy failonerror="false" file="${application.splash}" todir="${build.classes.dir}/META-INF"/>
- <manifest encoding="UTF-8" file="${tmp.manifest.file}" mode="update">
- <attribute name="SplashScreen-Image" value="META-INF/${splashscreen.basename}"/>
- </manifest>
- </target>
- <target depends="init,compile" name="-check-do-mkdist">
- <condition property="do.mkdist">
- <and>
- <isset property="do.archive"/>
- <isset property="libs.CopyLibs.classpath"/>
- <not>
- <istrue value="${mkdist.disabled}"/>
- </not>
- <not>
- <available file="${build.classes.dir}/module-info.class"/>
- </not>
- </and>
- </condition>
- </target>
- <target depends="init,-init-macrodef-copylibs,compile,-pre-pre-jar,-pre-jar,-do-jar-create-manifest,-do-jar-copy-manifest,-do-jar-set-mainclass,-do-jar-set-profile,-do-jar-set-splashscreen,-check-do-mkdist" if="do.mkdist" name="-do-jar-copylibs">
- <j2seproject3:copylibs manifest="${tmp.manifest.file}"/>
- <echo level="info">To run this application from the command line without Ant, try:</echo>
- <property location="${dist.jar}" name="dist.jar.resolved"/>
- <echo level="info">${platform.java} -jar "${dist.jar.resolved}"</echo>
- </target>
- <target depends="init,compile,-pre-pre-jar,-pre-jar,-do-jar-create-manifest,-do-jar-copy-manifest,-do-jar-set-mainclass,-do-jar-set-profile,-do-jar-set-splashscreen,-check-do-mkdist" if="do.archive" name="-do-jar-jar" unless="do.mkdist">
- <j2seproject1:jar manifest="${tmp.manifest.file}"/>
- <property location="${build.classes.dir}" name="build.classes.dir.resolved"/>
- <property location="${dist.jar}" name="dist.jar.resolved"/>
- <condition else="${dist.jar.resolved}" property="jar.usage.message.class.path.replacement" value="">
- <isset property="named.module.internal"/>
- </condition>
- <pathconvert property="run.classpath.with.dist.jar">
- <path path="${run.classpath}"/>
- <map from="${build.classes.dir.resolved}" to="${jar.usage.message.class.path.replacement}"/>
- </pathconvert>
- <pathconvert property="run.modulepath.with.dist.jar">
- <path location="${dist.jar.resolved}"/>
- <path path="${run.modulepath}"/>
- <map from="${build.classes.dir.resolved}" to="${dist.jar.resolved}"/>
- </pathconvert>
- <condition else="${run.modulepath}" property="jar.usage.message.run.modulepath.with.dist.jar" value="${run.modulepath.with.dist.jar}">
- <isset property="named.module.internal"/>
- </condition>
- <condition else="" property="jar.usage.message.module.path" value=" -p ${jar.usage.message.run.modulepath.with.dist.jar}">
- <and>
- <isset property="modules.supported.internal"/>
- <length length="0" string="${jar.usage.message.run.modulepath.with.dist.jar}" when="greater"/>
- </and>
- </condition>
- <condition else="" property="jar.usage.message.class.path" value=" -cp ${run.classpath.with.dist.jar}">
- <length length="0" string="${run.classpath.with.dist.jar}" when="greater"/>
- </condition>
- <condition else="/${main.class}" property="jar.usage.message.main.class.class.selector" value="">
- <isset property="do.module.main.class"/>
- </condition>
- <condition else=" ${main.class}" property="jar.usage.message.main.class" value=" -m ${module.name}${jar.usage.message.main.class.class.selector}">
- <isset property="named.module.internal"/>
- </condition>
- <condition else="" property="jar.usage.message" value="To run this application from the command line without Ant, try:${line.separator}${platform.java}${jar.usage.message.module.path}${jar.usage.message.class.path}${jar.usage.message.main.class}">
- <isset property="main.class.available"/>
- </condition>
- <condition else="debug" property="jar.usage.level" value="info">
- <isset property="main.class.available"/>
- </condition>
- <echo level="${jar.usage.level}" message="${jar.usage.message}"/>
- </target>
- <target depends="-do-jar-copylibs" if="do.archive" name="-do-jar-delete-manifest">
- <delete>
- <fileset file="${tmp.manifest.file}"/>
- </delete>
- </target>
- <target depends="init,compile,-pre-pre-jar,-pre-jar,-do-jar-create-manifest,-do-jar-copy-manifest,-do-jar-set-mainclass,-do-jar-set-profile,-do-jar-set-splashscreen,-do-jar-jar,-do-jar-delete-manifest" name="-do-jar-without-libraries"/>
- <target depends="init,compile,-pre-pre-jar,-pre-jar,-do-jar-create-manifest,-do-jar-copy-manifest,-do-jar-set-mainclass,-do-jar-set-profile,-do-jar-set-splashscreen,-do-jar-copylibs,-do-jar-delete-manifest" name="-do-jar-with-libraries"/>
- <target name="-post-jar">
- <!-- Empty placeholder for easier customization. -->
- <!-- You can override this target in the ../build.xml file. -->
- </target>
- <target depends="init,compile,-pre-jar,-set-module-main-class,-do-jar-without-libraries,-do-jar-with-libraries,-post-jar" name="-do-jar"/>
- <target depends="init,compile,-pre-jar,-do-jar,-post-jar,deploy" description="Build JAR." name="jar"/>
- <!--
- =================
- DEPLOY SECTION
- =================
- -->
- <target name="-pre-deploy">
- <!-- Empty placeholder for easier customization. -->
- <!-- You can override this target in the ../build.xml file. -->
- </target>
- <target depends="init" name="-check-jlink">
- <condition property="do.jlink.internal">
- <and>
- <istrue value="${do.jlink}"/>
- <isset property="do.archive"/>
- <isset property="named.module.internal"/>
- </and>
- </condition>
- </target>
- <target depends="init,-do-jar,-post-jar,-pre-deploy,-check-jlink" if="do.jlink.internal" name="-do-deploy">
- <delete dir="${dist.jlink.dir}" failonerror="false" quiet="true"/>
- <property name="jlink.launcher.name" value="${application.title}"/>
- <condition else="${module.name}" property="jlink.add.modules" value="${module.name},${jlink.additionalmodules}">
- <and>
- <isset property="jlink.additionalmodules"/>
- <length length="0" string="${jlink.additionalmodules}" when="greater"/>
- </and>
- </condition>
- <condition property="jlink.do.strip.internal">
- <and>
- <isset property="jlink.strip"/>
- <istrue value="${jlink.strip}"/>
- </and>
- </condition>
- <condition property="jlink.do.additionalparam.internal">
- <and>
- <isset property="jlink.additionalparam"/>
- <length length="0" string="${jlink.additionalparam}" when="greater"/>
- </and>
- </condition>
- <condition property="jlink.do.launcher.internal">
- <and>
- <istrue value="${jlink.launcher}"/>
- <isset property="main.class.available"/>
- </and>
- </condition>
- <property name="platform.jlink" value="${platform.home}/bin/jlink"/>
- <property name="jlink.systemmodules.internal" value="${platform.home}/jmods"/>
- <exec executable="${platform.jlink}">
- <arg value="--module-path"/>
- <arg path="${jlink.systemmodules.internal}:${run.modulepath}:${dist.jar}"/>
- <arg value="--add-modules"/>
- <arg value="${jlink.add.modules}"/>
- <arg if:set="jlink.do.strip.internal" value="--strip-debug"/>
- <arg if:set="jlink.do.launcher.internal" value="--launcher"/>
- <arg if:set="jlink.do.launcher.internal" value="${jlink.launcher.name}=${module.name}/${main.class}"/>
- <arg if:set="jlink.do.additionalparam.internal" line="${jlink.additionalparam}"/>
- <arg value="--output"/>
- <arg value="${dist.jlink.output}"/>
- </exec>
- </target>
- <target name="-post-deploy">
- <!-- Empty placeholder for easier customization. -->
- <!-- You can override this target in the ../build.xml file. -->
- </target>
- <target depends="-do-jar,-post-jar,-pre-deploy,-do-deploy,-post-deploy" name="deploy"/>
- <!--
- =================
- EXECUTION SECTION
- =================
- -->
- <target depends="init,compile" description="Run a main class." name="run">
- <j2seproject1:java>
- <customize>
- <arg line="${application.args}"/>
- </customize>
- </j2seproject1:java>
- </target>
- <target name="-do-not-recompile">
- <property name="javac.includes.binary" value=""/>
- </target>
- <target depends="init,compile-single" name="run-single">
- <fail unless="run.class">Must select one file in the IDE or set run.class</fail>
- <j2seproject1:java classname="${run.class}"/>
- </target>
- <target depends="init,compile-test-single" name="run-test-with-main">
- <fail unless="run.class">Must select one file in the IDE or set run.class</fail>
- <j2seproject1:java classname="${run.class}" classpath="${run.test.classpath}"/>
- </target>
- <!--
- =================
- DEBUGGING SECTION
- =================
- -->
- <target depends="init" if="netbeans.home" name="-debug-start-debugger">
- <j2seproject1:nbjpdastart name="${debug.class}"/>
- </target>
- <target depends="init" if="netbeans.home" name="-debug-start-debugger-main-test">
- <j2seproject1:nbjpdastart classpath="${debug.test.classpath}" name="${debug.class}"/>
- </target>
- <target depends="init,compile" name="-debug-start-debuggee">
- <j2seproject3:debug>
- <customizeDebuggee>
- <arg line="${application.args}"/>
- </customizeDebuggee>
- </j2seproject3:debug>
- </target>
- <target depends="init,compile,-debug-start-debugger,-debug-start-debuggee" description="Debug project in IDE." if="netbeans.home" name="debug"/>
- <target depends="init" if="netbeans.home" name="-debug-start-debugger-stepinto">
- <j2seproject1:nbjpdastart stopclassname="${main.class}"/>
- </target>
- <target depends="init,compile,-debug-start-debugger-stepinto,-debug-start-debuggee" if="netbeans.home" name="debug-stepinto"/>
- <target depends="init,compile-single" if="netbeans.home" name="-debug-start-debuggee-single">
- <fail unless="debug.class">Must select one file in the IDE or set debug.class</fail>
- <j2seproject3:debug classname="${debug.class}"/>
- </target>
- <target depends="init,compile-single,-debug-start-debugger,-debug-start-debuggee-single" if="netbeans.home" name="debug-single"/>
- <target depends="init,compile-test-single" if="netbeans.home" name="-debug-start-debuggee-main-test">
- <fail unless="debug.class">Must select one file in the IDE or set debug.class</fail>
- <j2seproject3:debug classname="${debug.class}" classpath="${debug.test.classpath}"/>
- </target>
- <target depends="init,compile-test-single,-debug-start-debugger-main-test,-debug-start-debuggee-main-test" if="netbeans.home" name="debug-test-with-main"/>
- <target depends="init" name="-pre-debug-fix">
- <fail unless="fix.includes">Must set fix.includes</fail>
- <property name="javac.includes" value="${fix.includes}.java"/>
- </target>
- <target depends="init,-pre-debug-fix,compile-single" if="netbeans.home" name="-do-debug-fix">
- <j2seproject1:nbjpdareload/>
- </target>
- <target depends="init,-pre-debug-fix,-do-debug-fix" if="netbeans.home" name="debug-fix"/>
- <!--
- =================
- PROFILING SECTION
- =================
- -->
- <!--
- pre NB7.2 profiler integration
- -->
- <target depends="profile-init,compile" description="Profile a project in the IDE." if="profiler.info.jvmargs.agent" name="-profile-pre72">
- <fail unless="netbeans.home">This target only works when run from inside the NetBeans IDE.</fail>
- <nbprofiledirect>
- <classpath>
- <path path="${run.classpath}"/>
- </classpath>
- </nbprofiledirect>
- <profile/>
- </target>
- <target depends="profile-init,compile-single" description="Profile a selected class in the IDE." if="profiler.info.jvmargs.agent" name="-profile-single-pre72">
- <fail unless="profile.class">Must select one file in the IDE or set profile.class</fail>
- <fail unless="netbeans.home">This target only works when run from inside the NetBeans IDE.</fail>
- <nbprofiledirect>
- <classpath>
- <path path="${run.classpath}"/>
- </classpath>
- </nbprofiledirect>
- <profile classname="${profile.class}"/>
- </target>
- <target depends="profile-init,compile-single" if="profiler.info.jvmargs.agent" name="-profile-applet-pre72">
- <fail unless="netbeans.home">This target only works when run from inside the NetBeans IDE.</fail>
- <nbprofiledirect>
- <classpath>
- <path path="${run.classpath}"/>
- </classpath>
- </nbprofiledirect>
- <profile classname="sun.applet.AppletViewer">
- <customize>
- <arg value="${applet.url}"/>
- </customize>
- </profile>
- </target>
- <target depends="-init-macrodef-junit,profile-init,compile-test-single" if="profiler.info.jvmargs.agent" name="-profile-test-single-pre72">
- <fail unless="netbeans.home">This target only works when run from inside the NetBeans IDE.</fail>
- <nbprofiledirect>
- <classpath>
- <path path="${run.test.classpath}"/>
- </classpath>
- </nbprofiledirect>
- <j2seproject3:junit excludes="${excludes}" includes="${includes}" testincludes="${profile.class}" testmethods="">
- <customize>
- <jvmarg value="-agentlib:jdwp=transport=${debug-transport},address=${jpda.address}"/>
- <env key="${profiler.info.pathvar}" path="${profiler.info.agentpath}:${profiler.current.path}"/>
- <jvmarg value="${profiler.info.jvmargs.agent}"/>
- <jvmarg line="${profiler.info.jvmargs}"/>
- <classpath>
- <path path="${run.test.classpath}"/>
- </classpath>
- </customize>
- </j2seproject3:junit>
- </target>
- <!--
- end of pre NB72 profiling section
- -->
- <target if="netbeans.home" name="-profile-check">
- <condition property="profiler.configured">
- <or>
- <contains casesensitive="true" string="${run.jvmargs.ide}" substring="-agentpath:"/>
- <contains casesensitive="true" string="${run.jvmargs.ide}" substring="-javaagent:"/>
- </or>
- </condition>
- </target>
- <target depends="-profile-check,-profile-pre72" description="Profile a project in the IDE." if="profiler.configured" name="profile" unless="profiler.info.jvmargs.agent">
- <startprofiler/>
- <antcall target="run"/>
- </target>
- <target depends="-profile-check,-profile-single-pre72" description="Profile a selected class in the IDE." if="profiler.configured" name="profile-single" unless="profiler.info.jvmargs.agent">
- <fail unless="run.class">Must select one file in the IDE or set run.class</fail>
- <startprofiler/>
- <antcall target="run-single"/>
- </target>
- <target depends="-profile-test-single-pre72" description="Profile a selected test in the IDE." name="profile-test-single"/>
- <target depends="-profile-check" description="Profile a selected test in the IDE." if="profiler.configured" name="profile-test" unless="profiler.info.jvmargs">
- <fail unless="test.includes">Must select some files in the IDE or set test.includes</fail>
- <startprofiler/>
- <antcall target="test-single"/>
- </target>
- <target depends="-profile-check" description="Profile a selected class in the IDE." if="profiler.configured" name="profile-test-with-main">
- <fail unless="run.class">Must select one file in the IDE or set run.class</fail>
- <startprofiler/>
- <antcall target="run-test-with-main"/>
- </target>
- <target depends="-profile-check,-profile-applet-pre72" if="profiler.configured" name="profile-applet" unless="profiler.info.jvmargs.agent">
- <fail unless="applet.url">Must select one file in the IDE or set applet.url</fail>
- <startprofiler/>
- <antcall target="run-applet"/>
- </target>
- <!--
- ===============
- JAVADOC SECTION
- ===============
- -->
- <target depends="init" if="have.sources" name="-javadoc-build">
- <mkdir dir="${dist.javadoc.dir}"/>
- <condition else="" property="javadoc.endorsed.classpath.cmd.line.arg" value="-J${endorsed.classpath.cmd.line.arg}">
- <and>
- <isset property="endorsed.classpath.cmd.line.arg"/>
- <not>
- <equals arg1="${endorsed.classpath.cmd.line.arg}" arg2=""/>
- </not>
- </and>
- </condition>
- <exec executable="${platform.java}" failonerror="false" outputproperty="platform.version.output">
- <arg value="-version"/>
- </exec>
- <condition else="" property="bug5101868workaround" value="*.java">
- <matches multiline="true" pattern="1\.[56](\..*)?" string="${platform.version.output}"/>
- </condition>
- <condition else="" property="javadoc.html5.cmd.line.arg" value="-html5">
- <and>
- <isset property="javadoc.html5"/>
- <available file="${platform.home}${file.separator}lib${file.separator}jrt-fs.jar"/>
- </and>
- </condition>
- <javadoc additionalparam="-J-Dfile.encoding=${file.encoding} ${javadoc.additionalparam}" author="${javadoc.author}" charset="UTF-8" destdir="${dist.javadoc.dir}" docencoding="UTF-8" encoding="${javadoc.encoding.used}" executable="${platform.javadoc}" failonerror="true" noindex="${javadoc.noindex}" nonavbar="${javadoc.nonavbar}" notree="${javadoc.notree}" private="${javadoc.private}" source="${javac.source}" splitindex="${javadoc.splitindex}" use="${javadoc.use}" useexternalfile="true" version="${javadoc.version}" windowtitle="${javadoc.windowtitle}">
- <classpath>
- <path path="${javac.classpath}"/>
- </classpath>
- <fileset dir="${src.dir}" excludes="${bug5101868workaround},${excludes}" includes="${includes}">
- <filename name="**/*.java"/>
- </fileset>
- <fileset dir="${build.generated.sources.dir}" erroronmissingdir="false">
- <include name="**/*.java"/>
- <exclude name="*.java"/>
- </fileset>
- <arg line="${javadoc.endorsed.classpath.cmd.line.arg}"/>
- <arg line="${javadoc.html5.cmd.line.arg}"/>
- </javadoc>
- <copy todir="${dist.javadoc.dir}">
- <fileset dir="${src.dir}" excludes="${excludes}" includes="${includes}">
- <filename name="**/doc-files/**"/>
- </fileset>
- <fileset dir="${build.generated.sources.dir}" erroronmissingdir="false">
- <include name="**/doc-files/**"/>
- </fileset>
- </copy>
- </target>
- <target depends="init,-javadoc-build" if="netbeans.home" name="-javadoc-browse" unless="no.javadoc.preview">
- <nbbrowse file="${dist.javadoc.dir}/index.html"/>
- </target>
- <target depends="init,-javadoc-build,-javadoc-browse" description="Build Javadoc." name="javadoc"/>
- <!--
- =========================
- TEST COMPILATION SECTION
- =========================
- -->
- <target depends="init,compile" if="have.tests" name="-pre-pre-compile-test">
- <mkdir dir="${build.test.classes.dir}"/>
- </target>
- <target name="-pre-compile-test">
- <!-- Empty placeholder for easier customization. -->
- <!-- You can override this target in the ../build.xml file. -->
- </target>
- <target depends="-init-source-module-properties" if="named.module.internal" name="-init-test-javac-module-properties-with-module">
- <j2seproject3:modulename property="test.module.name" sourcepath="${test.src.dir}"/>
- <condition else="${empty.dir}" property="javac.test.sourcepath" value="${test.src.dir}">
- <and>
- <isset property="test.module.name"/>
- <length length="0" string="${test.module.name}" when="greater"/>
- </and>
- </condition>
- <condition else="--patch-module ${module.name}=${test.src.dir} --add-reads ${module.name}=ALL-UNNAMED" property="javac.test.compilerargs" value="--add-reads ${test.module.name}=ALL-UNNAMED">
- <and>
- <isset property="test.module.name"/>
- <length length="0" string="${test.module.name}" when="greater"/>
- </and>
- </condition>
- </target>
- <target depends="-init-source-module-properties" if="named.module.internal" name="-init-test-run-module-properties">
- <condition else="${module.name}" property="run.test.addexport.source.module.internal" value="${test.module.name}">
- <and>
- <isset property="test.module.name"/>
- <length length="0" string="${test.module.name}" when="greater"/>
- </and>
- </condition>
- <fileset dir="${build.test.classes.dir}" id="run.test.packages.internal" includes="**/*.class"/>
- <property location="${build.test.classes.dir}" name="build.test.classes.dir.abs.internal"/>
- <pathconvert pathsep=" " property="run.test.addexports.internal" refid="run.test.packages.internal">
- <chainedmapper>
- <regexpmapper from="^(.*)\Q${file.separator}\E.*\.class$$" to="\1"/>
- <filtermapper>
- <uniqfilter/>
- <replacestring from="${build.test.classes.dir.abs.internal}" to=""/>
- </filtermapper>
- <cutdirsmapper dirs="1"/>
- <packagemapper from="*" to="--add-exports ${run.test.addexport.source.module.internal}/*=ALL-UNNAMED"/>
- </chainedmapper>
- </pathconvert>
- <condition else="--patch-module ${module.name}=${build.test.classes.dir} --add-modules ${module.name} --add-reads ${module.name}=ALL-UNNAMED ${run.test.addexports.internal}" property="run.test.jvmargs" value="--add-modules ${test.module.name} --add-reads ${test.module.name}=ALL-UNNAMED ${run.test.addexports.internal}">
- <and>
- <isset property="test.module.name"/>
- <length length="0" string="${test.module.name}" when="greater"/>
- </and>
- </condition>
- </target>
- <target depends="-init-source-module-properties" name="-init-test-module-properties-without-module" unless="named.module.internal">
- <property name="javac.test.sourcepath" value="${empty.dir}"/>
- <property name="javac.test.compilerargs" value=""/>
- <property name="run.test.jvmargs" value=""/>
- </target>
- <target depends="-init-test-javac-module-properties-with-module,-init-test-module-properties-without-module" name="-init-test-module-properties"/>
- <target if="do.depend.true" name="-compile-test-depend">
- <j2seproject3:depend classpath="${javac.test.classpath}" destdir="${build.test.classes.dir}" srcdir="${test.src.dir}"/>
- </target>
- <target depends="init,deps-jar,compile,-init-test-module-properties,-pre-pre-compile-test,-pre-compile-test,-compile-test-depend" if="have.tests" name="-do-compile-test">
- <j2seproject3:javac apgeneratedsrcdir="${build.test.classes.dir}" classpath="${javac.test.classpath}" debug="true" destdir="${build.test.classes.dir}" modulepath="${javac.test.modulepath}" processorpath="${javac.test.processorpath}" sourcepath="${javac.test.sourcepath}" srcdir="${test.src.dir}">
- <customize>
- <compilerarg line="${javac.test.compilerargs}"/>
- </customize>
- </j2seproject3:javac>
- <copy todir="${build.test.classes.dir}">
- <fileset dir="${test.src.dir}" excludes="${build.classes.excludes},${excludes}" includes="${includes}"/>
- </copy>
- </target>
- <target name="-post-compile-test">
- <!-- Empty placeholder for easier customization. -->
- <!-- You can override this target in the ../build.xml file. -->
- </target>
- <target depends="init,compile,-pre-pre-compile-test,-pre-compile-test,-do-compile-test,-post-compile-test" name="compile-test"/>
- <target name="-pre-compile-test-single">
- <!-- Empty placeholder for easier customization. -->
- <!-- You can override this target in the ../build.xml file. -->
- </target>
- <target depends="init,deps-jar,compile,-init-test-module-properties,-pre-pre-compile-test,-pre-compile-test-single" if="have.tests" name="-do-compile-test-single">
- <fail unless="javac.includes">Must select some files in the IDE or set javac.includes</fail>
- <j2seproject3:force-recompile destdir="${build.test.classes.dir}"/>
- <j2seproject3:javac apgeneratedsrcdir="${build.test.classes.dir}" classpath="${javac.test.classpath}" debug="true" destdir="${build.test.classes.dir}" excludes="" includes="${javac.includes}, module-info.java" modulepath="${javac.test.modulepath}" processorpath="${javac.test.processorpath}" sourcepath="${test.src.dir}" srcdir="${test.src.dir}">
- <customize>
- <compilerarg line="${javac.test.compilerargs}"/>
- </customize>
- </j2seproject3:javac>
- <copy todir="${build.test.classes.dir}">
- <fileset dir="${test.src.dir}" excludes="${build.classes.excludes},${excludes}" includes="${includes}"/>
- </copy>
- </target>
- <target name="-post-compile-test-single">
- <!-- Empty placeholder for easier customization. -->
- <!-- You can override this target in the ../build.xml file. -->
- </target>
- <target depends="init,compile,-pre-pre-compile-test,-pre-compile-test-single,-do-compile-test-single,-post-compile-test-single" name="compile-test-single"/>
- <!--
- =======================
- TEST EXECUTION SECTION
- =======================
- -->
- <target depends="init" if="have.tests" name="-pre-test-run">
- <mkdir dir="${build.test.results.dir}"/>
- </target>
- <target depends="init,compile-test,-init-test-run-module-properties,-pre-test-run" if="have.tests" name="-do-test-run">
- <j2seproject3:test includes="${includes}" testincludes="**/*Test.java"/>
- </target>
- <target depends="init,compile-test,-pre-test-run,-do-test-run" if="have.tests" name="-post-test-run">
- <fail if="tests.failed" unless="ignore.failing.tests">Some tests failed; see details above.</fail>
- </target>
- <target depends="init" if="have.tests" name="test-report"/>
- <target depends="init" if="netbeans.home+have.tests" name="-test-browse"/>
- <target depends="init,compile-test,-pre-test-run,-do-test-run,test-report,-post-test-run,-test-browse" description="Run unit tests." name="test"/>
- <target depends="init" if="have.tests" name="-pre-test-run-single">
- <mkdir dir="${build.test.results.dir}"/>
- </target>
- <target depends="init,compile-test-single,-init-test-run-module-properties,-pre-test-run-single" if="have.tests" name="-do-test-run-single">
- <fail unless="test.includes">Must select some files in the IDE or set test.includes</fail>
- <j2seproject3:test excludes="" includes="${test.includes}" testincludes="${test.includes}"/>
- </target>
- <target depends="init,compile-test-single,-pre-test-run-single,-do-test-run-single" if="have.tests" name="-post-test-run-single">
- <fail if="tests.failed" unless="ignore.failing.tests">Some tests failed; see details above.</fail>
- </target>
- <target depends="init,compile-test-single,-init-test-run-module-properties,-pre-test-run-single,-do-test-run-single,-post-test-run-single" description="Run single unit test." name="test-single"/>
- <target depends="init,compile-test-single,-pre-test-run-single" if="have.tests" name="-do-test-run-single-method">
- <fail unless="test.class">Must select some files in the IDE or set test.class</fail>
- <fail unless="test.method">Must select some method in the IDE or set test.method</fail>
- <j2seproject3:test excludes="" includes="${javac.includes}" testincludes="${test.class}" testmethods="${test.method}"/>
- </target>
- <target depends="init,compile-test-single,-pre-test-run-single,-do-test-run-single-method" if="have.tests" name="-post-test-run-single-method">
- <fail if="tests.failed" unless="ignore.failing.tests">Some tests failed; see details above.</fail>
- </target>
- <target depends="init,compile-test-single,-init-test-run-module-properties,-pre-test-run-single,-do-test-run-single-method,-post-test-run-single-method" description="Run single unit test." name="test-single-method"/>
- <!--
- =======================
- TEST DEBUGGING SECTION
- =======================
- -->
- <target depends="init,compile-test-single,-pre-test-run-single" if="have.tests" name="-debug-start-debuggee-test">
- <fail unless="test.class">Must select one file in the IDE or set test.class</fail>
- <j2seproject3:test-debug excludes="" includes="${javac.includes}" testClass="${test.class}" testincludes="${javac.includes}"/>
- </target>
- <target depends="init,compile-test-single,-pre-test-run-single" if="have.tests" name="-debug-start-debuggee-test-method">
- <fail unless="test.class">Must select one file in the IDE or set test.class</fail>
- <fail unless="test.method">Must select some method in the IDE or set test.method</fail>
- <j2seproject3:test-debug excludes="" includes="${javac.includes}" testClass="${test.class}" testMethod="${test.method}" testincludes="${test.class}" testmethods="${test.method}"/>
- </target>
- <target depends="init,compile-test" if="netbeans.home+have.tests" name="-debug-start-debugger-test">
- <j2seproject1:nbjpdastart classpath="${debug.test.classpath}" name="${test.class}"/>
- </target>
- <target depends="init,compile-test-single,-init-test-run-module-properties,-debug-start-debugger-test,-debug-start-debuggee-test" name="debug-test"/>
- <target depends="init,compile-test-single,-init-test-run-module-properties,-debug-start-debugger-test,-debug-start-debuggee-test-method" name="debug-test-method"/>
- <target depends="debug-test-method" name="debug-single-method"/>
- <target depends="init,-pre-debug-fix,compile-test-single" if="netbeans.home" name="-do-debug-fix-test">
- <j2seproject1:nbjpdareload dir="${build.test.classes.dir}"/>
- </target>
- <target depends="init,-pre-debug-fix,-do-debug-fix-test" if="netbeans.home" name="debug-fix-test"/>
- <!--
- =========================
- APPLET EXECUTION SECTION
- =========================
- -->
- <target depends="init,compile-single" name="run-applet">
- <fail unless="applet.url">Must select one file in the IDE or set applet.url</fail>
- <j2seproject1:java classname="sun.applet.AppletViewer">
- <customize>
- <arg value="${applet.url}"/>
- </customize>
- </j2seproject1:java>
- </target>
- <!--
- =========================
- APPLET DEBUGGING SECTION
- =========================
- -->
- <target depends="init,compile-single" if="netbeans.home" name="-debug-start-debuggee-applet">
- <fail unless="applet.url">Must select one file in the IDE or set applet.url</fail>
- <j2seproject3:debug classname="sun.applet.AppletViewer">
- <customizeDebuggee>
- <arg value="${applet.url}"/>
- </customizeDebuggee>
- </j2seproject3:debug>
- </target>
- <target depends="init,compile-single,-debug-start-debugger,-debug-start-debuggee-applet" if="netbeans.home" name="debug-applet"/>
- <!--
- ===============
- CLEANUP SECTION
- ===============
- -->
- <target name="-deps-clean-init" unless="built-clean.properties">
- <property location="${build.dir}/built-clean.properties" name="built-clean.properties"/>
- <delete file="${built-clean.properties}" quiet="true"/>
- </target>
- <target if="already.built.clean.${basedir}" name="-warn-already-built-clean">
- <echo level="warn" message="Cycle detected: pantools was already built"/>
- </target>
- <target depends="init,-deps-clean-init" name="deps-clean" unless="no.deps">
- <mkdir dir="${build.dir}"/>
- <touch file="${built-clean.properties}" verbose="false"/>
- <property file="${built-clean.properties}" prefix="already.built.clean."/>
- <antcall target="-warn-already-built-clean"/>
- <propertyfile file="${built-clean.properties}">
- <entry key="${basedir}" value=""/>
- </propertyfile>
- </target>
- <target depends="init" name="-do-clean">
- <delete dir="${build.dir}"/>
- <delete dir="${dist.jlink.output}"/>
- <delete dir="${dist.dir}" followsymlinks="false" includeemptydirs="true"/>
- </target>
- <target name="-post-clean">
- <!-- Empty placeholder for easier customization. -->
- <!-- You can override this target in the ../build.xml file. -->
- </target>
- <target depends="init,deps-clean,-do-clean,-post-clean" description="Clean build products." name="clean"/>
- <target name="-check-call-dep">
- <property file="${call.built.properties}" prefix="already.built."/>
- <condition property="should.call.dep">
- <and>
- <not>
- <isset property="already.built.${call.subproject}"/>
- </not>
- <available file="${call.script}"/>
- </and>
- </condition>
- </target>
- <target depends="-check-call-dep" if="should.call.dep" name="-maybe-call-dep">
- <ant antfile="${call.script}" inheritall="false" target="${call.target}">
- <propertyset>
- <propertyref prefix="transfer."/>
- <mapper from="transfer.*" to="*" type="glob"/>
- </propertyset>
- </ant>
- </target>
-</project>
diff --git a/nbproject/genfiles.properties b/nbproject/genfiles.properties
deleted file mode 100755
index bdac54f21d5336de505026968d0aa31515421266..0000000000000000000000000000000000000000
--- a/nbproject/genfiles.properties
+++ /dev/null
@@ -1,8 +0,0 @@
-build.xml.data.CRC32=33e0c080
-build.xml.script.CRC32=4a642e80
-build.xml.stylesheet.CRC32=8064a381@1.80.1.48
-# This file is used by a NetBeans-based IDE to track changes in generated files such as build-impl.xml.
-# Do not edit this file. You may delete it but then the IDE will never regenerate such files for you.
-nbproject/build-impl.xml.data.CRC32=2e8bc38d
-nbproject/build-impl.xml.script.CRC32=a09837ba
-nbproject/build-impl.xml.stylesheet.CRC32=12e0a6c2@1.100.0.48
diff --git a/nbproject/private/private.properties b/nbproject/private/private.properties
deleted file mode 100755
index f08d241410ec958c0b460e7f11d69ecd9e00c4fc..0000000000000000000000000000000000000000
--- a/nbproject/private/private.properties
+++ /dev/null
@@ -1,11 +0,0 @@
-application.args=map -dp /dev/shm/sheik005/4tomato/ -1 /mnt/scratch/sheik005/shared/tomato_siavash/accessions/001/illumina/pairedend_500/120512_I238_FCC0U42ACXX_L2_SZAXPI008746-45_1.fq.gz.clean.dup.clean.gz -2 /mnt/scratch/sheik005/shared/tomato_siavash/accessions/001/illumina/pairedend_500/120512_I238_FCC0U42ACXX_L2_SZAXPI008746-45_2.fq.gz.clean.dup.clean.gz -tn 16 -bf -gn numbers.txt
-compile.on.save=true
-do.depend=false
-do.jar=true
-do.jlink=false
-file.reference.neo4j-cypher-3.5.1.jar=/home/sheik005/neo4j-community-3.5.1/lib/neo4j-cypher-3.5.1.jar
-javac.debug=true
-javadoc.preview=true
-jlink.strip=false
-user.properties.file=/home/jonkh004/.netbeans/12.5/build.properties
-work.dir=/mnt/scratch/sheik005/read_mapping/tomato
diff --git a/nbproject/private/private.xml b/nbproject/private/private.xml
deleted file mode 100755
index 700418731b56aa13278cdb2013ee3dc9f6ac3338..0000000000000000000000000000000000000000
--- a/nbproject/private/private.xml
+++ /dev/null
@@ -1,21 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project-private xmlns="http://www.netbeans.org/ns/project-private/1">
- <editor-bookmarks xmlns="http://www.netbeans.org/ns/editor-bookmarks/2" lastBookmarkId="1">
- <file>
- <url>src/pangenome/MLSA.java</url>
- <bookmark id="1">
- <name/>
- <line>0</line>
- <key/>
- </bookmark>
- </file>
- </editor-bookmarks>
- <open-files xmlns="http://www.netbeans.org/ns/projectui-open-files/2">
- <group>
- <file>file:/local/jonkh004/git_branch/pantools/src/pangenome/Classification.java</file>
- <file>file:/local/jonkh004/git_branch/pantools/src/pangenome/Phylogeny.java</file>
- <file>file:/local/jonkh004/git_branch/pantools/src/pangenome/AnnotationLayer.java</file>
- <file>file:/local/jonkh004/git_branch/pantools/src/pantools/Pantools.java</file>
- </group>
- </open-files>
-</project-private>
diff --git a/nbproject/private/profiler/configurations.xml b/nbproject/private/profiler/configurations.xml
deleted file mode 100755
index 895fb7fae832a2bb522146cd842d4c09f571b948..0000000000000000000000000000000000000000
--- a/nbproject/private/profiler/configurations.xml
+++ /dev/null
@@ -1,116 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<!DOCTYPE properties SYSTEM "http://java.sun.com/dtd/properties.dtd">
-<properties>
-<entry key="2_profiler.settings.code.region.cpu.res.buf.size">1000</entry>
-<entry key="2_profiler.settings.sort.results.by.thread.cpu.time">false</entry>
-<entry key="0_profiler.settings.instrumentation.filter.selectedprofiler.filter.type">profiler.simple.filter</entry>
-<entry key="0_profiler.settings.instrument.empty.methods">false</entry>
-<entry key="0_profiler.settings.instrumentation.filter.selectedprofiler.simple.filter.name"/>
-<entry key="1_profiler.settings.profiling.type">8</entry>
-<entry key="0_profiler.settings.cpu.exclude.wait.time">true</entry>
-<entry key="0_profiler.settings.override.working.dir"/>
-<entry key="2_profiler.settings.cpu.sampling.frequency">10</entry>
-<entry key="0_profiler.settings.lockcontention.monitoring.enabled">false</entry>
-<entry key="1_profiler.settings.thread.cpu.timer.on">false</entry>
-<entry key="1_profiler.settings.instrumentation.root.methods.size">0</entry>
-<entry key="2_profiler.settings.override">false</entry>
-<entry key="1_profiler.settings.threads.sampling.enabled">true</entry>
-<entry key="profiler.settings.lastselected">1</entry>
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diff --git a/nbproject/private/profiler/settings.xml b/nbproject/private/profiler/settings.xml
deleted file mode 100755
index 1f8c352799381fa9c51f58bc5a4af3b76e06576b..0000000000000000000000000000000000000000
--- a/nbproject/private/profiler/settings.xml
+++ /dev/null
@@ -1,7 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<!DOCTYPE properties SYSTEM "http://java.sun.com/dtd/properties.dtd">
-<properties>
-<comment/>
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diff --git a/nbproject/private/profiler/snapshot-1476446607867.nps b/nbproject/private/profiler/snapshot-1476446607867.nps
deleted file mode 100755
index 266cc8f0136cf49eab441457e4c1268916616f2b..0000000000000000000000000000000000000000
Binary files a/nbproject/private/profiler/snapshot-1476446607867.nps and /dev/null differ
diff --git a/nbproject/private/profiler/snapshot-1476447547788.nps b/nbproject/private/profiler/snapshot-1476447547788.nps
deleted file mode 100755
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Binary files a/nbproject/private/profiler/snapshot-1476447547788.nps and /dev/null differ
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Binary files a/nbproject/private/profiler/snapshot-1476447977561.nps and /dev/null differ
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Binary files a/nbproject/private/profiler/snapshot-1476449552740.nps and /dev/null differ
diff --git a/nbproject/private/profiler/snapshot-1483444764796.nps b/nbproject/private/profiler/snapshot-1483444764796.nps
deleted file mode 100755
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Binary files a/nbproject/private/profiler/snapshot-1483444764796.nps and /dev/null differ
diff --git a/nbproject/private/profiler/snapshot-1524743170501.nps b/nbproject/private/profiler/snapshot-1524743170501.nps
deleted file mode 100644
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Binary files a/nbproject/private/profiler/snapshot-1524743170501.nps and /dev/null differ
diff --git a/nbproject/private/profiler/snapshot-1538072708552.nps b/nbproject/private/profiler/snapshot-1538072708552.nps
deleted file mode 100644
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Binary files a/nbproject/private/profiler/snapshot-1538072708552.nps and /dev/null differ
diff --git a/nbproject/project.properties b/nbproject/project.properties
deleted file mode 100755
index 10920c0216ec0d9241dbdcf19bc2390501d73fce..0000000000000000000000000000000000000000
--- a/nbproject/project.properties
+++ /dev/null
@@ -1,325 +0,0 @@
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-file.reference.neo4j-import-tool-3.5.3.jar=addons/java_libraries/neo4j-import-tool-3.5.3.jar
-file.reference.neo4j-index-3.5.3.jar=addons/java_libraries/neo4j-index-3.5.3.jar
-file.reference.neo4j-io-3.5.3.jar=addons/java_libraries/neo4j-io-3.5.3.jar
-file.reference.neo4j-jmx-3.5.3.jar=addons/java_libraries/neo4j-jmx-3.5.3.jar
-file.reference.neo4j-kernel-3.5.3.jar=addons/java_libraries/neo4j-kernel-3.5.3.jar
-file.reference.neo4j-kernel-api-3.5.3.jar=addons/java_libraries/neo4j-kernel-api-3.5.3.jar
-file.reference.neo4j-legacy-3.5.3.jar=addons/java_libraries/neo4j-legacy-3.5.3.jar
-file.reference.neo4j-logging-3.5.3.jar=addons/java_libraries/neo4j-logging-3.5.3.jar
-file.reference.neo4j-lucene-index-3.5.3.jar=addons/java_libraries/neo4j-lucene-index-3.5.3.jar
-file.reference.neo4j-lucene-upgrade-3.5.3.jar=addons/java_libraries/neo4j-lucene-upgrade-3.5.3.jar
-file.reference.neo4j-parser-3.5-3.5.3.jar=addons/java_libraries/neo4j-parser-3.5-3.5.3.jar
-file.reference.neo4j-procedure-api-3.5.3.jar=addons/java_libraries/neo4j-procedure-api-3.5.3.jar
-file.reference.neo4j-resource-3.5.3.jar=addons/java_libraries/neo4j-resource-3.5.3.jar
-file.reference.neo4j-rewriting-3.5-3.5.3.jar=addons/java_libraries/neo4j-rewriting-3.5-3.5.3.jar
-file.reference.neo4j-security-3.5.3.jar=addons/java_libraries/neo4j-security-3.5.3.jar
-file.reference.neo4j-server-3.5.3.jar=addons/java_libraries/neo4j-server-3.5.3.jar
-file.reference.neo4j-spatial-index-3.5.3.jar=addons/java_libraries/neo4j-spatial-index-3.5.3.jar
-file.reference.neo4j-ssl-3.5.3.jar=addons/java_libraries/neo4j-ssl-3.5.3.jar
-file.reference.neo4j-udc-3.5.3.jar=addons/java_libraries/neo4j-udc-3.5.3.jar
-file.reference.neo4j-unsafe-3.5.3.jar=addons/java_libraries/neo4j-unsafe-3.5.3.jar
-file.reference.neo4j-util-3.5-3.5.3.jar=addons/java_libraries/neo4j-util-3.5-3.5.3.jar
-file.reference.neo4j-values-3.5.3.jar=addons/java_libraries/neo4j-values-3.5.3.jar
-file.reference.netty-all-4.1.32.Final.jar=addons/java_libraries/netty-all-4.1.32.Final.jar
-file.reference.opencsv-2.3.jar=addons/java_libraries/opencsv-2.3.jar
-file.reference.openCypher-frontend-1-3.4.12.jar=addons/java_libraries/openCypher-frontend-1-3.4.12.jar
-file.reference.parboiled-core-1.1.7.jar=addons/java_libraries/parboiled-core-1.1.7.jar
-file.reference.parboiled-scala_2.11-1.1.7.jar=addons/java_libraries/parboiled-scala_2.11-1.1.7.jar
-file.reference.scala-library-2.11.12.jar=addons/java_libraries/scala-library-2.11.12.jar
-file.reference.scala-reflect-2.11.12.jar=addons/java_libraries/scala-reflect-2.11.12.jar
-file.reference.server-api-3.5.3.jar=addons/java_libraries/server-api-3.5.3.jar
-file.reference.stax-ex-1.7.8.jar=addons/java_libraries/stax-ex-1.7.8.jar
-file.reference.txw2-2.3.0.1.jar=addons/java_libraries/txw2-2.3.0.1.jar
-file.reference.WMI4Java-1.6.1.jar=addons/java_libraries/WMI4Java-1.6.1.jar
-javac.modulepath=
-javac.processormodulepath=
-javac.test.modulepath=\
- ${javac.modulepath}
-javadoc.html5=false
-javadoc.splitindex=true
-build.classes.excludes=**/*.java,**/*.form
-javadoc.author=false
-build.sysclasspath=ignore
-javac.target=1.8
-build.generated.dir=${build.dir}/generated
-jlink.launcher=false
-jlink.launcher.name=pantools
-run.classpath=\
- ${javac.classpath}:\
- ${build.classes.dir}
-debug.test.classpath=${run.test.classpath}
-build.dir=build
-javac.deprecation=false
-run.jvmargs=-server
-run.modulepath=\
- ${javac.modulepath}
-run.test.modulepath=\
- ${javac.test.modulepath}
-test.src.dir=test
-junit.selected.version=4
-includes=**
-application.vendor=sheik005
-mkdist.disabled=false
-jar.compress=false
-javac.external.vm=false
-annotation.processing.processors.list=
-javadoc.version=false
-build.classes.dir=${build.dir}/classes
-dist.dir=dist
-manifest.file=manifest.mf
-javac.source=1.8
-javac.test.processorpath=${javac.test.classpath}
-dist.archive.excludes=
-run.test.classpath=\
- ${javac.test.classpath}:\
- ${build.test.classes.dir}
-build.generated.sources.dir=${build.dir}/generated-sources
-javadoc.notree=false
-dist.jar=${dist.dir}/pantools.jar
-platform.active=JDK_1.8
-annotation.processing.enabled=true
-main.class=pantools.Pantools
-dist.javadoc.dir=${dist.dir}/javadoc
-javadoc.additionalparam=
-javac.classpath=\
- ${file.reference.htsjdk-2.16.0-12-g16704e6-SNAPSHOT-all.jar}:\
- ${file.reference.htsjdk-2.16.0-12-g16704e6-SNAPSHOT-javadoc.jar}:\
- ${file.reference.junit-4.11.jar-1}:\
- ${file.reference.WMI4Java-1.6.1.jar}:\
- ${file.reference.activation-1.1.1.jar}:\
- ${file.reference.bcpkix-jdk15on-1.60.jar}:\
- ${file.reference.bcprov-jdk15on-1.60.jar}:\
- ${file.reference.caffeine-2.6.2.jar}:\
- ${file.reference.colt.jar}:\
- ${file.reference.commons-compress-1.18.jar}:\
- ${file.reference.commons-configuration-1.10.jar}:\
- ${file.reference.commons-io-2.6.jar}:\
- ${file.reference.commons-lang-2.6.jar}:\
- ${file.reference.commons-lang3-3.8.jar}:\
- ${file.reference.commons-logging-1.1.1.jar}:\
- ${file.reference.commons-text-1.4.jar}:\
- ${file.reference.concurrent.jar}:\
- ${file.reference.concurrentlinkedhashmap-lru-1.4.2.jar}:\
- ${file.reference.eclipse-collections-9.2.0.jar}:\
- ${file.reference.eclipse-collections-api-9.2.0.jar}:\
- ${file.reference.htsjdk-2.16.0-12-g16704e6-SNAPSHOT-all.jar-1}:\
- ${file.reference.htsjdk-2.16.0-12-g16704e6-SNAPSHOT-javadoc.jar-1}:\
- ${file.reference.istack-commons-runtime-3.0.5.jar}:\
- ${file.reference.jPowerShell-1.9.jar}:\
- ${file.reference.jProcesses-1.6.4.jar}:\
- ${file.reference.jackson-core-asl-1.9.13.jar}:\
- ${file.reference.jackson-jaxrs-1.9.13.jar}:\
- ${file.reference.jackson-mapper-asl-1.9.13.jar}:\
- ${file.reference.javax.servlet-api-3.1.0.jar}:\
- ${file.reference.jaxb-api-2.3.0.jar}:\
- ${file.reference.jaxb-core-2.3.0.1.jar}:\
- ${file.reference.jaxb-runtime-2.3.0.1.jar}:\
- ${file.reference.jersey-core-1.19.3.jar}:\
- ${file.reference.jersey-server-1.19.3.jar}:\
- ${file.reference.jersey-servlet-1.19.3.jar}:\
- ${file.reference.jetty-http-9.4.11.v20180605.jar}:\
- ${file.reference.jetty-io-9.4.11.v20180605.jar}:\
- ${file.reference.jetty-security-9.4.11.v20180605.jar}:\
- ${file.reference.jetty-server-9.4.11.v20180605.jar}:\
- ${file.reference.jetty-servlet-9.4.11.v20180605.jar}:\
- ${file.reference.jetty-util-9.4.11.v20180605.jar}:\
- ${file.reference.jetty-webapp-9.4.11.v20180605.jar}:\
- ${file.reference.jetty-xml-9.4.11.v20180605.jar}:\
- ${file.reference.jsr311-api-1.1.2.r612.jar}:\
- ${file.reference.junit-4.11.jar-2}:\
- ${file.reference.lucene-analyzers-common-5.5.5.jar}:\
- ${file.reference.lucene-codecs-5.5.5.jar}:\
- ${file.reference.lucene-core-5.5.5.jar}:\
- ${file.reference.lucene-queryparser-5.5.5.jar}:\
- ${file.reference.neo4j-3.5.3.jar}:\
- ${file.reference.neo4j-ast-3.5-3.5.3.jar}:\
- ${file.reference.neo4j-bolt-3.5.3.jar}:\
- ${file.reference.neo4j-browser-3.2.16.jar}:\
- ${file.reference.neo4j-codegen-3.5.3.jar}:\
- ${file.reference.neo4j-collections-3.5.3.jar}:\
- ${file.reference.neo4j-command-line-3.5.3.jar}:\
- ${file.reference.neo4j-common-3.5.3.jar}:\
- ${file.reference.neo4j-concurrent-3.5.3.jar}:\
- ${file.reference.neo4j-configuration-3.5.3.jar}:\
- ${file.reference.neo4j-consistency-check-3.5.3.jar}:\
- ${file.reference.neo4j-csv-3.5.3.jar}:\
- ${file.reference.neo4j-cypher-3.5.3.jar}:\
- ${file.reference.neo4j-cypher-compiler-2.3-2.3.12.jar}:\
- ${file.reference.neo4j-cypher-compiler-3.1-3.1.9.jar}:\
- ${file.reference.neo4j-cypher-expression-3.4-3.4.12.jar}:\
- ${file.reference.neo4j-cypher-frontend-2.3-2.3.12.jar}:\
- ${file.reference.neo4j-cypher-frontend-3.1-3.1.9.jar}:\
- ${file.reference.neo4j-cypher-interpreted-runtime-3.5.3.jar}:\
- ${file.reference.neo4j-cypher-ir-3.4-3.4.12.jar}:\
- ${file.reference.neo4j-cypher-ir-3.5-3.5.3.jar}:\
- ${file.reference.neo4j-cypher-logical-plans-3.4-3.4.12.jar}:\
- ${file.reference.neo4j-cypher-logical-plans-3.5-3.5.3.jar}:\
- ${file.reference.neo4j-cypher-planner-3.4-3.4.12.jar}:\
- ${file.reference.neo4j-cypher-planner-3.5-3.5.3.jar}:\
- ${file.reference.neo4j-cypher-planner-spi-3.4-3.4.12.jar}:\
- ${file.reference.neo4j-cypher-planner-spi-3.5-3.5.3.jar}:\
- ${file.reference.neo4j-cypher-runtime-util-3.5.3.jar}:\
- ${file.reference.neo4j-cypher-util-3.4-3.4.12.jar}:\
- ${file.reference.neo4j-data-collector-3.5.3.jar}:\
- ${file.reference.neo4j-dbms-3.5.3.jar}:\
- ${file.reference.neo4j-diagnostics-3.5.3.jar}:\
- ${file.reference.neo4j-expressions-3.5-3.5.3.jar}:\
- ${file.reference.neo4j-front-end-3.5-3.5.3.jar}:\
- ${file.reference.neo4j-fulltext-index-3.5.3.jar}:\
- ${file.reference.neo4j-graph-algo-3.5.3.jar}:\
- ${file.reference.neo4j-graph-matching-3.1.9.jar}:\
- ${file.reference.neo4j-graphdb-api-3.5.3.jar}:\
- ${file.reference.neo4j-import-tool-3.5.3.jar}:\
- ${file.reference.neo4j-index-3.5.3.jar}:\
- ${file.reference.neo4j-io-3.5.3.jar}:\
- ${file.reference.neo4j-jmx-3.5.3.jar}:\
- ${file.reference.neo4j-kernel-3.5.3.jar}:\
- ${file.reference.neo4j-kernel-api-3.5.3.jar}:\
- ${file.reference.neo4j-legacy-3.5.3.jar}:\
- ${file.reference.neo4j-logging-3.5.3.jar}:\
- ${file.reference.neo4j-lucene-index-3.5.3.jar}:\
- ${file.reference.neo4j-lucene-upgrade-3.5.3.jar}:\
- ${file.reference.neo4j-parser-3.5-3.5.3.jar}:\
- ${file.reference.neo4j-procedure-api-3.5.3.jar}:\
- ${file.reference.neo4j-resource-3.5.3.jar}:\
- ${file.reference.neo4j-rewriting-3.5-3.5.3.jar}:\
- ${file.reference.neo4j-security-3.5.3.jar}:\
- ${file.reference.neo4j-server-3.5.3.jar}:\
- ${file.reference.neo4j-spatial-index-3.5.3.jar}:\
- ${file.reference.neo4j-ssl-3.5.3.jar}:\
- ${file.reference.neo4j-udc-3.5.3.jar}:\
- ${file.reference.neo4j-unsafe-3.5.3.jar}:\
- ${file.reference.neo4j-util-3.5-3.5.3.jar}:\
- ${file.reference.neo4j-values-3.5.3.jar}:\
- ${file.reference.netty-all-4.1.32.Final.jar}:\
- ${file.reference.openCypher-frontend-1-3.4.12.jar}:\
- ${file.reference.opencsv-2.3.jar}:\
- ${file.reference.parboiled-core-1.1.7.jar}:\
- ${file.reference.parboiled-scala_2.11-1.1.7.jar}:\
- ${file.reference.scala-library-2.11.12.jar}:\
- ${file.reference.scala-reflect-2.11.12.jar}:\
- ${file.reference.server-api-3.5.3.jar}:\
- ${file.reference.stax-ex-1.7.8.jar}:\
- ${file.reference.txw2-2.3.0.1.jar}:\
- ${file.reference.biojava-alignment-4.2.0.jar}:\
- ${file.reference.biojava-core-4.2.0.jar}
-javadoc.noindex=false
-annotation.processing.enabled.in.editor=false
-javadoc.private=false
-javadoc.encoding=${source.encoding}
-build.test.classes.dir=${build.dir}/test/classes
-javac.compilerargs=
-source.encoding=UTF-8
-meta.inf.dir=${src.dir}/META-INF
-annotation.processing.run.all.processors=true
-excludes=
-application.title=pantools
-javac.processorpath=\
- ${javac.classpath}
-build.test.results.dir=${build.dir}/test/results
-javadoc.use=true
-endorsed.classpath=
-javadoc.nonavbar=false
-javadoc.windowtitle=
-javac.test.classpath=\
- ${javac.classpath}:\
- ${build.classes.dir}:\
- ${libs.junit_4.classpath}:\
- ${libs.hamcrest.classpath}
-src.dir=src
-annotation.processing.source.output=${build.generated.sources.dir}/ap-source-output
-debug.classpath=${run.classpath}
diff --git a/nbproject/project.xml b/nbproject/project.xml
deleted file mode 100755
index 8fff2d77c672e7ba18cdc0c3166b2a5e7185d21d..0000000000000000000000000000000000000000
--- a/nbproject/project.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project xmlns="http://www.netbeans.org/ns/project/1">
- <type>org.netbeans.modules.java.j2seproject</type>
- <configuration>
- <data xmlns="http://www.netbeans.org/ns/j2se-project/3">
- <name>pantools</name>
- <explicit-platform explicit-source-supported="true"/>
- <source-roots>
- <root id="src.dir"/>
- </source-roots>
- <test-roots>
- <root id="test.src.dir"/>
- </test-roots>
- </data>
- </configuration>
-</project>
diff --git a/pom.xml b/pom.xml
new file mode 100644
index 0000000000000000000000000000000000000000..8bf3fb393021bb4f67ddaed04ab587302a3d367f
--- /dev/null
+++ b/pom.xml
@@ -0,0 +1,176 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+
+ <groupId>nl.wur.bif</groupId>
+ <artifactId>pantools</artifactId>
+ <version>3.4.0</version>
+
+ <properties>
+ <maven.compiler.source>8</maven.compiler.source>
+ <maven.compiler.target>8</maven.compiler.target>
+ <app.main.class>nl.wur.bif.pantools.pantools.Pantools</app.main.class>
+ <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+ </properties>
+
+ <dependencies>
+ <dependency>
+ <groupId>org.neo4j</groupId>
+ <artifactId>neo4j</artifactId>
+ <version>3.5.30</version>
+ </dependency>
+ <dependency>
+ <groupId>commons-io</groupId>
+ <artifactId>commons-io</artifactId>
+ <version>2.6</version>
+ </dependency>
+ <dependency>
+ <groupId>commons-lang</groupId>
+ <artifactId>commons-lang</artifactId>
+ <version>2.6</version>
+ </dependency>
+ <dependency>
+ <groupId>com.github.samtools</groupId>
+ <artifactId>htsjdk</artifactId>
+ <version>2.16.0</version>
+ </dependency>
+ <dependency>
+ <groupId>colt</groupId>
+ <artifactId>colt</artifactId>
+ <version>1.2.0</version>
+ </dependency>
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ <version>4.13.2</version>
+ <scope>test</scope>
+ </dependency>
+ <!-- https://mvnrepository.com/artifact/org.json/json -->
+ <dependency>
+ <groupId>org.json</groupId>
+ <artifactId>json</artifactId>
+ <version>20211205</version>
+ </dependency>
+
+ </dependencies>
+
+ <build>
+ <plugins>
+ <!-- Surefire plugin to run JUnit test in the test phase -->
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-surefire-plugin</artifactId>
+ <version>3.0.0-M5</version>
+ </plugin>
+ <!-- Shade plugin for creating a fat jar in the package phase -->
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-shade-plugin</artifactId>
+ <version>3.2.4</version>
+ <configuration>
+ <transformers>
+ <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
+ <!-- TODO: add version information, JDK source/target version -->
+ <manifestEntries>
+ <Main-Class>${app.main.class}</Main-Class>
+ </manifestEntries>
+ </transformer>
+ <!-- This transformer will make sure the shade plugin will not break org.apache.hadoop.fs.Filesystem -->
+ <!-- See: https://stackoverflow.com/questions/17265002/hadoop-no-filesystem-for-scheme-file/27532248#27532248 -->
+ <transformer implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer"/>
+ </transformers>
+ <filters>
+ <filter>
+ <artifact>*:*</artifact>
+ <excludes>
+ <exclude>module-info.class</exclude>
+ <exclude>META-INF/*.SF</exclude>
+ <exclude>META-INF/*.DSA</exclude>
+ <exclude>META-INF/*.RSA</exclude>
+ </excludes>
+ </filter>
+ </filters>
+ </configuration>
+ <executions>
+ <execution>
+ <phase>package</phase>
+ <goals>
+ <goal>shade</goal>
+ </goals>
+ </execution>
+ </executions>
+ </plugin>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-dependency-plugin</artifactId>
+ <version>3.2.0</version>
+ <executions>
+ <execution>
+ <id>copy-dependencies</id>
+ <phase>package</phase>
+ <goals>
+ <goal>copy-dependencies</goal>
+ </goals>
+ <configuration>
+ <outputDirectory>${project.build.directory}/alternateLocation</outputDirectory>
+ <overWriteReleases>false</overWriteReleases>
+ <overWriteSnapshots>false</overWriteSnapshots>
+ <overWriteIfNewer>true</overWriteIfNewer>
+ </configuration>
+ </execution>
+ </executions>
+ </plugin>
+ <!-- Plugin for creating a git.properties file that contains build and commit IDs -->
+ <plugin>
+ <groupId>pl.project13.maven</groupId>
+ <artifactId>git-commit-id-plugin</artifactId>
+ <version>4.0.5</version>
+ <executions>
+ <execution>
+ <id>get-the-git-infos</id>
+ <goals>
+ <goal>revision</goal>
+ </goals>
+ <phase>initialize</phase>
+ </execution>
+ </executions>
+ <configuration>
+ <generateGitPropertiesFile>true</generateGitPropertiesFile>
+ <generateGitPropertiesFilename>${project.build.outputDirectory}/git.properties</generateGitPropertiesFilename>
+ <includeOnlyProperties>
+ <includeOnlyProperty>^git.build.(time|version)$</includeOnlyProperty>
+ <includeOnlyProperty>^git.commit.id.(abbrev|full)$</includeOnlyProperty>
+ </includeOnlyProperties>
+ <commitIdGenerationMode>full</commitIdGenerationMode>
+ </configuration>
+ </plugin>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-enforcer-plugin</artifactId>
+ <version>3.0.0</version>
+ <executions>
+ <execution>
+ <id>enforce-versions</id>
+ <goals>
+ <goal>enforce</goal>
+ </goals>
+ <configuration>
+ <rules>
+ <requireMavenVersion>
+ <version>>=3.8.1</version>
+ <message>Maven version must be >= 3.8.1.</message>
+ </requireMavenVersion>
+ <requireJavaVersion>
+ <version>[1.8.0-0,1.8.0-500]</version>
+ <message>JDK version must be 1.8.0-x.</message>
+ </requireJavaVersion>
+ </rules>
+ </configuration>
+ </execution>
+ </executions>
+ </plugin>
+ </plugins>
+ </build>
+</project>
\ No newline at end of file
diff --git a/src/alignment/BoundedLocalSequenceAlignment.java b/src/main/java/nl/wur/bif/pantools/alignment/BoundedLocalSequenceAlignment.java
similarity index 99%
rename from src/alignment/BoundedLocalSequenceAlignment.java
rename to src/main/java/nl/wur/bif/pantools/alignment/BoundedLocalSequenceAlignment.java
index 4d2978dd535e86c4ae74070177cb577aee35efaa..a40d5c99518a7ff1e0f25b0ffb92f3898a3dbab1 100755
--- a/src/alignment/BoundedLocalSequenceAlignment.java
+++ b/src/main/java/nl/wur/bif/pantools/alignment/BoundedLocalSequenceAlignment.java
@@ -1,4 +1,4 @@
-package alignment;
+package nl.wur.bif.pantools.alignment;
import java.util.Stack;
diff --git a/src/alignment/LocalSequenceAlignment.java b/src/main/java/nl/wur/bif/pantools/alignment/LocalSequenceAlignment.java
similarity index 99%
rename from src/alignment/LocalSequenceAlignment.java
rename to src/main/java/nl/wur/bif/pantools/alignment/LocalSequenceAlignment.java
index 97a67b290fe7215bec7654f3f8f791fde2a46edc..b0925a58786632ea72ca9af4f43692b48df6e21e 100755
--- a/src/alignment/LocalSequenceAlignment.java
+++ b/src/main/java/nl/wur/bif/pantools/alignment/LocalSequenceAlignment.java
@@ -1,4 +1,4 @@
-package alignment;
+package nl.wur.bif.pantools.alignment;
import java.util.Stack;
diff --git a/src/index/IndexDatabase.java b/src/main/java/nl/wur/bif/pantools/index/IndexDatabase.java
similarity index 98%
rename from src/index/IndexDatabase.java
rename to src/main/java/nl/wur/bif/pantools/index/IndexDatabase.java
index 702ce524acb9b26e05b8637d9e1081fc548d6e03..fa29b8f9861dd274b514df4e3fd5a1f80fa25a4d 100755
--- a/src/index/IndexDatabase.java
+++ b/src/main/java/nl/wur/bif/pantools/index/IndexDatabase.java
@@ -1,7 +1,7 @@
-package index;
+package nl.wur.bif.pantools.index;
-import sequence.SequenceDatabase;
-import static index.kmer.copy_and_adjust;
+import nl.wur.bif.pantools.sequence.SequenceDatabase;
+import static nl.wur.bif.pantools.index.kmer.copy_and_adjust;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
@@ -19,12 +19,12 @@ import java.nio.file.Files;
import java.nio.file.Paths;
import java.util.logging.Level;
import java.util.logging.Logger;
-import pangenome.ExecCommand;
-import static pantools.Pantools.LOG;
-import static pantools.Pantools.cores;
-import static pantools.Pantools.degenerate_label;
-import static pantools.Pantools.executeCommand;
-import static pantools.Pantools.nucleotide_label;
+import nl.wur.bif.pantools.pangenome.ExecCommand;
+import static nl.wur.bif.pantools.pantools.Pantools.LOG;
+import static nl.wur.bif.pantools.pantools.Pantools.cores;
+import static nl.wur.bif.pantools.pantools.Pantools.degenerate_label;
+import static nl.wur.bif.pantools.pantools.Pantools.executeCommand;
+import static nl.wur.bif.pantools.pantools.Pantools.nucleotide_label;
/**
* Implements all the functionality to build a KMC-based kmer index.
@@ -63,7 +63,6 @@ public final class IndexDatabase {
public MappedByteBuffer pre_buff[];
public String KMC = "kmc";
-
/**
* Mounts an available index database to the index database object
*
@@ -280,7 +279,7 @@ public final class IndexDatabase {
* @param genomes_path_file A text file containing path to the new genomes
* @param genomeDb The genome database
* @param graphDb The graph database
- * @param old_darabase The existing index database
+ * @param old_database The existing index database
* @param previous_num_genomes Number of the genomes available in the index
*/
public IndexDatabase(String index_path, String genomes_path_file, SequenceDatabase genomeDb, GraphDatabaseService graphDb, IndexDatabase old_database, int previous_num_genomes) {
diff --git a/src/index/IndexPointer.java b/src/main/java/nl/wur/bif/pantools/index/IndexPointer.java
similarity index 97%
rename from src/index/IndexPointer.java
rename to src/main/java/nl/wur/bif/pantools/index/IndexPointer.java
index f6e6f7faf0288ee22597016bb35a2298ab70ebd0..a590c415ab7aa689e530df2d519b3a59922c2b23 100755
--- a/src/index/IndexPointer.java
+++ b/src/main/java/nl/wur/bif/pantools/index/IndexPointer.java
@@ -1,4 +1,4 @@
-package index;
+package nl.wur.bif.pantools.index;
/**
* Implements the data structure for index pointer.
diff --git a/src/index/IndexScanner.java b/src/main/java/nl/wur/bif/pantools/index/IndexScanner.java
similarity index 98%
rename from src/index/IndexScanner.java
rename to src/main/java/nl/wur/bif/pantools/index/IndexScanner.java
index edd655c007a9f05d196cde3b8b6da516dfbd5806..a52616886c6f67fa0dc05dedabbfcdf4a5edfe5d 100644
--- a/src/index/IndexScanner.java
+++ b/src/main/java/nl/wur/bif/pantools/index/IndexScanner.java
@@ -1,6 +1,6 @@
-package index;
+package nl.wur.bif.pantools.index;
-import static index.kmer.compare_suffix;
+import static nl.wur.bif.pantools.index.kmer.compare_suffix;
import java.io.IOException;
import java.nio.MappedByteBuffer;
@@ -70,7 +70,7 @@ public final class IndexScanner {
*
* @param buff The memory mapped page of the pointer database
* @param pos The position in the buffer to start writing bytes.
- * @param offset The long integer to be written as node ID.
+ * @param id The long integer to be written as node ID.
*/
private void write_node_id(MappedByteBuffer buff, int pos, long id) {
for (int i = database.id_len - 1; i >= 0; --i, ++pos) {
@@ -81,7 +81,7 @@ public final class IndexScanner {
/**
* Reads a kmer from th index database.
*
- * @param kmer The kmer object to be filled
+ * @param key The kmer object to be filled
* @param number The number of kmer in the kmer index
*/
public void get_kmer(kmer key, long number) {
diff --git a/src/index/kmer.java b/src/main/java/nl/wur/bif/pantools/index/kmer.java
similarity index 98%
rename from src/index/kmer.java
rename to src/main/java/nl/wur/bif/pantools/index/kmer.java
index ef95c775fee5995c7ba88043f31281f8449c4b8c..4c2e0fe69997ec724f167347e78d6727d745cb38 100755
--- a/src/index/kmer.java
+++ b/src/main/java/nl/wur/bif/pantools/index/kmer.java
@@ -1,4 +1,4 @@
-package index;
+package nl.wur.bif.pantools.index;
import org.bouncycastle.util.Arrays;
@@ -105,7 +105,7 @@ public class kmer {
/**
* Sets the suffix of the forward kmer
*
- * @param p The suffix to set
+ * @param s The suffix to set
*/
public void set_fwd_suffix(byte[] s) {
fwd_suffix = s;
@@ -114,7 +114,7 @@ public class kmer {
/**
* Sets the suffix of the reverse kmer
*
- * @param p The suffix to set
+ * @param s The suffix to set
*/
public void set_rev_suffix(byte[] s) {
rev_suffix = s;
diff --git a/src/pangenome/AnnotationLayer.java b/src/main/java/nl/wur/bif/pantools/pangenome/AnnotationLayer.java
similarity index 83%
rename from src/pangenome/AnnotationLayer.java
rename to src/main/java/nl/wur/bif/pantools/pangenome/AnnotationLayer.java
index 063d98b017a2e49c9a985651c73ad7579808e4af..96a4e176e02f1527fd9c97736106a4ba3148502b 100755
--- a/src/pangenome/AnnotationLayer.java
+++ b/src/main/java/nl/wur/bif/pantools/pangenome/AnnotationLayer.java
@@ -3,10 +3,10 @@
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
-package pangenome;
+package nl.wur.bif.pantools.pangenome;
-import index.IndexPointer;
-import index.IndexScanner;
+import nl.wur.bif.pantools.index.IndexPointer;
+import nl.wur.bif.pantools.index.IndexScanner;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
@@ -26,6 +26,7 @@ import java.util.Arrays;
import java.util.Date;
import java.util.HashSet;
import java.util.Map;
+import java.util.TreeSet;
import java.util.Scanner;
import org.apache.commons.lang.ArrayUtils;
import org.neo4j.graphdb.Direction;
@@ -35,52 +36,53 @@ import org.neo4j.graphdb.NotFoundException;
import org.neo4j.graphdb.Relationship;
import org.neo4j.graphdb.ResourceIterator;
import org.neo4j.graphdb.Transaction;
-import static pangenome.Classification.try_incr_hashmap;
-import static pangenome.GenomeLayer.locate;
+import static nl.wur.bif.pantools.pangenome.Classification.try_incr_hashmap;
+import static nl.wur.bif.pantools.pangenome.GenomeLayer.locate;
-import static pantools.Pantools.FEATURE;
-import static pantools.Pantools.RelTypes;
-import static pantools.Pantools.labels;
-import static pantools.Pantools.CDS_label;
-import static pantools.Pantools.CONNECT_ANNOTATIONS;
-import static pantools.Pantools.K_SIZE;
-import static pantools.Pantools.MAX_TRANSACTION_SIZE;
-import static pantools.Pantools.OUTPUT_PATH;
-import static pantools.Pantools.PATH_TO_THE_ANNOTATIONS_FILE;
-import static pantools.Pantools.PATH_TO_THE_GENOME_NUMBERS_FILE;
-import static pantools.Pantools.WORKING_DIRECTORY;
-import static pantools.Pantools.annotation_label;
-import static pantools.Pantools.coding_gene_label;
-import static pantools.Pantools.connect_pangenome;
-import static pantools.Pantools.disconnect_pangenome;
-import static pantools.Pantools.exon_label;
-import static pantools.Pantools.feature_label;
-import static pantools.Pantools.gene_label;
-import static pantools.Pantools.genome_label;
-import static pantools.Pantools.intron_label;
-import static pantools.Pantools.mRNA_label;
-import static pantools.Pantools.rRNA_label;
-import static pantools.Pantools.reverse_complement;
-import static pantools.Pantools.sequence_label;
-import static pantools.Pantools.tRNA_label;
-import static pantools.Pantools.write_fasta;
-import sequence.SequenceScanner;
-import static pantools.Pantools.genomeDb;
-import static pantools.Pantools.genomeSc;
-import static pantools.Pantools.graphDb;
-import static pantools.Pantools.indexDb;
-import static pantools.Pantools.indexSc;
-import static pantools.Pantools.target_genome;
-import static pantools.Pantools.skip_genomes;
-import static pantools.Pantools.check_if_graphDb_is_available;
-import static pantools.Pantools.count_nodes;
-import static pantools.Pantools.SELECTED_LABEL;
-import static pantools.Pantools.delete_file_in_DB;
-import static pantools.Pantools.stop_if_panproteome;
-import static pantools.Pantools.pangenome_label;
-import static pangenome.create_skip_arrays.create_skip_arrays;
-import static pantools.Pantools.skip_array;
-import static pantools.Pantools.write_string_to_file_in_DB;
+import static nl.wur.bif.pantools.pantools.Pantools.RelTypes;
+import static nl.wur.bif.pantools.pantools.Pantools.labels;
+import static nl.wur.bif.pantools.pantools.Pantools.CDS_label;
+import static nl.wur.bif.pantools.pantools.Pantools.CONNECT_ANNOTATIONS;
+import static nl.wur.bif.pantools.pantools.Pantools.K_SIZE;
+import static nl.wur.bif.pantools.pantools.Pantools.MAX_TRANSACTION_SIZE;
+import static nl.wur.bif.pantools.pantools.Pantools.OUTPUT_PATH;
+import static nl.wur.bif.pantools.pantools.Pantools.PATH_TO_THE_ANNOTATIONS_FILE;
+import static nl.wur.bif.pantools.pantools.Pantools.PATH_TO_THE_GENOME_NUMBERS_FILE;
+import static nl.wur.bif.pantools.pantools.Pantools.WORKING_DIRECTORY;
+import static nl.wur.bif.pantools.pantools.Pantools.annotation_label;
+import static nl.wur.bif.pantools.pantools.Pantools.coding_gene_label;
+import static nl.wur.bif.pantools.pantools.Pantools.connect_pangenome;
+import static nl.wur.bif.pantools.pantools.Pantools.disconnect_pangenome;
+import static nl.wur.bif.pantools.pantools.Pantools.exon_label;
+import static nl.wur.bif.pantools.pantools.Pantools.feature_label;
+import static nl.wur.bif.pantools.pantools.Pantools.gene_label;
+import static nl.wur.bif.pantools.pantools.Pantools.genome_label;
+import static nl.wur.bif.pantools.pantools.Pantools.intron_label;
+import static nl.wur.bif.pantools.pantools.Pantools.mRNA_label;
+import static nl.wur.bif.pantools.pantools.Pantools.rRNA_label;
+import static nl.wur.bif.pantools.pantools.Pantools.reverse_complement;
+import static nl.wur.bif.pantools.pantools.Pantools.sequence_label;
+import static nl.wur.bif.pantools.pantools.Pantools.tRNA_label;
+import static nl.wur.bif.pantools.pantools.Pantools.write_fasta;
+import nl.wur.bif.pantools.sequence.SequenceScanner;
+import static nl.wur.bif.pantools.pantools.Pantools.genomeDb;
+import static nl.wur.bif.pantools.pantools.Pantools.genomeSc;
+import static nl.wur.bif.pantools.pantools.Pantools.graphDb;
+import static nl.wur.bif.pantools.pantools.Pantools.indexDb;
+import static nl.wur.bif.pantools.pantools.Pantools.indexSc;
+import static nl.wur.bif.pantools.pantools.Pantools.target_genome;
+import static nl.wur.bif.pantools.pantools.Pantools.skip_genomes;
+import static nl.wur.bif.pantools.pantools.Pantools.check_if_graphDb_is_available;
+import static nl.wur.bif.pantools.pantools.Pantools.count_nodes;
+import static nl.wur.bif.pantools.pantools.Pantools.SELECTED_LABEL;
+import static nl.wur.bif.pantools.pantools.Pantools.delete_file_in_DB;
+import static nl.wur.bif.pantools.pantools.Pantools.stop_if_panproteome;
+import static nl.wur.bif.pantools.pantools.Pantools.pangenome_label;
+import static nl.wur.bif.pantools.pangenome.create_skip_arrays.create_skip_arrays;
+import static nl.wur.bif.pantools.pantools.Pantools.create_directory_in_DB;
+import static nl.wur.bif.pantools.pantools.Pantools.skip_array;
+import static nl.wur.bif.pantools.pantools.Pantools.total_genomes;
+import static nl.wur.bif.pantools.pantools.Pantools.write_string_to_file_in_DB;
/**
* Implements all the functionalities related to the annotation layer of the pangenome
@@ -288,7 +290,7 @@ public class AnnotationLayer {
* Creates annotation_overview.txt, an overview of the .gff and .gbk files incorporated in the pangenome
*/
public static void create_annotation_overview() {
- int total_genomes = (int) graphDb.findNodes(pangenome_label).next().getProperty("num_genomes");
+ total_genomes = (int) graphDb.findNodes(pangenome_label).next().getProperty("num_genomes");
StringBuilder output_builder = new StringBuilder();
int annotation_count = 0;
for (int i = 1; i <= total_genomes; i++) {
@@ -335,7 +337,9 @@ public class AnnotationLayer {
* @param annotation_file Path to the GFF3 file
* @param proteins_directory The directory to write protein FASTA files in
*/
- private void parse_gff(int genome, String annotation_id, BufferedWriter log_file, String annotation_file, String proteins_directory, Node annotation_node) {
+ private void parse_gff(int genome, String annotation_id, BufferedWriter log_file, String annotation_file,
+ String proteins_directory, Node annotation_node) {
+
int i, trsc, num_genes, num_mRNAs, num_tRNAs, num_rRNAs, feature_len, offset, num_cds_without_genes;
MAX_TRANSACTION_SIZE = 50000; // commit changes every 50k lines
long seq_len = -1, line_nr = 0;
@@ -561,10 +565,16 @@ public class AnnotationLayer {
} // while lines
in.close();
- System.out.println("\r" + address[0] + "\t" + (num_genes + num_cds_without_genes) + "\t" + num_mRNAs + "\t" + num_tRNAs + "\t" + num_rRNAs + "\t");
+ System.out.print("\r" + address[0] + "\t" + (num_genes + num_cds_without_genes) + "\t" + num_mRNAs + "\t"
+ + num_tRNAs + "\t" + num_rRNAs + "\t");
if (num_genes == 0 && num_cds_without_genes == 0) {
- System.out.println("\nNo genes could be added for genome " + address[0] +"!\n");
+ System.out.println("-> No gene nodes could be created!\n");
+ undo_failed_annotation(annotation_node);
+ System.out.println("\rNone of the final GFF's annotations were included to the pangenome\n"
+ + "Please verify the correctness of: " + annotation_file + "\n");
System.exit(1);
+ } else {
+ System.out.println("");
}
try (Transaction tx = graphDb.beginTx()) {
@@ -584,7 +594,54 @@ public class AnnotationLayer {
System.out.println("Could not open " + annotation_file + "!");
}
}
-
+
+ /**
+ * Use in case something went wrong during the annotation and you want to rollback the latest annotation
+ * @param annotation_node an 'annotation' node
+ */
+ private void undo_failed_annotation(Node annotation_node) {
+ int trsc = 0;
+ long node_counter = 0;
+ Transaction tx = graphDb.beginTx(); // start database transaction
+ try {
+ String id = (String) annotation_node.getProperty("identifier");
+ Iterable<Relationship> anno_relations = annotation_node.getRelationships();
+ for (Relationship rel : anno_relations) {
+ rel.delete();
+ }
+ annotation_node.delete();
+ ResourceIterator<Node> annotated_nodes = graphDb.findNodes(feature_label, "annotation_id", id);
+ while (annotated_nodes.hasNext()) {
+ node_counter ++;
+ Node new_node = annotated_nodes.next();
+ Iterable<Relationship> new_relations = new_node.getRelationships();
+ for (Relationship rel : new_relations) {
+ rel.delete();
+ trsc ++;
+ if (trsc >= 100000) { // 100k actions
+ tx.success();
+ tx.close();
+ trsc = 0;
+ tx = graphDb.beginTx(); // start a new database transaction
+ }
+ }
+ trsc ++;
+ if (trsc >= 100000) { // 100k actions
+ tx.success();
+ tx.close();
+ trsc = 0;
+ tx = graphDb.beginTx(); // start a new database transaction
+ }
+ if (node_counter % 5000 == 0){
+ System.out.print("\rRolling back annotated features: " + node_counter);
+ }
+ }
+ } finally {
+ tx.close();
+ }
+ }
+
+
/**
* Parses a GenBank file and annotates the genomes at the same time.
*
@@ -906,13 +963,13 @@ public class AnnotationLayer {
for (int i = 0; i < fields.length; ++i)
if (fields[i].startsWith(property)) {
if (fields[i].contains("=")) {
- if (fields[i].trim().split("=")[1].contains("/")){
+ if (fields[i].trim().split("=")[1].contains("/")) {
return fields[i].trim().split("=")[1].split("/")[0]; // remove string after /
} else {
return fields[i].trim().split("=")[1];
}
} else {
- if (fields[i].trim().split("\\s+")[1].contains("/")){
+ if (fields[i].trim().split("\\s+")[1].contains("/")) {
return fields[i].trim().split("\\s+")[1].split("/")[0]; // remove string after /
} else {
return fields[i].trim().split("\\s+")[1];
@@ -971,124 +1028,140 @@ public class AnnotationLayer {
/**
* Retrieves sequence of the features and stores them in a FASTA file.
*/
- public void retrieve_feature() {
- BufferedReader in;
- ResourceIterator<Node> feature_nodes;
- //Relationship rstart;
- Node feature;//start,
- String ID;
- String line;
- boolean forward;
- int i, j, num_genomes, begin, end, genome = 0;
- int[] address, genome_numbers;
- StringBuilder feature_seq;
- Label feature_label = labels.get(FEATURE);
- if (PATH_TO_THE_GENOME_NUMBERS_FILE == null) {
- System.out.println("PATH_TO_THE_GENOME_NUMBERS_FILE is empty.");
+ public void retrieve_features() {
+ System.out.println("\nRetrieve sequences of annotated (GFF) features from the pangenome.\n");
+ // Verify if the provided --label argument is correct
+ if (SELECTED_LABEL == null) {
+ System.out.println("No GFF annotation feature/node was provided via --label\n");
+ System.exit(1);
+ }
+ if (!labels.containsKey(SELECTED_LABEL)) {
+ System.out.println(SELECTED_LABEL + " is not a known node type.\n"
+ + "Allowed features: gene, coding_gene, mRNA, CDS, exon, intron, tRNA, rRNA");
+ }
+
+ // Verify if the genomes were correctly selected
+ if (PATH_TO_THE_GENOME_NUMBERS_FILE != null && (skip_genomes != null || target_genome != null)) {
+ System.out.println("Select genomes via --feature-type, --skip or --reference. Using multiple arguments is not allowed.\n");
+ System.exit(1);
+ } else if (PATH_TO_THE_GENOME_NUMBERS_FILE == null && skip_genomes == null && target_genome == null) {
+ System.out.println("Missing a genome selection via --feature-type, --skip or --reference. Using multiple arguments is not allowed.\n");
System.exit(1);
}
+
+ Label feature_label = labels.get(SELECTED_LABEL);
connect_pangenome();
- K_SIZE = indexDb.get_K();
+ try (Transaction tx = graphDb.beginTx()) { // start database transaction
+ Node pangenome_node = graphDb.findNodes(pangenome_label).next();
+ stop_if_panproteome(pangenome_node, "retrieve_features"); // stops the progam when run on a panproteome, retrieves K_size & total_genomes
+ create_skip_arrays(false, true); // create skip array if -skip/-ref is provided by user
+ tx.success(); // transaction successful, commit changes
+ } catch (NotFoundException nfe) {
+ System.out.println("\nUnable to start the database\n");
+ System.exit(1);
+ }
+ create_directory_in_DB("retrieval/features/");
genomeSc = new SequenceScanner(genomeDb, 1, 1, K_SIZE, indexDb.get_pre_len());
- num_genomes = 0;
- feature_seq = new StringBuilder();
- BufferedWriter[] out = new BufferedWriter[genomeDb.num_genomes + 1];
- try {
- in = new BufferedReader(new FileReader(PATH_TO_THE_GENOME_NUMBERS_FILE));
- while ((line = in.readLine()) != null) {
- line = line.trim();
- if (line.equals("")) {
- continue;
- }
- try{
- genome = Integer.parseInt(line.trim());
- }catch(NumberFormatException e) {
- System.out.println(genome + "is not a valid genome number.");
+
+ // skip_array is used to control for which genomes the sequences are extracted.
+ // By using --skip or --reference, the array is already prepared.
+ // When using --label, the array is prepared below
+
+ BufferedWriter[] out = new BufferedWriter[genomeDb.num_genomes];
+ if (PATH_TO_THE_GENOME_NUMBERS_FILE != null) { // skip_array is prepared
+ skip_array = new boolean[total_genomes];
+ TreeSet<Integer> genome_numbers_set = retrieve_numbers_from_genome_numbers_file();
+ for (int i = 1; i <= total_genomes; i++) {
+ skip_array[i-1] = !genome_numbers_set.contains(i); // sets true or false in array
+ }
+ }
+
+ try { // start the file writers
+ for (int i = 0; i < total_genomes; i++) { // i+1 is the genome number
+ if (skip_array[i]) {
continue;
}
- num_genomes++;
+ out[i] = new BufferedWriter(new FileWriter(WORKING_DIRECTORY + "retrieval/features/" + SELECTED_LABEL + "s_" + (i+1) + ".fasta"));
}
- in.close();
- } catch (IOException e) {
- System.out.println(e.getMessage());
+ } catch (IOException ioe) {
+ System.out.println("Failed to read: " + PATH_TO_THE_GENOME_NUMBERS_FILE + "\n");
System.exit(1);
}
- genome_numbers = new int[num_genomes];
+
+ // retrieve nodes that match the provided --label and extract sequences
+ int extract_counter = 0;
try (Transaction tx = graphDb.beginTx()) {
try {
- in = new BufferedReader(new FileReader(PATH_TO_THE_GENOME_NUMBERS_FILE));
- // fill all the records in an array to be sorted
- for (i = 0; (line = in.readLine()) != null;) {
- line = line.trim();
- if (line.equals("")) {
+ ResourceIterator<Node> feature_nodes = graphDb.findNodes(feature_label);
+ while (feature_nodes.hasNext()) {
+ Node feature = feature_nodes.next();
+ int genome = (int) feature.getProperty("genome");
+ String feature_id = (String) feature.getProperty("id");
+ StringBuilder feature_seq = new StringBuilder();
+ if (skip_array[genome-1]) { // genome was not selected by user
continue;
}
- try{
- genome = genome_numbers[i] = Integer.parseInt(line.trim());
- }catch(NumberFormatException e) {
- System.out.println(genome + " skipped.");
+ if (SELECTED_LABEL.equals("mRNA")) {
+ feature_seq.append(feature.getProperty("sequence"));
+ } else {
+ int[] address = (int[]) feature.getProperty("address");
+ boolean forward = feature.getProperty("strand").equals("+"); // returns a boolean
+ int region_length = address[3] - address[2] + 1;
+ genomeSc.get_sub_sequence(feature_seq, address[0], address[1], address[2]-1, region_length, forward);
+ }
+ extract_counter ++;
+ out[genome-1].write(">" + feature_id + "\n");
+ write_fasta(out[genome-1], feature_seq.toString(), 70);
+ }
+
+ System.out.println("\r" + extract_counter + " " + SELECTED_LABEL + "s found and retrieved successfully.");
+ for (int i = 0; i < total_genomes; i++) { // i+1 is the genome number
+ if (skip_array[i]) {
continue;
}
- out[genome] = new BufferedWriter(new FileWriter(OUTPUT_PATH + "/" + FEATURE + "s." + genome + ".fasta"));
- ++i;
+ out[i].close();
}
- in.close();
- Arrays.sort(genome_numbers);
- } catch (IOException ioe) {
- System.out.println("Failed to read file names!");
- System.exit(1);
- }
- try {
- // for all the genes in the database
- for (i = 0, j = 0, feature_nodes = graphDb.findNodes(feature_label); feature_nodes.hasNext();) {
- feature = feature_nodes.next();
- genome = (int) feature.getProperty("genome");
- ID = (String) feature.getProperty("id");
- feature_seq.setLength(0);
- if (Arrays.binarySearch(genome_numbers, genome) >= 0) {
- ++i;
- if (FEATURE.equals("mRNA"))
- feature_seq.append(feature.getProperty("sequence"));
- else{
- //rstart = feature.getSingleRelationship(RelTypes.starts, Direction.OUTGOING);
- // start = rstart.getEndNode();
- address = (int[]) feature.getProperty("address");
- begin = address[2];
- end = address[3];
- forward = feature.getProperty("strand").equals("+");
- //extract_sequence(gene_seq, new IndexPointer(start.getId(), (boolean) rstart.getProperty("forward"), (int) rstart.getProperty("offset"),-1l), address, K);//
- address[2] -= 1;
- address[3] -= 1;
- genomeSc.get_sub_sequence(feature_seq, address[0], address[1], address[2], address[3] - address[2] + 1 , forward);
- //genomeDb=new sequence_database(pangenome_path+GENOME_DATABASE_PATH);
- //if(gene_seq.toString().equals(genomeDb.get_sequence(genome, sequence, begin-1, end-begin+1, strand))
- //|| gene_seq.toString().equals(genomeDb.get_sequence(genome, sequence, begin-1, end-begin+1, !strand)) )//gene_seq.length() == end-begin+1)//
- }
- ++j;
- out[genome].write(">" + ID + "\n");
- //if (strand) {
- write_fasta(out[genome], feature_seq.toString(), 70);
- //} else {
- // reverse_complement(gene_seq);
- // write_fasta(out, gene_seq.toString(), 70);
- //}
- }
- //if (i % (num_genes / 100 + 1) == 0) {
- // System.out.print((long) i * 100 / num_genes + 1 + "%\r");
- //}
- }//for i
- System.out.println(j + " out of " + i + " " + FEATURE + "s found and retrieved successfully.");
- for (i = 0; i < genome_numbers.length; ++i)
- out[genome_numbers[i]].close();
} catch (IOException ioe) {
- System.out.println("Failed to read file names!");
+ System.out.println("Failed to write files to " + WORKING_DIRECTORY + "retrieval/features/\n");
System.exit(1);
}
tx.success();
}
disconnect_pangenome();
+ System.out.println("\nOutput written to:\n"
+ + " " + WORKING_DIRECTORY + "retrieval/features/\n");
}
+ /**
+ * Read --genome-numbers or -gn. Places the numbers in a Set that automatically sorts the numbers in ascending order
+ * @return
+ */
+ public TreeSet<Integer> retrieve_numbers_from_genome_numbers_file() {
+ String line;
+ TreeSet<Integer> genome_numbers = new TreeSet<>();
+ try {
+ BufferedReader in; in = new BufferedReader(new FileReader(PATH_TO_THE_GENOME_NUMBERS_FILE));
+ while ((line = in.readLine()) != null) {
+ line = line.trim();
+ if (line.equals("")) {
+ continue;
+ }
+ try {
+ int genome = Integer.parseInt(line.trim());
+ genome_numbers.add(genome);
+ } catch(NumberFormatException e) {
+ System.out.println(line.trim() + "is not a valid genome number.");
+ }
+
+ }
+ in.close();
+ } catch (IOException e) {
+ System.out.println(e.getMessage());
+ System.exit(1);
+ }
+ return genome_numbers;
+ }
+
/**
* Translates a transcript to a protein sequence
*
@@ -1129,7 +1202,7 @@ public class AnnotationLayer {
tx.success();
} catch (NotFoundException nfe) {
System.out.println("Unable to start the database\n");
- return;
+ System.exit(1);
}
if (total_annotations == 0) {
System.out.println("No annotations are present\n");
@@ -1143,7 +1216,8 @@ public class AnnotationLayer {
create_skip_arrays(false, true); // create skip arrays for sequences and genomes if -skip/-ref is provided by user
String genome_or_identifier = "genome";
- if ((target_genome != null || skip_genomes != null) && PATH_TO_THE_ANNOTATIONS_FILE == null) { // option 1, remove all from selected genomes
+
+ if ((target_genome != null || skip_genomes != null) && PATH_TO_THE_ANNOTATIONS_FILE == null) { // option 1, remove all from selected genomes
try (Transaction tx = graphDb.beginTx()) {
ResourceIterator<Node> annotation_nodes = graphDb.findNodes(annotation_label);
while (annotation_nodes.hasNext()) {
@@ -1207,8 +1281,8 @@ public class AnnotationLayer {
/**
*
- * @param target_label
- * @param identifier
+ * @param target_label a node label
+ * @param identifier an annotation identifier
* @param genome_or_identifier
*/
public void remove_node_rels_matching_genome_or_identifier(Label target_label, String identifier, String genome_or_identifier) {
@@ -1234,8 +1308,9 @@ public class AnnotationLayer {
rel.delete();
trsc1 ++;
rel_counter ++;
- if (rel_counter % 100 == 0 || rel_counter == rel_set.size()) {
- System.out.print("\rRemoving " + target_label + " relationships of annotation " + identifier + ": " + rel_counter + "/" + rel_set.size() + " ");
+ if (rel_counter % 10000 == 0 || rel_counter == rel_set.size()) {
+ System.out.print("\rRemoving " + target_label + " relationships of annotation " + identifier + ": "
+ + rel_counter + "/" + rel_set.size() + " ");
}
if (trsc1 >= MAX_TRANSACTION_SIZE) {
tx.success();
@@ -1257,8 +1332,9 @@ public class AnnotationLayer {
trsc1 ++;
node1.delete();
node_counter ++;
- if (node_counter % 1000 == 0 || node_counter == node_set.size()) {
- System.out.print("\rRemoving " + target_label + " nodes of annotation " + identifier + ": " + node_counter + "/" + node_set.size() + " ");
+ if (node_counter % 10000 == 0 || node_counter == node_set.size()) {
+ System.out.print("\rRemoving " + target_label + " nodes of annotation " + identifier + ": "
+ + node_counter + "/" + node_set.size() + " ");
}
if (trsc1 >= MAX_TRANSACTION_SIZE) {
tx.success();
diff --git a/src/pangenome/Classification.java b/src/main/java/nl/wur/bif/pantools/pangenome/Classification.java
similarity index 78%
rename from src/pangenome/Classification.java
rename to src/main/java/nl/wur/bif/pantools/pangenome/Classification.java
index 0709d60bdf894b1c3831591c9970a75bd3725014..3e3aea33b2b496ec787ed4fdf11cc57f3268c81a 100644
--- a/src/pangenome/Classification.java
+++ b/src/main/java/nl/wur/bif/pantools/pangenome/Classification.java
@@ -4,164 +4,162 @@
* and open the template in the editor.
*/
-package pangenome;
+package nl.wur.bif.pantools.pangenome;
-import index.kmer;
-import static pantools.Pantools.count_nodes;
+import static nl.wur.bif.pantools.pantools.Pantools.count_nodes;
import java.util.Arrays;
import java.util.ArrayList;
-import static pantools.Pantools.COG_label;
-import static pantools.Pantools.find_program_location;
+import static nl.wur.bif.pantools.pantools.Pantools.COG_label;
+import static nl.wur.bif.pantools.pantools.Pantools.find_program_location;
import java.util.List;
import java.util.HashMap;
import java.util.LinkedHashMap;
import org.neo4j.graphdb.Label;
import java.util.Scanner;
-import static pantools.Pantools.PROTEOME;
+import static nl.wur.bif.pantools.pantools.Pantools.PROTEOME;
import java.util.stream.Collectors;
import java.util.Map;
import org.apache.commons.lang.ArrayUtils;
-import static pantools.Pantools.copy_directory;
-import index.IndexPointer;
+import static nl.wur.bif.pantools.pantools.Pantools.copy_directory;
+import nl.wur.bif.pantools.index.IndexPointer;
import org.neo4j.graphdb.Node;
import org.neo4j.graphdb.Relationship;
import org.neo4j.graphdb.RelationshipType;
import org.neo4j.graphdb.ResourceIterator;
import org.neo4j.graphdb.Transaction;
import org.neo4j.graphdb.Direction;
-import static pantools.Pantools.repeat_label;
-import static alignment.BoundedLocalSequenceAlignment.match;
-import static alignment.BoundedLocalSequenceAlignment.initialize_BLOSUM_matrix;
-import static pantools.Pantools.GAP_OPEN;
-import static pantools.Pantools.PATH_TO_THE_REGIONS_FILE;
-import static pantools.Pantools.PATH_TO_THE_ANNOTATIONS_FILE;
-import static pantools.Pantools.homology_group_label;
-import static pantools.Pantools.pangenome_label;
-import static pantools.Pantools.busco_label;
+import static nl.wur.bif.pantools.pantools.Pantools.repeat_label;
+import static nl.wur.bif.pantools.alignment.BoundedLocalSequenceAlignment.match;
+import static nl.wur.bif.pantools.alignment.BoundedLocalSequenceAlignment.initialize_BLOSUM_matrix;
+import static nl.wur.bif.pantools.pantools.Pantools.GAP_OPEN;
+import static nl.wur.bif.pantools.pantools.Pantools.PATH_TO_THE_REGIONS_FILE;
+import static nl.wur.bif.pantools.pantools.Pantools.PATH_TO_THE_ANNOTATIONS_FILE;
+import static nl.wur.bif.pantools.pantools.Pantools.homology_group_label;
+import static nl.wur.bif.pantools.pantools.Pantools.pangenome_label;
+import static nl.wur.bif.pantools.pantools.Pantools.busco_label;
import java.io.BufferedReader;
import java.io.BufferedWriter;
-import static pantools.Pantools.adj_total_genomes;
-import static pantools.Pantools.target_genome;
-import static pantools.Pantools.WORKING_DIRECTORY;
-import static pantools.Pantools.WD_full_path;
-import static pantools.Pantools.skip_genomes;
-import static pantools.Pantools.PHENOTYPE;
-import static pantools.Pantools.LOG;
-import static pantools.Pantools.write_log;
+import static nl.wur.bif.pantools.pantools.Pantools.adj_total_genomes;
+import static nl.wur.bif.pantools.pantools.Pantools.target_genome;
+import static nl.wur.bif.pantools.pantools.Pantools.WORKING_DIRECTORY;
+import static nl.wur.bif.pantools.pantools.Pantools.WD_full_path;
+import static nl.wur.bif.pantools.pantools.Pantools.skip_genomes;
+import static nl.wur.bif.pantools.pantools.Pantools.PHENOTYPE;
+import static nl.wur.bif.pantools.pantools.Pantools.LOG;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import org.neo4j.graphdb.NotFoundException;
-import static pantools.Pantools.phenotype_label;
-import static pantools.Pantools.degenerate_label;
-import static pantools.Pantools.genome_label;
-import static pantools.Pantools.nucleotide_label;
-import static pantools.Pantools.gene_label;
-import static pantools.Pantools.coding_gene_label;
-import static pantools.Pantools.mRNA_label;
-import static pantools.Pantools.CDS_label;
-import static pantools.Pantools.sequence_label;
-import static pantools.Pantools.go_label;
-import static pantools.Pantools.phobius_label;
-import static pantools.Pantools.pfam_label;
-import static pantools.Pantools.intron_label;
-import static pantools.Pantools.exon_label;
-import static pantools.Pantools.tigrfam_label;
-import static pantools.Pantools.interpro_label;
-import static pantools.Pantools.bgc_label;
-import static pantools.Pantools.inactive_homology_group_label;
-import static pantools.Pantools.tRNA_label;
-import static pantools.Pantools.rRNA_label;
-import static pantools.Pantools.check_if_graphDb_is_available;
-import static pantools.Pantools.check_if_file_exists;
-import static pantools.Pantools.NODE_ID;
+import static nl.wur.bif.pantools.pantools.Pantools.phenotype_label;
+import static nl.wur.bif.pantools.pantools.Pantools.degenerate_label;
+import static nl.wur.bif.pantools.pantools.Pantools.genome_label;
+import static nl.wur.bif.pantools.pantools.Pantools.nucleotide_label;
+import static nl.wur.bif.pantools.pantools.Pantools.gene_label;
+import static nl.wur.bif.pantools.pantools.Pantools.coding_gene_label;
+import static nl.wur.bif.pantools.pantools.Pantools.mRNA_label;
+import static nl.wur.bif.pantools.pantools.Pantools.CDS_label;
+import static nl.wur.bif.pantools.pantools.Pantools.sequence_label;
+import static nl.wur.bif.pantools.pantools.Pantools.go_label;
+import static nl.wur.bif.pantools.pantools.Pantools.phobius_label;
+import static nl.wur.bif.pantools.pantools.Pantools.pfam_label;
+import static nl.wur.bif.pantools.pantools.Pantools.intron_label;
+import static nl.wur.bif.pantools.pantools.Pantools.exon_label;
+import static nl.wur.bif.pantools.pantools.Pantools.tigrfam_label;
+import static nl.wur.bif.pantools.pantools.Pantools.interpro_label;
+import static nl.wur.bif.pantools.pantools.Pantools.bgc_label;
+import static nl.wur.bif.pantools.pantools.Pantools.inactive_homology_group_label;
+import static nl.wur.bif.pantools.pantools.Pantools.tRNA_label;
+import static nl.wur.bif.pantools.pantools.Pantools.rRNA_label;
+import static nl.wur.bif.pantools.pantools.Pantools.check_if_graphDb_is_available;
+import static nl.wur.bif.pantools.pantools.Pantools.check_if_file_exists;
+import static nl.wur.bif.pantools.pantools.Pantools.NODE_ID;
import java.io.File;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.text.DecimalFormat;
-import static pantools.Pantools.SELECTED_HMGROUPS;
+import static nl.wur.bif.pantools.pantools.Pantools.SELECTED_HMGROUPS;
import java.util.HashSet;
import java.util.Set;
import org.neo4j.graphdb.ResourceIterable;
-import static pantools.Pantools.K_SIZE;
-import static pantools.Pantools.KMinOne;
-import static pantools.Pantools.skip_list;
-import static pantools.Pantools.skip_array;
-import static pantools.Pantools.seqLayer;
-import static pantools.Pantools.APPEND;
-import pantools.Pantools.RelTypes;
-import static pantools.Pantools.SELECTED_LABEL;
-import static pantools.Pantools.Mode;
-import static pantools.Pantools.SELECTED_NAME;
-import static pantools.Pantools.annotation_label;
-import static pantools.Pantools.genomeDb;
-import static pantools.Pantools.graphDb;
-import static pantools.Pantools.indexDb;
-import static pantools.Pantools.FAST;
-import sequence.SequenceScanner;
-import index.IndexScanner;
+import static nl.wur.bif.pantools.pantools.Pantools.K_SIZE;
+import static nl.wur.bif.pantools.pantools.Pantools.KMinOne;
+import static nl.wur.bif.pantools.pantools.Pantools.skip_list;
+import static nl.wur.bif.pantools.pantools.Pantools.skip_array;
+import static nl.wur.bif.pantools.pantools.Pantools.seqLayer;
+import static nl.wur.bif.pantools.pantools.Pantools.APPEND;
+import nl.wur.bif.pantools.pantools.Pantools.RelTypes;
+import static nl.wur.bif.pantools.pantools.Pantools.SELECTED_LABEL;
+import static nl.wur.bif.pantools.pantools.Pantools.Mode;
+import static nl.wur.bif.pantools.pantools.Pantools.SELECTED_NAME;
+import static nl.wur.bif.pantools.pantools.Pantools.annotation_label;
+import static nl.wur.bif.pantools.pantools.Pantools.genomeDb;
+import static nl.wur.bif.pantools.pantools.Pantools.graphDb;
+import static nl.wur.bif.pantools.pantools.Pantools.indexDb;
+import static nl.wur.bif.pantools.pantools.Pantools.FAST;
+import nl.wur.bif.pantools.sequence.SequenceScanner;
+import nl.wur.bif.pantools.index.IndexScanner;
import java.util.Collections;
import java.util.Random;
import java.util.TreeSet;
import java.util.concurrent.atomic.AtomicInteger;
import java.util.concurrent.atomic.AtomicLong;
-import static pantools.Pantools.indexSc;
-import static pantools.Pantools.genomeSc;
-import static pantools.Pantools.connect_pangenome;
-import static pantools.Pantools.phenotype_threshold;
-import static pantools.Pantools.phenotype_threshold_map;
-import static pantools.Pantools.geno_pheno_map;
-import static pantools.Pantools.phenotype_map;
+import static nl.wur.bif.pantools.pantools.Pantools.indexSc;
+import static nl.wur.bif.pantools.pantools.Pantools.genomeSc;
+import static nl.wur.bif.pantools.pantools.Pantools.connect_pangenome;
+import static nl.wur.bif.pantools.pantools.Pantools.phenotype_threshold;
+import static nl.wur.bif.pantools.pantools.Pantools.phenotype_threshold_map;
+import static nl.wur.bif.pantools.pantools.Pantools.geno_pheno_map;
+import static nl.wur.bif.pantools.pantools.Pantools.phenotype_map;
import java.util.concurrent.ConcurrentHashMap;
-import static pantools.Pantools.NODE_VALUE;
-import static pantools.Pantools.delete_directory;
-import static pantools.Pantools.delete_directory_in_DB;
-import static pantools.Pantools.write_SB_to_file_in_DB;
-import static pantools.Pantools.append_SB_to_file_in_DB;
-import static pantools.Pantools.write_string_to_file_in_DB;
-import static pantools.Pantools.write_string_to_file_full_path;
-import static pantools.Pantools.write_SB_to_file_full_path;
-import static pantools.Pantools.copy_file;
-import static pantools.Pantools.printProgressBar;
-import static pantools.Pantools.check_if_program_exists_stdout;
-import static pantools.Pantools.check_if_program_exists_stderr;
-import static pangenome.create_skip_arrays.create_skip_arrays;
-import static pantools.Pantools.test_if_correct_label;
-import static pantools.Pantools.retrieve_phenotypes;
-import static pantools.Pantools.grouping_version;
-import static pantools.Pantools.delete_file_in_DB;
-import static pantools.Pantools.delete_file_full_path;
-import static pantools.Pantools.annotation_identifiers;
-import static pantools.Pantools.append_SB_to_file_full_path;
-import static pantools.Pantools.append_string_to_file_full_path;
-import static pantools.Pantools.check_current_grouping_version;
-import static pantools.Pantools.check_if_panproteome;
-import static pantools.Pantools.remove_first_position_array;
-import static pantools.Pantools.report_number_of_threads;
-import static pantools.Pantools.stop_if_panproteome;
-import static pantools.Pantools.total_genomes;
+import static nl.wur.bif.pantools.pantools.Pantools.NODE_VALUE;
+import static nl.wur.bif.pantools.pantools.Pantools.delete_directory;
+import static nl.wur.bif.pantools.pantools.Pantools.delete_directory_in_DB;
+import static nl.wur.bif.pantools.pantools.Pantools.write_SB_to_file_in_DB;
+import static nl.wur.bif.pantools.pantools.Pantools.append_SB_to_file_in_DB;
+import static nl.wur.bif.pantools.pantools.Pantools.write_string_to_file_in_DB;
+import static nl.wur.bif.pantools.pantools.Pantools.write_string_to_file_full_path;
+import static nl.wur.bif.pantools.pantools.Pantools.write_SB_to_file_full_path;
+import static nl.wur.bif.pantools.pantools.Pantools.copy_file;
+import static nl.wur.bif.pantools.pantools.Pantools.printProgressBar;
+import static nl.wur.bif.pantools.pantools.Pantools.check_if_program_exists_stdout;
+import static nl.wur.bif.pantools.pantools.Pantools.check_if_program_exists_stderr;
+import static nl.wur.bif.pantools.pangenome.create_skip_arrays.create_skip_arrays;
+import static nl.wur.bif.pantools.pantools.Pantools.test_if_correct_label;
+import static nl.wur.bif.pantools.pantools.Pantools.retrieve_phenotypes;
+import static nl.wur.bif.pantools.pantools.Pantools.grouping_version;
+import static nl.wur.bif.pantools.pantools.Pantools.delete_file_in_DB;
+import static nl.wur.bif.pantools.pantools.Pantools.delete_file_full_path;
+import static nl.wur.bif.pantools.pantools.Pantools.annotation_identifiers;
+import static nl.wur.bif.pantools.pantools.Pantools.append_SB_to_file_full_path;
+import static nl.wur.bif.pantools.pantools.Pantools.append_string_to_file_full_path;
+import static nl.wur.bif.pantools.pantools.Pantools.check_current_grouping_version;
+import static nl.wur.bif.pantools.pantools.Pantools.check_if_panproteome;
+import static nl.wur.bif.pantools.pantools.Pantools.remove_first_position_array;
+import static nl.wur.bif.pantools.pantools.Pantools.report_number_of_threads;
+import static nl.wur.bif.pantools.pantools.Pantools.stop_if_panproteome;
+import static nl.wur.bif.pantools.pantools.Pantools.total_genomes;
import java.util.concurrent.BlockingQueue;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.concurrent.LinkedBlockingQueue;
import java.util.concurrent.TimeUnit;
-import static pantools.Pantools.INPUT_FILE;
-import static pantools.Pantools.THREADS;
-import static pantools.Pantools.VERSION;
-import static pantools.Pantools.MAX_TRANSACTION_SIZE;
-import static pantools.Pantools.core_threshold;
-import static pantools.Pantools.unique_threshold;
-import static pantools.Pantools.create_directory_in_DB;
-import static pantools.Pantools.check_r_libraries_environment;
-import static pantools.Pantools.longest_transcripts;
-import static pantools.Pantools.signalp_label;
-import static pantools.Pantools.skip_seq_array;
-import static pantools.Pantools.BLOSUM;
-import static pangenome.FunctionalAnnotations.function_overview_per_group;
-import static pantools.Pantools.compare_sequences;
-import static pantools.Pantools.compare_genomes;
-import static pantools.Pantools.append_file_to_other_file;
+import static nl.wur.bif.pantools.pantools.Pantools.INPUT_FILE;
+import static nl.wur.bif.pantools.pantools.Pantools.THREADS;
+import static nl.wur.bif.pantools.pantools.Pantools.VERSION;
+import static nl.wur.bif.pantools.pantools.Pantools.MAX_TRANSACTION_SIZE;
+import static nl.wur.bif.pantools.pantools.Pantools.core_threshold;
+import static nl.wur.bif.pantools.pantools.Pantools.unique_threshold;
+import static nl.wur.bif.pantools.pantools.Pantools.create_directory_in_DB;
+import static nl.wur.bif.pantools.pantools.Pantools.check_r_libraries_environment;
+import static nl.wur.bif.pantools.pantools.Pantools.longest_transcripts;
+import static nl.wur.bif.pantools.pantools.Pantools.signalp_label;
+import static nl.wur.bif.pantools.pantools.Pantools.skip_seq_array;
+import static nl.wur.bif.pantools.pantools.Pantools.BLOSUM;
+import static nl.wur.bif.pantools.pangenome.FunctionalAnnotations.function_overview_per_group;
+import static nl.wur.bif.pantools.pantools.Pantools.compare_sequences;
+import static nl.wur.bif.pantools.pantools.Pantools.compare_genomes;
+import static nl.wur.bif.pantools.pantools.Pantools.append_file_to_other_file;
/**
* @author Eef Jonkheer, Bioinformatics group, Wageningen University, the Netherlands.
@@ -170,19 +168,14 @@ public class Classification {
public static String[] regions_to_search;
private static int total_loops = 1000;
- final private String[] COLOR_CODES = new String[]{"#fabebe","#bfef45","#42d4f4","#ffd8b1","#aaffc3","#fffac8","#e6beff","#469990","#e6194B","#f58231", "#ffe119",
- "#3cb44b","#4363d8","#911eb4","#a9a9a9","#800000","#808000","#9A6324","#000075","#f032e6"};
- final private String[] COLOR_NAMES = new String[]{"Pink","Lime","Cyan","Apricot","Mint","Beige","Lavender","Teal","Red","Orange","Yellow","Green","Blue","Purple","Grey","Maroon",
- "Olive", "Brown", "Navy","Magenta"};
private static BlockingQueue<Integer> loop_numbers;
private static String percentage_counter;
private static AtomicLong atomic_counter1;
private static AtomicLong atomic_counter2;
private static AtomicLong distinct_node_count;
private static AtomicLong total_node_count;
- public static ConcurrentHashMap<String, String> keys = new ConcurrentHashMap<>();
boolean compressed_kmers;
- private static ArrayList<String> all_sequences;
+ private static ArrayList<String> selected_sequences;
ConcurrentHashMap<Integer, ArrayList<Integer>> sequences_per_genome;
public static boolean phased = false;
@@ -221,7 +214,7 @@ public class Classification {
tx.success(); // transaction successful, commit changes
} catch (NotFoundException nfe) {
System.out.println("\nUnable to start the database\n");
- return;
+ System.exit(1);
}
graphDb.shutdown();
if (PROTEOME) { // when run against a panproteome
@@ -238,16 +231,22 @@ public class Classification {
ProteomeLayer proLayer = new ProteomeLayer();
StringBuilder output_builder = new StringBuilder();
- StringBuilder genome_csv_builder = create_header_for_csv_statistics_file();
+
System.out.print("\rGathering pangenome statistics");
+ ArrayList<String> phenotype_properties = retrieve_phenotypes_properties();
+ HashMap<String, String> all_phenotypes_map = retrieve_phenotypes_for_metrics();
+ StringBuilder genome_csv_builder = create_header_for_genome_metrics_csv_file(phenotype_properties);
+ HashMap<Integer, ArrayList<String>> annotations_map = get_all_annotation_identifiers();
try (Transaction tx = graphDb.beginTx()) { // start database transaction
- HashMap<Integer, ArrayList<String>> annotations_map = get_all_annotation_identifiers();
annotation_identifiers = get_annotation_identifiers(false, false); // do not print, USE the -af input file
longest_transcripts = true;
proLayer.find_longest_transcript_per_gene(false, 0);
+ tx.success();
+ }
+ try (Transaction tx = graphDb.beginTx()) { // start database transaction
HashMap<Integer, StringBuilder> busco_map = create_busco_summary();
get_and_append_pangenome_statistics(output_builder);
- int[] annotations_array = count_nodes_per_genome(annotation_label, false);
+ int[] annotations_array = count_nodes_per_genome(annotation_label);
HashMap<String, int[]> function_count_map = count_functions_for_metrics();
int[][] hmgroup_counts = count_homology_groups_per_genome();
int[] degenerate_nodes = gather_all_degenerate_nodes(true);
@@ -264,7 +263,7 @@ public class Classification {
continue;
}
- if (PROTEOME) {
+ if (PROTEOME) { // panproteome
write_panproteome_anno_stats_to_builders(output_builder, genome_csv_builder, i, hmgroup_counts);
} else { // pangenome
ArrayList<String> annotation_ids = annotations_map.get(i);
@@ -273,7 +272,7 @@ public class Classification {
calculate_gc_content(i, (long) sequence_values[0], nuc_count_per_seq);
long[] nucleotide_count = nuc_count_per_seq.get(i +""); // total number of A T C G in genome
write_genome_statistics_to_builders(output_builder, genome_csv_builder, i, sequence_values, nucleotide_count, annotation_ids,
- annotations_array, degenerate_nodes[(i*2)-2]);
+ annotations_array, degenerate_nodes[(i*2)-2], phenotype_properties, all_phenotypes_map);
if (busco_map.containsKey(i)) {
String busco_scores = busco_map.get(i).toString();
@@ -309,63 +308,29 @@ public class Classification {
/**
* Count nodes with a specific label. The nodes must have the 'genome' property
- * @param label1
- * @param print
- * @return
- */
- public static int[] count_nodes_per_genome(Label label1, boolean print) {
- int[] total_array = new int[total_genomes];
- for (int i=1; i<= total_genomes; i++) {
- if (skip_array[i-1]) {
- continue;
- }
- int total_nodes = 0;
- if (print) {
- System.out.print("\rCounting " + label1 + " nodes: Genome " + i);
- }
- ResourceIterator<Node> all_nodes = graphDb.findNodes(label1, "genome", i);
- while (all_nodes.hasNext()) {
- all_nodes.next();
- total_nodes ++;
- }
- total_array[i-1] = total_nodes;
- }
- return total_array;
- }
-
- /**
- * Count nodes with a specific label. The nodes must have the 'genome' property
- * @param label1
- * @param property
- * @param print
- * @param property_value
- * @return
+ * @param node_label a node label
+ * @return count per genome
*/
- public static int[] count_nodes_with_property_per_genome(Label label1, String property, boolean property_value, boolean print) {
- int[] total_array = new int[total_genomes];
- int total_nodes = 0;
- ResourceIterator<Node> all_nodes = graphDb.findNodes(label1, property, property_value);
- while (all_nodes.hasNext()) {
- Node node = all_nodes.next();
+ public static int[] count_nodes_per_genome(Label node_label) {
+ int[] count_array = new int[total_genomes];
+ ResourceIterator<Node> nodes = graphDb.findNodes(node_label);
+ while (nodes.hasNext()) {
+ Node node = nodes.next();
int genome_nr = (int) node.getProperty("genome");
- total_array[genome_nr-1] = total_nodes;
- if (total_nodes % 10000 == 0) {
- System.out.print("\rCounting " + label1 + " " + property + " nodes");
- }
- total_nodes ++;
+ count_array[genome_nr-1] ++;
}
- return total_array;
+ return count_array;
}
-
+
/**
* Write the already retrieved values for functional annotations to the two output builders
- * @param output_builder
- * @param csv_builder
- * @param genome_nr
- * @param mrnas_with_functions
+ * @param output_builder genome.txt file
+ * @param csv_builder genome.csv file
+ * @param genome_nr a genome number
+ * @param function_count_map
*/
public void write_function_stats_to_builders(StringBuilder output_builder, StringBuilder csv_builder, int genome_nr,
- HashMap<String, int[]> mrnas_with_functions) {
+ HashMap<String, int[]> function_count_map) {
int[] total_go = new int[1];
int[] total_pfam = new int[1];
@@ -376,30 +341,30 @@ public class Classification {
int[] total_cog = new int[1];
int[] mrna_with_function = new int[1];
- if (mrnas_with_functions.containsKey(genome_nr + "#GO")) {
- total_go = mrnas_with_functions.get(genome_nr + "#GO"); // [function nodes, connect to mRNAs, total relations]
+ if (function_count_map.containsKey(genome_nr + "#GO")) {
+ total_go = function_count_map.get(genome_nr + "#GO"); // [function nodes, connect to mRNAs, total relations]
}
- if (mrnas_with_functions.containsKey(genome_nr + "#pfam")) {
- total_pfam = mrnas_with_functions.get(genome_nr + "#pfam");
+ if (function_count_map.containsKey(genome_nr + "#pfam")) {
+ total_pfam = function_count_map.get(genome_nr + "#pfam");
}
- if (mrnas_with_functions.containsKey(genome_nr + "#interpro")) {
- total_interpro = mrnas_with_functions.get(genome_nr + "#interpro");
+ if (function_count_map.containsKey(genome_nr + "#interpro")) {
+ total_interpro = function_count_map.get(genome_nr + "#interpro");
}
- if (mrnas_with_functions.containsKey(genome_nr + "#tigrfam")) {
- total_tigrfam = mrnas_with_functions.get(genome_nr + "#tigrfam");
+ if (function_count_map.containsKey(genome_nr + "#tigrfam")) {
+ total_tigrfam = function_count_map.get(genome_nr + "#tigrfam");
}
- if (mrnas_with_functions.containsKey(genome_nr + "#phobius_signalp")) {
- phobius_signalp = mrnas_with_functions.get(genome_nr + "#phobius_signalp"); // [ phobius signalpeptide, phobius tranmembrane, signalp]
+ if (function_count_map.containsKey(genome_nr + "#phobius_signalp")) {
+ phobius_signalp =function_count_map.get(genome_nr + "#phobius_signalp"); // [ phobius signalpeptide, phobius tranmembrane, signalp]
}
- if (mrnas_with_functions.containsKey(genome_nr + "#bgc")) {
- total_bgc = mrnas_with_functions.get(genome_nr + "#bgc");
+ if (function_count_map.containsKey(genome_nr + "#bgc")) {
+ total_bgc = function_count_map.get(genome_nr + "#bgc");
}
- if (mrnas_with_functions.containsKey(genome_nr + "#cog")) {
- total_cog = mrnas_with_functions.get(genome_nr + "#cog");
+ if (function_count_map.containsKey(genome_nr + "#cog")) {
+ total_cog = function_count_map.get(genome_nr + "#cog");
}
- if (mrnas_with_functions.containsKey(genome_nr + "#all")) {
- mrna_with_function = mrnas_with_functions.get(genome_nr + "#all");
+ if (function_count_map.containsKey(genome_nr + "#all")) {
+ mrna_with_function = function_count_map.get(genome_nr + "#all");
}
String prot_or_mrna = " mRNA's", prot_or_mrna_cap = "mRNA's";
@@ -481,14 +446,19 @@ public class Classification {
* @param annotation_id_list
* @param annotations_array
* @param degenerate_nodes
+ * @param phenotype_properties
+ * @param all_phenotypes_map
*/
public void write_genome_statistics_to_builders(StringBuilder output_builder, StringBuilder csv_builder, int genome_nr,
- double[] sequence_values, long[] nucleotide_count, ArrayList<String> annotation_id_list, int[] annotations_array, int degenerate_nodes) {
+ double[] sequence_values, long[] nucleotide_count, ArrayList<String> annotation_id_list, int[] annotations_array, int degenerate_nodes,
+ ArrayList<String> phenotype_properties, HashMap<String, String> all_phenotypes_map) {
- String phenotype = "";
- if (PHENOTYPE != null) {
- phenotype = geno_pheno_map.get(genome_nr) + ",";
+ String pheno_properties_string = "";
+ for (String phenotype : phenotype_properties) {
+ String pheno_value = all_phenotypes_map.get(genome_nr + "#" + phenotype);
+ pheno_properties_string += pheno_value + ",";
}
+
String genome_name = get_genome_name(genome_nr);
long[] n_statistics = calculate_N_statistics(genome_nr, (long) sequence_values[0]); // N25, L25, N50, L50, L75, N75, L90, N90, L95, N95,
String gc_genome = get_percentage_str(nucleotide_count[2] + nucleotide_count[3],
@@ -531,7 +501,7 @@ public class Classification {
.append("\n\nN25: ").append(n25)
.append("\nL25: ").append(n_statistics[1])
.append("\nN50: ").append(n50)
- .append("\nN50: ").append(n_statistics[3])
+ .append("\nL50: ").append(n_statistics[3])
.append("\nN75: ").append(n75)
.append("\nL75: ").append(n_statistics[5])
.append("\nN90: ").append(n90)
@@ -544,7 +514,8 @@ public class Classification {
if (annotation_id.endsWith("_0")) {
annotation_id = "No annotation";
}
- csv_builder.append(genome_nr).append(",").append(phenotype)
+ csv_builder.append(genome_nr).append(",")
+ .append(pheno_properties_string) // already includes a comma
.append(annotation_id).append(",")
.append(genome_size_str).append(",")
.append(sequence_values[1]).append(",")
@@ -622,8 +593,7 @@ public class Classification {
int[] phobius_signalp_array = function_count_map.get("pangenome#phobius_signalp");
int[] total_COG = function_count_map.get("pangenome#cog");
- //long total_bcg = get_BGCs_per_sequence(mrnas_with_annotations);
- long total_functions = total_go[0] + phobius_signalp_array[0] + phobius_signalp_array[1] + phobius_signalp_array[2]
+ long total_functions = total_go[0] + phobius_signalp_array[0] + phobius_signalp_array[1] + phobius_signalp_array[2]
+ total_pfam[0] + total_interpro[0] + total_tigrfam[2] + total_COG[0];
long total_annotations = sum_of_array(annotations_array);
int total_genes = (int) count_nodes(gene_label);
@@ -684,18 +654,21 @@ public class Classification {
}
}
+
/**
* Prepare the first row for metrics_per_genome.csv
+ * @param phenotype_properties
* @return StringBuilder
*/
- public StringBuilder create_header_for_csv_statistics_file() {
+ public StringBuilder create_header_for_genome_metrics_csv_file(ArrayList<String> phenotype_properties) {
StringBuilder genome_csv_builder;
- String phenotype = "";
- if (PHENOTYPE != null) {
- phenotype = "Phenotype,";
- }
+ StringBuilder pheno_properties_string = new StringBuilder();
+ for (String phenotype : phenotype_properties) {
+ pheno_properties_string.append("Phenotype ").append(phenotype).append(",");
+ }
+
if (PROTEOME) {
- genome_csv_builder = new StringBuilder("Genome," + phenotype + "Protein count,Total protein length,Shortest protein,Longest protein,Average protein length,"
+ genome_csv_builder = new StringBuilder("Genome," + pheno_properties_string + "Protein count,Total protein length,Shortest protein,Longest protein,Average protein length,"
+ "Median protein length,Homology groups,"
+ "Singletons,mRNA with functional annotation,Phobius signal peptides,Phobius transmembrane domains,SignalP signal peptides,"
+ "Biosynthetic gene clusters,COG proteins,"
@@ -704,7 +677,7 @@ public class Classification {
+ "InterPro domains,Total InterPro connections,Total mRNAs with InterPro,"
+ "TIGRFAMS,Total TIGRFAM connections,Total mRNAs with TIGRFAMS\n");
} else {
- genome_csv_builder = new StringBuilder("Genome," + phenotype + "Annotation,Genome size,Sequences,Annotations,Degenerate k-mer nodes,"
+ genome_csv_builder = new StringBuilder("Genome," + pheno_properties_string + "Annotation,Genome size,Sequences,Annotations,Degenerate k-mer nodes,"
+ "Shortest sequence,Longest sequence,Average sequence length,GC content (%),Percentage of genome unknown,"
+ "Total A,Total T,Total C, Total G, Total N, Total other letters,N25,L25,N50,L50,N75,L75,N90,L90,N95,L95,"
+ "Gene count,Total gene length,Shortest gene,Longest gene,Average gene length,Median gene length,Genome covered by genes (%),Gene density per Mb,"
@@ -725,84 +698,49 @@ public class Classification {
//add phenotype, hashmap met string en string[]array
return genome_csv_builder;
}
-
- /**
- * Add BGC nodes to hashmap. No geneclusters can be present in a panproteome
- * @param mrnas_with_annotations
- * @return
- */
- public long get_BGCs_per_sequence(HashMap<String, Integer> mrnas_with_annotations) {
- ResourceIterator<Node> bgc_nodes = graphDb.findNodes(bgc_label);
- long total_bgcs = 0;
- while (bgc_nodes.hasNext()) {
- Node bgc_node = bgc_nodes.next();
- int[] address = (int[]) bgc_node.getProperty("address");
- total_bgcs ++;
- try_incr_hashmap(mrnas_with_annotations, address[0] + "#bgc", 1);
- try_incr_hashmap(mrnas_with_annotations, address[1] + "_" + address[1] + "#bgc", 1);
- }
- return total_bgcs;
- }
/**
* Add BGC nodes to hashmap. No geneclusters can be present in a panproteome
- * @param mrnas_with_functions
+ * @param mrnas_with_function_set key is genome nr or sequence id. value are mrna's with at least one function
+ * @param function_count_map key is genome or sequence id + type of function or "ALL"
*/
- public void get_BGCs_per_sequence2(HashMap<String, int[]> mrnas_with_functions) {
+ public void get_BGCs_per_sequence(HashMap<String, HashSet<Node>> mrnas_with_function_set, HashMap<String, int[]> function_count_map) {
+ if (PROTEOME) { // no geneclusters can be added to panproteome
+ return;
+ }
HashMap<String, Integer> mrnas_with_annotations = new HashMap<>();
ResourceIterator<Node> bgc_nodes = graphDb.findNodes(bgc_label);
- long total_bgcs = 0;
while (bgc_nodes.hasNext()) {
Node bgc_node = bgc_nodes.next();
- int[] address = (int[]) bgc_node.getProperty("address");
- total_bgcs ++;
+ int[] address = (int[]) bgc_node.getProperty("address_genes");
try_incr_hashmap(mrnas_with_annotations, address[0] +"", 1);
- try_incr_hashmap(mrnas_with_annotations, address[1] + "_" + address[1], 1);
+ try_incr_hashmap(mrnas_with_annotations, address[0] + "_" + address[1], 1);
+ Iterable<Relationship> rels = bgc_node.getRelationships();
+ for (Relationship rel : rels) {
+ Node gene_node = rel.getStartNode();
+ Iterable<Relationship> gene_rels = gene_node.getRelationships(RelTypes.codes_for);
+ for (Relationship gene_rel : gene_rels) {
+ Node mrna_node = gene_rel.getEndNode();
+ if (!mrna_node.hasProperty("longest_transcript")) {
+ continue; // will only be counted if they are part of the longest transcript
+ }
+ try_incr_hashset_hashmap(mrnas_with_function_set,address[0] +"", mrna_node);
+ try_incr_hashset_hashmap(mrnas_with_function_set,address[0] + "_" + address[1], mrna_node);
+ }
+ }
}
for (String key : mrnas_with_annotations.keySet()) {
- int[] total_bgc = new int[]{ mrnas_with_annotations.get(key)};
- mrnas_with_functions.put(key, total_bgc);
- }
-
- }
-
- /**
- * Add COG nodes to hashmap. COG nodes are mRNA nodes
- * @param mrnas_with_annotations
- * @return
- */
- public long count_cog_nodes_per_sequence(HashMap<String, Integer> mrnas_with_annotations) {
- int cog_counter = 0;
- int total_cog = (int) count_nodes(COG_label);
- ResourceIterator<Node> mrna_nodes = graphDb.findNodes(COG_label);
- while (mrna_nodes.hasNext()) {
- cog_counter ++;
- if (cog_counter < 100 || cog_counter % 101 == 0 || cog_counter == total_cog) {
- System.out.print("\rGathering genes with assigned COG functions: " + cog_counter + "/" + total_cog + " ");
- }
- Node mrna_node = mrna_nodes.next();
- int genome_nr, sequence_nr = 0;
- if (PROTEOME) {
- genome_nr = (int) mrna_node.getProperty("genome");
- } else {
- int[] address = (int[]) mrna_node.getProperty("address");
- genome_nr = address[0];
- sequence_nr = address[1];
- }
- cog_counter ++;
- try_incr_hashmap(mrnas_with_annotations, genome_nr + "#cog", 1);
- try_incr_hashmap(mrnas_with_annotations, genome_nr + "_" + sequence_nr + "#cog", 1);
+ int[] total_bgc = new int[]{mrnas_with_annotations.get(key)};
+ function_count_map.put(key + "#bgc", total_bgc);
}
- System.out.print("\r "); // spaces are intentional
- return cog_counter;
}
/**
- * Add COG nodes to hashmap. COG nodes are mRNA nodes
- * @param mrnas_with_function_set
- * @param mrnas_with_functions
+ * Add COG mRNA counts to 'function_count_map' hashmap. COG nodes are mRNA nodes
+ * @param mrnas_with_function_set key is genome nr or sequence id. value are mrna's with at least one function
+ * @param function_count_map
*/
- public void count_cog_for_metrics(HashMap<String, HashSet<Node>> mrnas_with_function_set, HashMap<String, int[]> mrnas_with_functions) {
+ public void count_cog_for_metrics(HashMap<String, HashSet<Node>> mrnas_with_function_set, HashMap<String, int[]> function_count_map) {
HashMap<String, Integer> cog_count = new HashMap<>();
int cog_counter = 0;
int total_cog = (int) count_nodes(COG_label);
@@ -814,7 +752,7 @@ public class Classification {
Node mrna_node = mrna_nodes.next();
if (!PROTEOME && !mrna_node.hasProperty("longest_transcript")) {
continue; // will only be counted if they are part of the longest transcript
- }
+ }
int genome_nr, sequence_nr = 0;
if (PROTEOME) {
genome_nr = (int) mrna_node.getProperty("genome");
@@ -822,8 +760,8 @@ public class Classification {
int[] address = (int[]) mrna_node.getProperty("address");
genome_nr = address[0];
sequence_nr = address[1];
- }
-
+ }
+
if (PROTEOME && skip_array[genome_nr-1]) { // skip the mRNAs from annotations that are not currently selected.
continue;
} else if (!PROTEOME) {
@@ -832,7 +770,7 @@ public class Classification {
continue;
}
}
-
+
cog_counter ++;
try_incr_hashmap(cog_count, genome_nr +"", 1);
try_incr_hashset_hashmap(mrnas_with_function_set, genome_nr +"", mrna_node);
@@ -841,19 +779,19 @@ public class Classification {
try_incr_hashset_hashmap(mrnas_with_function_set, genome_nr + "_" + sequence_nr, mrna_node);
}
}
- System.out.print("\r "); // spaces are intentional
+ System.out.print("\r "); // spaces are intentional
for (String key : cog_count.keySet()) {
int nr_of_mrnas = cog_count.get(key);
int[] nr_of_mrnas_array = new int[]{nr_of_mrnas};
- mrnas_with_functions.put(key + "#cog", nr_of_mrnas_array);
+ function_count_map.put(key + "#cog", nr_of_mrnas_array);
}
- mrnas_with_functions.put("pangenome#cog", new int[]{cog_counter});
+ function_count_map.put("pangenome#cog", new int[]{cog_counter});
}
/**
* Find name of genome input file (includes .fasta extension)
- * @param genome_nr
- * @return
+ * @param genome_nr a genome number
+ * @return file name of the genome
*/
public static String get_genome_name(int genome_nr) {
if (PROTEOME) { // No 'genome' nodes are available in panproteome
@@ -864,59 +802,10 @@ public class Classification {
String[] path_array = path.split("/");
return path_array[path_array.length-1];
}
-
- /**
- * Create input file for CIRCOS plots
- * Use the forward or reverse orientation of a gene to construct blocks genes with the same orientation
- * @param genome_nr
- * @param number_of_sequences
- */
- public static void calculate_gene_orientation_blocks(int genome_nr, long number_of_sequences) {
- boolean disabled = true;
- if (disabled) { // this function is currently disabled. do not remove
- return;
- }
- create_directory_in_DB("metrics/orientation/");
- boolean exists = check_if_file_exists(WORKING_DIRECTORY + "metrics/orientation/" + genome_nr);
- if (exists || PROTEOME) { // Files were already created on a previous run, or proteomes don't have position information
- return;
- }
-
- StringBuilder output_builder = new StringBuilder();
- for (int i=1; i <= number_of_sequences; i++) {
- ResourceIterator<Node> gene_nodes = graphDb.findNodes(gene_label, "genome", genome_nr, "sequence", i);
- String current_strand = "";
- int start_pos = 0, end_pos = 0;
- while (gene_nodes.hasNext()) {
- Node gene_node = gene_nodes.next();
- int[] address = (int[]) gene_node.getProperty("address");
- String strand = (String) gene_node.getProperty("strand");
- if (strand.equals("+")) {
- strand = "black";
- } else {
- strand = "red";
- }
- if (strand.equals(current_strand)) {
- end_pos = address[3];
- } else {
- if (start_pos > 0) {
- output_builder.append("chr").append(i).append(" ").append(start_pos).append(" ").append(end_pos).append(" color=").append(current_strand).append("\n");
- }
- start_pos = address[2];
- end_pos = address[3];
- }
- current_strand = strand;
- }
- if (start_pos > 0) {
- output_builder.append("chr").append(i).append(" ").append(start_pos).append(" ").append(end_pos).append(" color=").append(current_strand).append("\n");
- }
- }
- write_SB_to_file_in_DB(output_builder, "metrics/orientation/" + genome_nr);
- }
-
+
/**
- * Retrieve BUSCO scores for metrics function
- * @return
+ * Retrieve BUSCO scores for 'metrics' command line function
+ * @return hashmap. key is genome number. value is a stringbuilder with overview of busco scores
*/
public static HashMap<Integer, StringBuilder> create_busco_summary() {
HashMap<Integer, StringBuilder> busco_map = new HashMap<>();
@@ -925,7 +814,7 @@ public class Classification {
Node busco_node = busco_nodes.next();
int genome_nr = (int) busco_node.getProperty("genome");
Iterable<String> properties = busco_node.getPropertyKeys();
- for (String property : properties) {
+ for (String property : properties) { // take all properties from busco node
if (property.equals("genome")) {
continue;
}
@@ -942,10 +831,10 @@ public class Classification {
* @param annotation_counts_per_seq
* @param seq_length_map
* @param nuc_count_per_seq
- * @param mrnas_with_functions
+ * @param function_count_map
*/
public static void create_per_sequence_statistics_csv(HashMap<String, double[]> annotation_counts_per_seq, HashMap<String, Long> seq_length_map,
- HashMap<String, long[]> nuc_count_per_seq, HashMap<String, int[]> mrnas_with_functions) {
+ HashMap<String, long[]> nuc_count_per_seq, HashMap<String, int[]> function_count_map) {
System.out.println("");
if (PROTEOME) {
@@ -999,57 +888,57 @@ public class Classification {
add_anno_stats_to_seq_builder(sequence_id, "rRNA", sequence_length, csv_builder, annotation_counts_per_seq);
add_anno_stats_to_seq_builder(sequence_id, "repeat", sequence_length, csv_builder, annotation_counts_per_seq);
- if (mrnas_with_functions.containsKey(sequence_id + "#all")) {
- int[] nodes_with_function = mrnas_with_functions.get(sequence_id + "#all");
+ if (function_count_map.containsKey(sequence_id + "#all")) {
+ int[] nodes_with_function = function_count_map.get(sequence_id + "#all");
csv_builder.append(nodes_with_function[0]).append(",");
} else {
csv_builder.append(",");
}
- if (mrnas_with_functions.containsKey(sequence_id + "#bgc")) {
- int[] bgc_nodes = mrnas_with_functions.get(sequence_id + "#bgc");
+ if (function_count_map.containsKey(sequence_id + "#bgc")) {
+ int[] bgc_nodes = function_count_map.get(sequence_id + "#bgc");
csv_builder.append(bgc_nodes[0]).append(",");
} else {
csv_builder.append(",");
}
- if (mrnas_with_functions.containsKey(sequence_id + "#cog")) {
- int[] cog_count = mrnas_with_functions.get(sequence_id + "#cog");
+ if (function_count_map.containsKey(sequence_id + "#cog")) {
+ int[] cog_count = function_count_map.get(sequence_id + "#cog");
csv_builder.append(cog_count[0]).append(",");
} else {
csv_builder.append(",");
}
- if (mrnas_with_functions.containsKey(sequence_id + "#phobius_signalp")) { // [ phobius signalpeptide, phobius tranmembrane, signalp]
- int[] phobius_counts = mrnas_with_functions.get(sequence_id + "#phobius_signalp");
+ if (function_count_map.containsKey(sequence_id + "#phobius_signalp")) { // [ phobius signalpeptide, phobius tranmembrane, signalp]
+ int[] phobius_counts = function_count_map.get(sequence_id + "#phobius_signalp");
csv_builder.append(phobius_counts[0]).append(",").append(phobius_counts[1]).append(",").append(phobius_counts[2]).append(",");
} else {
csv_builder.append(",,,");
}
- if (mrnas_with_functions.containsKey(sequence_id + "#GO")) {
- int[] go_counts = mrnas_with_functions.get(sequence_id + "#GO"); // [nr of function nodes, nr of mrnas with function, total relationships]
+ if (function_count_map.containsKey(sequence_id + "#GO")) {
+ int[] go_counts = function_count_map.get(sequence_id + "#GO"); // [nr of function nodes, nr of mrnas with function, total relationships]
csv_builder.append(go_counts[1]).append(",").append(go_counts[2]).append(",").append(go_counts[0]).append(",");
} else {
csv_builder.append(",,,");
}
- if (mrnas_with_functions.containsKey(sequence_id + "#pfam")) {
- int[] pfam_counts = mrnas_with_functions.get(sequence_id + "#pfam");
+ if (function_count_map.containsKey(sequence_id + "#pfam")) {
+ int[] pfam_counts = function_count_map.get(sequence_id + "#pfam");
csv_builder.append(pfam_counts[1]).append(",").append(pfam_counts[2]).append(",").append(pfam_counts[0]).append(",");
} else {
csv_builder.append(",,,");
}
- if (mrnas_with_functions.containsKey(sequence_id + "#interpro")) {
- int[] ipro_counts = mrnas_with_functions.get(sequence_id + "#interpro");
+ if (function_count_map.containsKey(sequence_id + "#interpro")) {
+ int[] ipro_counts = function_count_map.get(sequence_id + "#interpro");
csv_builder.append(ipro_counts[1]).append(",").append(ipro_counts[2]).append(",").append(ipro_counts[0]).append(",");
} else {
csv_builder.append(",,,");
}
- if (mrnas_with_functions.containsKey(sequence_id + "#tigrfam")) {
- int[] tigrfam_counts = mrnas_with_functions.get(sequence_id + "#tigrfam");
+ if (function_count_map.containsKey(sequence_id + "#tigrfam")) {
+ int[] tigrfam_counts = function_count_map.get(sequence_id + "#tigrfam");
csv_builder.append(tigrfam_counts[1]).append(",").append(tigrfam_counts[2]).append(",").append(tigrfam_counts[0]).append(",");
} else {
csv_builder.append(",,,");
@@ -1211,8 +1100,8 @@ public class Classification {
}
}
try_incr_AL_hashmap(lengths_per_seq, address[0] + "_" + address[1], feature_length);
-
}
+
for (String key : lengths_per_seq.keySet()) {
ArrayList<Integer> lengths = lengths_per_seq.get(key);
int total_count = counts_per_seq.get(key);
@@ -1313,6 +1202,7 @@ public class Classification {
HashSet<String> groups_with_function = new HashSet<>();
HashMap<String, HashSet<String>> groups_with_function_or_name = new HashMap<>();
StringBuilder node_builder = new StringBuilder("#To visualize in the Neo4j browser:\n MATCH (n) where id(n) in [ PLACE,NODES,HERE ] return n\n\n");
+ create_directory_in_DB("group_info");
delete_file_in_DB("group_info/group_functional_annotations.txt");
if (Mode.contains("K-MER")) { // user (that does not look at code) cannot see this mode
@@ -1332,7 +1222,7 @@ public class Classification {
tx.success(); // transaction successful, commit changes
} catch (NotFoundException nfe) {
System.out.println("Unable to start the database\n");
- return;
+ System.exit(1);
}
if (Mode.contains("K-MER")) { // user (that does not look at code) cannot see this mode
indexSc = new IndexScanner(indexDb);
@@ -1345,8 +1235,8 @@ public class Classification {
}
ArrayList<String> name_list = new ArrayList<>(Arrays.asList(SELECTED_NAME.split("\\s*,\\s*")));
+
try (Transaction tx = graphDb.beginTx()) { // start database transaction
- prepare_msa_sequences(hm_node_list, true);
function_overview_per_group(hm_node_list, WORKING_DIRECTORY + "group_info/");
int counter = 0;
for (Node hm_node : hm_node_list) {
@@ -1454,10 +1344,7 @@ public class Classification {
*
*/
public void print_output_files_for_grp_info() {
- System.out.print("\n\nSequences written to:\n "
- + WORKING_DIRECTORY + "/alignments/grouping_v" + grouping_version + "/groups/\n"
- +"\n"
- + " Output written to:\n "
+ System.out.print("\n\nOutput written to:\n "
+ WORKING_DIRECTORY + "group_info/group_info.txt\n "
+ WORKING_DIRECTORY + "group_info/functions_per_group_and_mrna.csv\n "
+ WORKING_DIRECTORY + "group_info/functions_counts_per_group.csv\n ");
@@ -1579,37 +1466,6 @@ public class Classification {
return output.toString().replaceFirst(".$", "").replaceFirst(".$", ""); // remove last character (2x)
}
- /**
- *
- * @param size_list
- * @return
- */
- public static String determine_frequency_list_str(ArrayList<String> size_list) {
- ArrayList<String> distinct_size_list = remove_duplicates_from_AL_str(size_list);
- StringBuilder output = new StringBuilder();
- for (String size : distinct_size_list) {
- int occurrences = Collections.frequency(size_list, size);
- output.append(size).append("(").append(occurrences).append("x), ");
- }
- return output.toString().replaceFirst(".$", "").replaceFirst(".$", "");
- }
-
- /**
- *
- * @param array
- * @return
- */
- public static String determine_genome_freq_absence_presence_freq(long[] array) {
- StringBuilder output = new StringBuilder();
- for (int i = 0; i < array.length; ++i) {
- if (array[i] > 0) {
- output.append((i+1)).append("(").append(array[i]).append("x),");
- }
- }
- String output_str = output.toString().replaceFirst(".$", "");
- return output_str;
- }
-
/**
*
* @param array
@@ -1626,18 +1482,6 @@ public class Classification {
return output_str;
}
- /**
- *
- * @param str
- * @return
- */
- public static String capitalize_first_letter(String str) {
- if(str == null) {
- return str;
- }
- return str.substring(0, 1).toUpperCase() + str.substring(1);
- }
-
/**
*
* @param all_nodes_set
@@ -1662,65 +1506,7 @@ public class Classification {
}
node_builder_temp.append(fasta_header).append(node_str.replaceFirst(".$","")).append("\n\n"); // remove last character
}
-
- /**
- *
- * @param sequence
- * @return
- */
- public static kmer string_to_kmer(String sequence) {
- kmer current_kmer = new kmer(K_SIZE, indexSc.get_pre_len());
- kmer tmp_kmer = new kmer(current_kmer);
- tmp_kmer.reset();
- for (int i = 0; i < sequence.length(); i++) {
- char c = sequence.charAt(i);
- int code = 0;
- switch (c) {
- case 'T':
- code = 3;
- break;
- case 'C':
- code = 1;
- break;
- case 'G':
- code = 2;
- break;
- default:
- break;
- }
- tmp_kmer.next_fwd_kmer(code);
- }
- return tmp_kmer;
- }
-
- /**
- Create the reverse complement of a sequence
- * @param sequence
- * @return
- */
- public static String get_rv_complement(String sequence) {
- String rev_complement = "";
- char[] char_array = sequence.toCharArray();
- for (int counter = char_array.length - 1; counter >= 0; counter--) {
- char nuc = char_array[counter];
- switch (nuc) {
- case 'A':
- rev_complement += "T";
- break;
- case 'T':
- rev_complement += "A";
- break;
- case 'C':
- rev_complement += "G";
- break;
- default: // G
- rev_complement += "C";
- break;
- }
- }
- return rev_complement;
- }
-
+
/**
* VERSION is set by --version argument
*/
@@ -1757,24 +1543,29 @@ public class Classification {
/**
* Create 'busco' nodes if these don't exists yet
*/
- public static void check_if_busco_info_node_already_exists() {
- ResourceIterator<Node> nodes = graphDb.findNodes(busco_label);
- boolean exists = false;
- if (nodes.hasNext()) {
- exists = true;
- }
-
- if (!exists) {
- for(int i=1; i<= total_genomes; i++) {
- Node busco_node = graphDb.createNode(busco_label);
- busco_node.setProperty("genome", i);
- Node genome_node = graphDb.findNode(genome_label, "number", i);
- if (!PROTEOME) { // panproteome does not have genome nodes
- busco_node.createRelationshipTo(genome_node, RelTypes.has_busco);
- }
- }
- }
- }
+ public static void create_busco_node_if_missing() {
+ ResourceIterator<Node> busco_nodes = graphDb.findNodes(busco_label);
+ if (busco_nodes.hasNext()) {
+ return; // busco nodes already exist
+ }
+
+ // busco nodes do not exist, create one for every genome (even when skipped)
+ if (PROTEOME) { // panproteome does not have genome nodes
+ for(int i=1; i <= total_genomes; i++) {
+ Node busco_node = graphDb.createNode(busco_label);
+ busco_node.setProperty("genome", i);
+ }
+ } else {
+ ResourceIterator<Node> genome_nodes = graphDb.findNodes(genome_label);
+ while (genome_nodes.hasNext()) {
+ Node genome_node = genome_nodes.next();
+ int genome_nr = (int) genome_node.getProperty("number");
+ Node busco_node = graphDb.createNode(busco_label);
+ busco_node.setProperty("genome", genome_nr);
+ genome_node.createRelationshipTo(busco_node, RelTypes.has_busco);
+ }
+ }
+ }
/**
* Checks if the required input file is available depending on the --mode argument that was included
@@ -1836,7 +1627,7 @@ public class Classification {
tx.success(); // transaction successful, commit changes
} catch (NotFoundException nfe) {
System.out.println("Unable to start the pangenome database\n");
- return;
+ System.exit(1);
}
String[] anno_path_array = INPUT_FILE.split("/");
@@ -1920,9 +1711,9 @@ public class Classification {
+ WORKING_DIRECTORY + "busco/" + db_name + "/" + output_name + "/busco_scores.txt\n");
}
- /*
- Gather all mrna nodes of a genome and put this in a hashmap. key is the protein_id, value is the node.
- Interpro/eggnog/BLAST2GO output must have the protein_id or the information cannot be added.
+ /**
+ * Gather all mrna nodes of a genome and put this in a hashmap. key is the protein_id, value is the node.
+ * Interpro/eggnog/BLAST2GO output must have the protein_id or the information cannot be added.
*/
public static HashMap<String, Node> create_mrna_node_map_for_genome(int genome_nr, String info, String mrna_or_gene) {
HashMap<String, Node> mrna_node_map = new HashMap<>();
@@ -1985,8 +1776,8 @@ public class Classification {
* @param busco_mode
* @param busco_scores_map
*/
- public static void update_busco_nodes(String db_name, String busco_mode, HashMap<Integer, String> busco_scores_map) {
- check_if_busco_info_node_already_exists();
+ public static void update_busco_nodes(String db_name, String busco_mode, HashMap<Integer, String> busco_scores_map) {
+ create_busco_node_if_missing();
ResourceIterator<Node> busco_nodes = graphDb.findNodes(busco_label);
System.out.println("\nUpdating BUSCO nodes");
while (busco_nodes.hasNext()) {
@@ -2561,6 +2352,7 @@ public class Classification {
System.out.println("Unable to start the pangenome database\n");
System.exit(1);
}
+
if (PHENOTYPE == null) {
System.out.println("\rPlease provide a CSV formatted input file with '--phenotype'\n");
return;
@@ -2571,6 +2363,10 @@ public class Classification {
HashMap<Integer, String> column_value_map = new HashMap<>();
HashSet<String> existing_phenotypes = new HashSet<>();
ArrayList<String> already_present = new ArrayList<>();
+
+
+ HashMap<String, ArrayList<Object>> valuesPerPhenotype = new HashMap<>();
+
try (Transaction tx = graphDb.beginTx()) { // start database transaction
check_existing_phenotype_nodes(existing_phenotypes, pheno_node_array);
try (BufferedReader in = new BufferedReader(new FileReader(PHENOTYPE))) {
@@ -2590,7 +2386,7 @@ public class Classification {
}
Node pheno_node = create_pheno_node_if_not_present(line_array, pheno_node_array);
for (int l = 0; l < header_length; l++) {
- set_property_to_pheno_node(line_array, l, column_value_map, already_present, pheno_node);
+ set_property_to_pheno_node(line_array, l, column_value_map, already_present, pheno_node, valuesPerPhenotype);
}
}
line_count ++;
@@ -2602,10 +2398,84 @@ public class Classification {
}
tx.success(); // transaction successful, commit changes
}
+ binPhenotypeValues(valuesPerPhenotype);
phenotype_overview();
graphDb.shutdown();
}
-
+
+ public void binPhenotypeValues(HashMap<String, ArrayList<Object>> valuesPerPhenotype) {
+ HashMap<Integer, Node> genomePhenoNode = new HashMap<>();
+ boolean first = true;
+ try (Transaction tx = graphDb.beginTx()) { // start database transaction
+ ResourceIterator<Node> phenoNodes = graphDb.findNodes(phenotype_label);
+ while (phenoNodes.hasNext()) {
+ Node phenoNode = phenoNodes.next();
+ int genomeNr = (int) phenoNode.getProperty("genome");
+ genomePhenoNode.put(genomeNr, phenoNode);
+ }
+
+ //System.out.println("kijk");
+ int categories = 3;
+ for (String key : valuesPerPhenotype.keySet()) {
+ ArrayList<Object> valuesList = valuesPerPhenotype.get(key);
+ double lowest = 999999999;
+ double highest = -999999999;
+ for (Object value : valuesList) {
+ try {
+ double d = Double.parseDouble((String) value);
+ if (d > highest) {
+ highest = d;
+ }
+ if (d < lowest) {
+ lowest = d;
+ }
+ } catch (Exception ex) {
+ //System.out.println("no " + value);
+ }
+ }
+ if (lowest == 999999999) {
+ continue;
+ }
+ //System.out.println(key + " " + valuesPerPhenotype.get(key));
+ double difference = highest - lowest;
+ double step = difference / categories;
+ //System.out.println(lowest + "-" + highest + " = " + difference + " en " + step);
+ ArrayList<Double> levels = new ArrayList<>();
+ levels.add(lowest);
+ for (int i = 1; i < categories; i++) {
+ //System.out.println((i *step) + lowest); // + " " + (i *step) + " " + lowest);
+ levels.add((i * step) + lowest);
+ }
+ levels.add(highest);
+ if (first) {
+ System.out.println("\nPhenotypes with numerical values recognized! " +
+ "If the values do not exactly match they are not considered to be different phenotypes.\n" +
+ "Extra phenotypes are generated that for equally sized bins on " + categories + " levels.\n");
+ first = false;
+ }
+ System.out.println(key + " -> " + key + "_binned. Level ranges " + levels);
+ int genomeNr = 0;
+ for (Object value : valuesList) {
+ genomeNr++;
+ Node phenoNode = genomePhenoNode.get(genomeNr);
+ phenoNode.removeProperty(key + "_binned");
+ try {
+ double d = Double.parseDouble((String) value);
+ for (int i = 0; i < levels.size() - 1; i++) {
+ if (d >= levels.get(i) && d <= levels.get(i + 1)) {
+ phenoNode.setProperty(key + "_binned", "bin " + (i + 1));
+ break;
+ }
+ }
+ } catch (Exception ex) {
+ phenoNode.setProperty(key + "_binned", "Unknown");
+ }
+ }
+ }
+ tx.success();
+ }
+ }
+
/**
* Removes additional spaces around commas or semicolons
* @param line
@@ -2684,10 +2554,10 @@ public class Classification {
pheno_node = graphDb.createNode(phenotype_label);
pheno_node.setProperty("genome", genome_nr);
}
- if (PROTEOME == false && !APPEND) {
+ if (!PROTEOME && !APPEND) {
Node genome_node = graphDb.findNode(genome_label, "number", genome_nr);
if (genome_node == null) {
- System.out.println("No genome has been found with number: " + genome_nr + "\n");
+ System.out.println("\rNo genome has been found with number: " + genome_nr + "\n");
System.exit(1);
}
genome_node.createRelationshipTo(pheno_node, RelTypes.has_phenotype);
@@ -2697,14 +2567,19 @@ public class Classification {
/**
* Convert the string to the correct type of variable and store in a phenotype node.
+ *
+ * Most of this function can be replaced with "instanceof"
+ *
* @param line_array
* @param column
* @param column_value_map
* @param already_present
* @param pheno_node
*/
- public static void set_property_to_pheno_node(String[] line_array, int column, HashMap<Integer, String> column_value_map,
- ArrayList<String> already_present, Node pheno_node) {
+ public static String set_property_to_pheno_node(String[] line_array, int column, HashMap<Integer, String> column_value_map,
+ ArrayList<String> already_present, Node pheno_node, HashMap<String, ArrayList<Object>> valuesPerPhenotype) {
+
+ String type = "string";
String value;
try {
value = line_array[column];
@@ -2719,7 +2594,7 @@ public class Classification {
if (column > 0) {
String current_pheno = column_value_map.get(column);
if (current_pheno == null) {
- return;
+ return "";
}
if (APPEND && already_present.contains(current_pheno)) { // remove the current value
pheno_node.removeProperty(current_pheno);
@@ -2730,30 +2605,35 @@ public class Classification {
} else if (value.equals("FALSE") || value.equals("False") || value.equals("false")) { // boolean
boolean add = false;
pheno_node.setProperty(current_pheno, add);
- } else if (test == true) {// integer or long
+ } else if (test) { // integer or long
if (value.length() < 10) {
int add = Integer.parseInt(value);
pheno_node.setProperty(current_pheno, add);
+ type = "integer";
} else {
long add = Long.parseLong(value);
pheno_node.setProperty(current_pheno, add);
+ type = "long";
}
- } else if (test1 == true) { // String
+ } else if (test1) { // String
value = value.replace(" ","_").replace("\"","").replace("(","").replace(")","");
pheno_node.setProperty(current_pheno, value);
} else if (value.equals("") || value.equals(" ")) { // no value
pheno_node.setProperty(current_pheno, "?");
- } else if (test2 == true) { // String
+ } else if (test2) { // String
value = value.replace(" ","_").replace("\"","").replace("(","").replace(")","");
pheno_node.setProperty(current_pheno, value);
- } else if (test3 == true) { // Double
+ } else if (test3) { // Double
double add = Double.parseDouble(value);
pheno_node.setProperty(current_pheno, add);
+ type = "double";
} else {
value = value.replace(" ","_").replace("\"","").replace("(","").replace(")","");
pheno_node.setProperty(current_pheno, value);
}
+ try_incr_AL_hashmap(valuesPerPhenotype, current_pheno, value);
}
+ return type;
}
/**
@@ -2815,7 +2695,7 @@ public class Classification {
tx.success(); // transaction successful, commit changes
} catch (NotFoundException nfe) {
System.out.println("\nUnable to start the database\n");
- return;
+ System.exit(1);
}
ArrayList<Node> sco_nodes = new ArrayList<>();
@@ -3080,7 +2960,7 @@ public class Classification {
counter ++;
Node hm_node = homology_groups.next();
hm_nodes.add(hm_node);
- if (counter % 100 == 0) {
+ if (counter % 10000 == 0) {
System.out.print("\rGathering homology groups: " + counter);
}
}
@@ -3615,53 +3495,57 @@ public class Classification {
write_string_to_file_in_DB("Total genomes with a phenotype: " + total_with_pheno + "\n\n" + output_builder.toString(),
"gene_classification/gene_classification_phenotype_overview.txt");
}
+
+//PLEASE DO NOT REMOVE
+// /**
+// * Create an rscript that can infer a gene tree of an homology group based on SNP distances
+// */
+// public void rscript_for_group_var_inf_site_distances() {
+// String path1 = WD_full_path + "alignments/grouping_v" + grouping_version +"/";
+// String path2 = WD_full_path + "alignments/grouping_v" + grouping_version + "/?????/output/var_inf_positions/";
+// String R_LIB = check_r_libraries_environment();
+// StringBuilder rscript = new StringBuilder();
+// rscript.append("#! /usr/bin/env RScript\n\n")
+// .append("\n")
+// .append("# Infer a gene tree based on SNP distances\n")
+// .append("# Use one of the following files\n")
+// .append("# ").append(path2).append("informative_nuc_trimmed_distance.csv\n")
+// .append("# ").append(path2).append("informative_nuc_distance.csv\n")
+// .append("# ").append(path2).append("variable_nuc_distance.csv\n")
+// .append("# ").append(path2).append("variable_nuc_trimmed_distance.csv\n")
+// .append("\n")
+// .append("# ").append(path2).append("informative_prot_trimmed_distance.csv\n")
+// .append("# ").append(path2).append("informative_prot_distance.csv\n")
+// .append("# ").append(path2).append("variable_prot_trimmed_distance.csv\n")
+// .append("# ").append(path2).append("variable_prot_distance.csv\n")
+// .append("\n")
+// .append("#Assuming the R libraries were installed via Conda, the next line can be ignored. If not, use it to manually install the required package\n")
+// .append("#install.packages(\"ape\", \"").append(R_LIB).append("\", \"https://cran.us.r-project.org\")\n")
+// .append("library(ape)\n\n")
+// .append("input = read.csv(\"INSERT FILE HERE\", sep=\",\", header = TRUE)\n")
+// .append("df2 = subset(input, select = -c(Genomes))\n")
+// .append("df.dist2 = as.matrix(df2, labels=TRUE)\n")
+// .append("colnames(df.dist2) <- rownames(df.dist2) <- input[['Genomes']]\n")
+// .append("NJ_tree <- nj(df.dist2)\n")
+// .append("\n")
+// .append("pdf(NULL)\n")
+// .append("plot(NJ_tree, main = \"Neighbor Joining\")\n")
+// .append("write.tree(NJ_tree, tree.names = TRUE, file=\"").append(path1).append("snp_distance.tree\")\n")
+// .append("cat(\"\\nGene tree written to: ").append(path1).append("snp_distance.tree\\n\\n\")");
+// write_SB_to_file_full_path(rscript, path1 + "snp_distance_tree.R");
+// }
/**
- * Create an rscript that can infer a gene tree of an homology group based on SNP distances
+ *
+ * @param shared_snps_map
+ * @param output_path
+ * @param total_sites
+ * @param informative
+ * @param nuc_or_prot_short
+ * @param genome_order_file
*/
- public void rscript_for_group_var_inf_site_distances() {
- String path1 = WD_full_path + "alignments/grouping_v" + grouping_version +"/";
- String path2 = WD_full_path + "alignments/grouping_v" + grouping_version + "/groups/?????/output/var_inf_positions/";
- String R_LIB = check_r_libraries_environment();
- StringBuilder rscript = new StringBuilder();
- rscript.append("#! /usr/bin/env RScript\n\n")
- .append("# Use one of the following files\n")
- .append("# ").append(path2).append("informative_nuc_trimmed_distance.csv\n")
- .append("# ").append(path2).append("informative_nuc_distance.csv\n")
- .append("# ").append(path2).append("variable_nuc_trimmed_distance.csv\n")
- .append("# ").append(path2).append("variable_nuc_trimmed_distance.csv\n")
- .append("\n")
- .append("# ").append(path2).append("informative_prot_trimmed_distance.csv\n")
- .append("# ").append(path2).append("informative_prot_distance.csv\n")
- .append("# ").append(path2).append("variable_prot_trimmed_distance.csv\n")
- .append("# ").append(path2).append("variable_prot_distance.csv\n")
- .append("\n")
- .append("#Assuming the R libraries were installed via Conda, the next line can be ignored. If not, use it to manually install the required package\n")
- .append("#install.packages(\"ape\", \"").append(R_LIB).append("\", \"https://cran.us.r-project.org\")\n")
- .append("library(ape)\n\n")
- .append("input = read.csv(\"INSERT FILE HERE\", sep=\",\", header = TRUE)\n")
- .append("df2 = subset(input, select = -c(Genomes))\n")
- .append("df.dist2 = as.matrix(df2, labels=TRUE)\n")
- .append("colnames(df.dist2) <- rownames(df.dist2) <- input[['Genomes']]\n")
- .append("NJ_tree <- nj(df.dist2)\n")
- .append("pdf(NULL)\n")
- .append("plot(NJ_tree, main = \"Neighbor Joining\")\n")
- .append("write.tree(NJ_tree, tree.names = TRUE, file=\"").append(path1).append("snp_distance.tree\")\n")
- .append("cat(\"\\nGene tree written to: ").append(path1).append("snp_distance.tree\\n\\n\")");
- write_SB_to_file_full_path(rscript, path1 + "snp_distance_tree.R");
- }
-
- /**
- *
- * @param shared_snps_map
- * @param output_path
- * @param total_sites
- * @param informative
- * @param nuc_or_prot_short
- * @param genome_order_file
- */
- public void create_shared_site_matrices(HashMap<String, Integer> shared_snps_map, String output_path, int total_sites, String informative,
- String nuc_or_prot_short, String genome_order_file) {
+ public static void create_shared_site_matrices(HashMap<String, Integer> shared_snps_map, String output_path, int total_sites, String informative,
+ String nuc_or_prot_short, String genome_order_file) {
if (total_sites == 0) {
return;
@@ -3851,7 +3735,7 @@ public class Classification {
try (Transaction tx = graphDb.beginTx()) { // start database transaction
StringBuilder sco_builder = new StringBuilder();
StringBuilder mlsa_builder = new StringBuilder("# Suitable genes for 'MLSA_find_genes'\n");
- StringBuilder mlsa_builder2 = new StringBuilder("# Possible gene names when using --mode1\n");
+ StringBuilder mlsa_builder2 = new StringBuilder("\n# Possible gene names when including --mode extensive\n");
if (sco_nodes.isEmpty()) {
sco_builder.append("No single copy orthologs were found");
}
@@ -4321,7 +4205,8 @@ public class Classification {
}
/**
- * Key is annotation identifers and also stores the genome number as key. The genome number matches the annotation id from annotation_identifiers
+ * Key is annotation identifers and also stores the genome number as key.
+ * The genome number matches the annotation id from annotation_identifiers
* On a panproteome the returned hashmap is empty as no annotation nodes are present
* @return
*/
@@ -4414,21 +4299,24 @@ public class Classification {
}
/**
- *
+ * Get all the annotation identifiers of annotation nodes
* @return
*/
public static HashMap<Integer, ArrayList<String>> get_all_annotation_identifiers() {
- ResourceIterator<Node> annotation_nodes = graphDb.findNodes(annotation_label);
HashMap<Integer, ArrayList<String>> annotations_map = new HashMap<>();
- while (annotation_nodes.hasNext()) {
- Node annotation_node = annotation_nodes.next();
- String identifier = (String) annotation_node.getProperty("identifier");
- String[] id_array = identifier.split("_");
- int genome_nr = Integer.parseInt(id_array[0]);
- if (skip_array[genome_nr-1]) {
- continue;
+ try (Transaction tx = graphDb.beginTx()) { // start database transaction
+ ResourceIterator<Node> annotation_nodes = graphDb.findNodes(annotation_label);
+ while (annotation_nodes.hasNext()) {
+ Node annotation_node = annotation_nodes.next();
+ String identifier = (String) annotation_node.getProperty("identifier");
+ String[] id_array = identifier.split("_");
+ int genome_nr = Integer.parseInt(id_array[0]);
+ if (skip_array[genome_nr - 1]) {
+ continue;
+ }
+ try_incr_AL_hashmap(annotations_map, genome_nr, identifier);
}
- try_incr_AL_hashmap(annotations_map, genome_nr, identifier);
+ tx.success();
}
return annotations_map;
}
@@ -4534,7 +4422,7 @@ public class Classification {
* Stop PanTools when less than ? genomes are included in the analysis
* @param genome_threshold minimum required genomes
*/
- public static void stop_with_less_than_X_genomes(int genome_threshold) {
+ public static void stopWithLessThanGenomes(int genome_threshold) {
if (adj_total_genomes < genome_threshold) {
System.out.println("The pangenome should contain at least " + genome_threshold + " genomes for this analysis. \n");
System.exit(1);
@@ -4542,6 +4430,8 @@ public class Classification {
}
/**
+ * Known as pangenome_structure_gene() in manual
+ *
* Requires
* -dp
*
@@ -4566,11 +4456,11 @@ public class Classification {
tx.success(); // transaction successful, commit changes
} catch (NotFoundException nfe) {
System.out.println("Unable to start the database\n");
- return;
+ System.exit(1);
}
try (Transaction tx = graphDb.beginTx()) { // start database transaction
- stop_with_less_than_X_genomes(3);
+ stopWithLessThanGenomes(3);
ResourceIterator<Node> hm_nodes = graphDb.findNodes(homology_group_label);
int total_hmgroups = (int) count_nodes(homology_group_label);
all_core = new int[total_loops][adj_total_genomes-1];
@@ -4768,11 +4658,11 @@ public class Classification {
tx.success(); // transaction successful, commit changes
} catch (NotFoundException nfe) {
System.out.println("Unable to start the database");
- return;
+ System.exit(1);
}
create_skip_arrays(false, true); // create skip array if -skip/-ref is provided by user
- stop_with_less_than_X_genomes(3);
+ stopWithLessThanGenomes(3);
long one_procent = (num_nodes-1)/100;
long procent_threshold = one_procent;
int total_procent = 0;
@@ -4821,16 +4711,7 @@ public class Classification {
System.out.println("\nOutput written to:\n "
+ WORKING_DIRECTORY + "pangenome_size/kmer/pangenome_size_kmer.txt\n "
+ WORKING_DIRECTORY + "pangenome_size/kmer/pangenome_growth.R\n");
- }
- /**
- * Take a value from a random position and return it
- * @param list
- * @return
- */
- public static String getRandomElement(ArrayList<String> list) {
- Random rand = new Random();
- return list.get(rand.nextInt(list.size()));
- }
+ }
/**
*
@@ -5360,7 +5241,7 @@ public class Classification {
}
ArrayList<Integer> genome_list = create_genome_list();
ArrayList<Integer> new_genome_list = new ArrayList<>();
- if (i+1 % 10 == 0) {
+ if ((i+1) % 10 == 0) {
printProgressBar(total_loops, (i+1), "loops", false);
}
while (!genome_list.isEmpty()) {
@@ -5663,19 +5544,19 @@ public class Classification {
if (label1.equals(selected_label)) {
found_label = true;
break;
- }
+ }
present_labels += label1 + ",";
- }
+ }
if (!found_label) {
System.out.println("\rProvided label '" + selected_label + "' does not match with anything in the pangenome\n"
- + "Present labels: " + present_labels.replaceFirst(".$","") + "\n");
+ + "Present labels: " + present_labels.replaceFirst(".$", "") + "\n");
System.exit(1);
}
return selected_label;
}
/**
- * Not allowed to remove anything from 'build_pangenome' and annotation nodes
+ * Not allowed to remove anything from 'build_pangenome' and 'annotation' nodes
*/
public void remove_nodes() {
System.out.println("\nRemoving nodes from the pangenome\n");
@@ -5685,12 +5566,13 @@ public class Classification {
create_skip_arrays(false, true); // create skip array if --skip/-ref is provided by user
tx.success(); // transaction successful, commit changes
} catch (NotFoundException nee ) {
- System.out.println("Unable to start the pangenome\n");
- return;
+ System.out.println("Unable to start the database\n");
+ System.exit(1);
}
if (NODE_ID == null && SELECTED_LABEL == null) {
- System.out.println("\rProvide either --node or --label");
+ System.out.println("\rProvide either --node or --label\n");
+ System.exit(1);
} else if (NODE_ID != null && SELECTED_LABEL == null) { // --node argument was used
remove_selected_nodes();
} else if (SELECTED_LABEL != null && NODE_ID == null) { // --label argument was used
@@ -6085,7 +5967,7 @@ public class Classification {
tx.success(); // transaction successful, commit changes
} catch (NotFoundException nfe) {
System.out.println("Unable to start the database\n");
- return;
+ System.exit(1);
}
if (Mode.equals("0")) {
@@ -6118,17 +6000,20 @@ public class Classification {
} else {
retrieve_phenotypes(); // Creates and fills geno_pheno_map and phenotype_map when a phenotype was provided by the user
}
- retrieve_selected_sequences();
- if (compare_sequences && !compare_genomes) {
- System.out.println("\r--sequence is selected. Number of sequences in analysis: " + all_sequences.size());
- } else if(compare_sequences && compare_genomes) {
+ retrieve_selected_sequences();
+
+ if (compare_sequences && compare_genomes) {
System.out.println("\rBoth the--sequence and --genome arguments were included. Please select one");
- return;
- } else { // both are false
- //System.out.println("\rNo --sequence argument was included. Only comparing genomes");
+ System.exit(1);
+ } else if (compare_sequences) {
+ System.out.println("\r--sequence is selected. Number of sequences in analysis: " + selected_sequences.size());
+ if (selected_sequences.size() > 50000) {
+ System.out.println("Can only analyze up to 50.000 sequences. Please make a selection using the --skip argument");
+ System.exit(1);
+ }
}
- core_unique_thresholds_for_classification("k-mers"); // set core_threshold and unique_threshold
+ core_unique_thresholds_for_classification("k-mers"); // set 'core_threshold' and 'unique_threshold' variables
if (!Mode.contains("OCCURANCE")) {
kmer_occur_map = null;
freq_per_genome = null;
@@ -6152,7 +6037,7 @@ public class Classification {
}
HashMap<String, long[]> degen_node_per_seq_genome = gather_degen_nodes_per_seq();
- long[] node_count = gather_kmer_information2(kmer_occur_map, kmer_freq_map, pheno_kmer_map, freq_per_genome, kmer_class_count);
+ long[] node_count = gather_kmer_information(kmer_occur_map, kmer_freq_map, pheno_kmer_map, freq_per_genome, kmer_class_count);
try (Transaction tx = graphDb.beginTx()) { // start database transaction
System.out.print("\nGenerating output files");
create_kmer_occurance_output(kmer_occur_map, highest_frequency, freq_per_genome);
@@ -6180,10 +6065,10 @@ public class Classification {
return;
}
int write_every_sequence = 1000;
- if (all_sequences.size() > 999) {
+ if (selected_sequences.size() > 999) {
write_every_sequence = 500;
}
- if (all_sequences.size() >= 10000) { // 10k genomes
+ if (selected_sequences.size() >= 10000) { // 10k genomes
write_every_sequence = 100;
}
@@ -6202,8 +6087,8 @@ public class Classification {
StringBuilder genome_j_distinct_shared_builder = new StringBuilder();
StringBuilder header_builder2 = new StringBuilder("Sequences,");
- for (int i = 0; i < all_sequences.size(); i ++) {
- String seq_id = all_sequences.get(i);
+ for (int i = 0; i < selected_sequences.size(); i ++) {
+ String seq_id = selected_sequences.get(i);
String add = "", add2 = "";
if (phased) {
add = " (" + subgenome_nr_map.get(seq_id + "_phasing_id") + ")";
@@ -6212,15 +6097,15 @@ public class Classification {
//header_builder.append(seq_id).append(add).append(",");
header_builder2.append(seq_id).append(add2);
- if (i != all_sequences.size()-1) {
+ if (i != selected_sequences.size()-1) {
header_builder2.append(",");
}
}
String header2 = header_builder2.toString() + "\n";
long pairwise_counter = 0;
int sequence_counter = 0;
- for (int i = 0; i < all_sequences.size(); i ++) {
- String seq_id = all_sequences.get(i);
+ for (int i = 0; i < selected_sequences.size(); i ++) {
+ String seq_id = selected_sequences.get(i);
String add = "", add2 = "";
if (phased) {
add = " (" + subgenome_nr_map.get(seq_id + "_phasing_id") + ")";
@@ -6242,7 +6127,7 @@ public class Classification {
if (sequence_counter % 100 == 0 ) {
System.out.print("\rWriting shared k-mers between sequences " + (i+1));
}
- for (int j = 0; j < all_sequences.size(); j ++) {
+ for (int j = 0; j < selected_sequences.size(); j ++) {
pairwise_counter ++;
int all_shared_kmers = seq_all_shared_kmers[i][j];
int all_total_kmers = seq_all_total_kmers[i][j];
@@ -6272,7 +6157,7 @@ public class Classification {
distinct_kmer_shared.append(distinct_shared_kmers);
kmer_count_all_total.append(all_total_kmers);
kmer_count_distinct_total.append(distinct_total_kmers);
- if (j != all_sequences.size()-1) {
+ if (j != selected_sequences.size()-1) {
mash_distance.append(",");
distinct_kmer_distance.append(",");
all_kmer_distance.append(",");
@@ -6372,7 +6257,7 @@ public class Classification {
*
* @return
*/
- public long[] gather_kmer_information2(ConcurrentHashMap<Long, ArrayList<Node>> kmer_occur_map,
+ public long[] gather_kmer_information(ConcurrentHashMap<Long, ArrayList<Node>> kmer_occur_map,
ConcurrentHashMap<Integer, long[]> kmer_freq_map, ConcurrentHashMap<String, ArrayList<Node>> pheno_kmer_map,
ConcurrentHashMap<Integer, HashMap<Long,Long>> freq_per_genome,
long[] kmer_class_count) {
@@ -6386,11 +6271,13 @@ public class Classification {
string_queue = new LinkedBlockingQueue<>();
node_queue = new LinkedBlockingQueue<>();
hashmap_ni_queue = new LinkedBlockingQueue<>();
-
- seq_distinct_total_kmers = new int[all_sequences.size()][all_sequences.size()];
- seq_distinct_shared_kmers = new int [all_sequences.size()][all_sequences.size()];
- seq_all_total_kmers = new int[all_sequences.size()][all_sequences.size()];
- seq_all_shared_kmers = new int [all_sequences.size()][all_sequences.size()];
+
+ if (compare_sequences) {
+ seq_distinct_total_kmers = new int[selected_sequences.size()][selected_sequences.size()];
+ seq_distinct_shared_kmers = new int[selected_sequences.size()][selected_sequences.size()];
+ seq_all_total_kmers = new int[selected_sequences.size()][selected_sequences.size()];
+ seq_all_shared_kmers = new int[selected_sequences.size()][selected_sequences.size()];
+ }
genome_distinct_total_kmers = new int[total_genomes][total_genomes];
genome_distinct_shared_kmers = new int[total_genomes][total_genomes];
@@ -6423,11 +6310,11 @@ public class Classification {
*/
public class count_kmers_per_sequence_class implements Runnable {
int thread_nr;
- int[][] distinct_shared_array = new int[all_sequences.size()][all_sequences.size()];
- int[][] distinct_total_array = new int[all_sequences.size()][all_sequences.size()];
- int[][] all_shared_array = new int[all_sequences.size()][all_sequences.size()];
- int[][] all_total_array = new int[all_sequences.size()][all_sequences.size()];
- int[] freq_array = new int[all_sequences.size()];
+ int[][] distinct_shared_array = new int[selected_sequences.size()][selected_sequences.size()];
+ int[][] distinct_total_array = new int[selected_sequences.size()][selected_sequences.size()];
+ int[][] all_shared_array = new int[selected_sequences.size()][selected_sequences.size()];
+ int[][] all_total_array = new int[selected_sequences.size()][selected_sequences.size()];
+ int[] freq_array = new int[selected_sequences.size()];
public count_kmers_per_sequence_class(int thread_nr) {
this.thread_nr = thread_nr;
@@ -6514,12 +6401,12 @@ public class Classification {
*/
public long determine_appropriate_nr_for_printing() {
- long nr_for_printing = 1000;
- if (all_sequences.size() >= 1000) {
- nr_for_printing = 100;
+ long nr_for_printing = 10000;
+ if (selected_sequences.size() >= 1000) {
+ nr_for_printing = 1000;
}
- if (all_sequences.size() >= 10000) {
- nr_for_printing = 10;
+ if (selected_sequences.size() >= 10000) {
+ nr_for_printing = 100;
}
return nr_for_printing;
}
@@ -6548,7 +6435,7 @@ public class Classification {
}
ArrayList<Integer> missing_positions = new ArrayList<>();
- for (int i = 0; i < all_sequences.size(); i++) {
+ for (int i = 0; i < selected_sequences.size(); i++) {
if (!positions.contains(i)) {
missing_positions.add(i);
}
@@ -6659,7 +6546,7 @@ public class Classification {
public static HashMap<String, Integer> create_seq_nr_map() {
HashMap<String, Integer> seq_nr_map = new HashMap<>();
int counter = 0;
- for (String seq_id : all_sequences) {
+ for (String seq_id : selected_sequences) {
seq_nr_map.put(seq_id, counter);
counter ++;
}
@@ -7033,6 +6920,7 @@ public class Classification {
boolean frequencies_present = false;
int genomes_present = 0;
for (int i = 1; i <= total_genomes; i++) { // i is a genome number
+ //nuc_node.removeProperty("freq_per_seq_genome_" + i);
if (nuc_node.hasProperty("freq_per_seq_genome_" + i)) {
frequencies_present = true; // if one is present, the frequency was added for all genomes
if (skip_array[i-1]) {
@@ -7558,10 +7446,10 @@ public class Classification {
try {
ExecutorService es = Executors.newFixedThreadPool(THREADS);
if (compare_sequences) {
- es.execute(new find_degen_nodes_sequence(degen_node_count));
- //for (int i = 1; i <= THREADS-1; i++) {
- es.execute(new add_freq_per_seq(1));
- //}
+ es.execute(new find_degen_nodes_sequence(degen_node_count));
+ //for (int i = 1; i <= THREADS-1; i++) {
+ es.execute(new add_freq_per_seq(1));
+ //}
} else { // genome level, only 1 thread
es.execute(new find_degen_nodes_genome(degen_node_count));
}
@@ -7764,7 +7652,7 @@ public class Classification {
Genome nodes are not always retrieved in the correct order (1,2,3)
*/
public void retrieve_selected_sequences() {
- all_sequences = new ArrayList<>();
+ selected_sequences = new ArrayList<>();
HashMap<Integer, Integer> sequence_count_per_genome = new HashMap<>();
sequences_per_genome = new ConcurrentHashMap<>();
int counter = 0;
@@ -7786,267 +7674,15 @@ public class Classification {
for (int i = 1; i <= total_genomes; i++) { // i is genome nr
int num_sequences = sequence_count_per_genome.get(i);
for (int j = 1; j <= num_sequences; ++j) {
+ try_incr_AL_chashmap(sequences_per_genome, i, j); // holds all sequences per genome, use skip_seq_array to through list faster
if (skip_seq_array[i-1][j-1]) {
continue;
}
- all_sequences.add(i + "_" + j);
- try_incr_AL_chashmap(sequences_per_genome, i, j);
+ selected_sequences.add(i + "_" + j);
}
}
}
- /*
- OLD version. to be removed
- */
- /*
- public void kmer_classification() {
- long highest_frequency = 0;
- System.out.println("\nCalculating CORE, UNIQUE, and ACCESSORY k-mer sequences\n");
- report_number_of_threads(true, false); //do not print how many threads were given, only when more than 1 thread was selected
- THREADS = 1; // do not remove
- check_if_graphDb_is_available(); // starts up the graph database if needed
- try (Transaction tx = graphDb.beginTx()) { // start database transaction
- Node pangenome_node = graphDb.findNodes(pangenome_label).next();
- stop_if_panproteome(pangenome_node, "kmer_classification"); // stops the progam when run on a panproteome, retrieves K_size & total_genomes
- if (pangenome_node.hasProperty("k_mer_highest_frequency")) {
- highest_frequency = (long) pangenome_node.getProperty("k_mer_highest_frequency"); // this is set by 'build_pangenome' in Pantools v3
- } else {
- highest_frequency = 52564L;
- System.out.println("Rebuilt the pangenome with a new pantools version");
- }
- KMinOne = K_SIZE -1;
- tx.success(); // transaction successful, commit changes
- } catch (NotFoundException nfe) {
- System.out.println("Unable to start the database\n");
- return;
- }
-
- if (Mode.equals("0")) {
- System.out.println("No --mode has been selected, counting all k-mers in compressed k-mers."
- + " K-mer size is " + K_SIZE + ", extracting " + KMinOne + " of every compressed k-mer");
- } else if (Mode.contains("COMPRESSED")) {
- System.out.println("--mode " + Mode + " is selected. Considering a compressed k-mer as a single k-mer.");
- } else if (Mode.contains("OCCURANCE")) {
-
- } else {
- System.out.println("--mode " + Mode + " is not recognized");
- return;
- }
-
- try (Transaction tx = graphDb.beginTx()) { // start database transaction
- create_skip_arrays(false, true); // create skip array if -skip/-ref is provided by user
- create_directory_in_DB("kmer_classification");
- if (PHENOTYPE == null) {
- System.out.println("\rNo --phenotype was provided. Unable to find phenotype shared/specific k-mers.");
- } else {
- retrieve_phenotypes(); // Creates and fills geno_pheno_map and phenotype_map when a phenotype was provided by the user
- }
- core_unique_thresholds_for_classification("k-mers"); // set core_threshold and unique_threshold
- ConcurrentHashMap<Integer, long[]> kmer_freq_map = new ConcurrentHashMap<>(); // key is genome number, long[] with total, core, access, unique, distinct total, distinct core, distinct access, distinct uni
- ConcurrentHashMap<String, ArrayList<Node>> pheno_kmer_map = new ConcurrentHashMap<>(); // key is phenotype + "#exclusive" or + "#specific" or "shared"
- ConcurrentHashMap<Integer, ArrayList<Node>> kmer_genome_presence = new ConcurrentHashMap<>(); // key is total number of genomes present
- ConcurrentHashMap<Integer, ArrayList<Node>> unique_kmers = new ConcurrentHashMap<>(); // key is genome number
- ConcurrentHashMap<String, long[]> shared_kmers_map = new ConcurrentHashMap<>(); // key is combination of genomes //total all, total distinct, shared all, shared distinct
-
- ConcurrentHashMap<Long, ArrayList<Node>> kmer_occur_map = new ConcurrentHashMap<>(); // key is frequency of kmer. This can become quite large, written to log every 250k keys
- ConcurrentHashMap<Integer, HashMap<Long, Long>> freq_per_genome = new ConcurrentHashMap<>(); // key is genome. second key is the frequency.
- if (!Mode.contains("OCCURANCE")) {
- kmer_occur_map = null;
- freq_per_genome = null;
- }
- long[] kmer_class_count = new long[3]; // distinct: core, accessory, unique
- for (int i=1; i <= total_genomes; i++) {
- if (freq_per_genome != null) {
- HashMap<Long, Long> empty_map = new HashMap<>();
- freq_per_genome.put(i, empty_map);
-
- }
- long[] empty_array = new long[8]; // total, core, access, unique, distinct total, distinct core, distinct access, distinct uni
- kmer_freq_map.put(i, empty_array);
- for (int j=1; j <= total_genomes; j++) {
- long[] empty_array2 = new long[8]; //total all, total distinct, shared all, shared distinct, inf total distinct, inf shared distinct
- if (j > i) {
- shared_kmers_map.put(i + "_" + j, empty_array2);
- } else {
- shared_kmers_map.put(j + "_" + i, empty_array2);
- }
- }
- }
- int[] degenerate_count = gather_all_degenerate_nodes(false);
- long[] node_count = gather_kmer_information(kmer_occur_map, kmer_genome_presence, kmer_freq_map, pheno_kmer_map,
- unique_kmers, freq_per_genome, shared_kmers_map, kmer_class_count);
- System.out.println("\nGenerating output files ");
- kmer_classi_pheno_overview(pheno_kmer_map);
- create_kmer_occurance_output(kmer_occur_map, highest_frequency, freq_per_genome);
- create_kmer_unique_output(unique_kmers);
- create_kmer_core_accessory_output(kmer_genome_presence);
- calculate_kmer_distances_btwn_genomes(shared_kmers_map, kmer_freq_map);
- create_kmer_classification_overview(kmer_freq_map, node_count, kmer_class_count, degenerate_count);
- create_kmer_distance_rscript(WD_full_path + "kmer_classification/");
- tx.success(); // transaction successful, commit changes
- }
- print_kmer_classification_output();
- graphDb.shutdown();
- }*/
-
- /**
- * Print which files are created depending on input arguments
- */
- /*
- public void print_kmer_classification_output() {
- String dir = WORKING_DIRECTORY + "kmer_classification/";
- String pheno_overview = "";
- if (PHENOTYPE != null) {
- pheno_overview = dir + "kmer_classification_phenotype_overview.txt\n ";
- }
- String highly_occuring_kmers = "";
- if (NODE_VALUE != null) {
- highly_occuring_kmers = dir + "highly_occuring_kmers.txt\n ";
- }
- String kmer_occurance = "";
- if (Mode.contains("OCCURANCE")) {
- highly_occuring_kmers = dir + "kmer_occurance.txt\n ";
- }
-
- System.out.print("\rOutput written to:\n "
- + dir + "kmer_classification_overview.txt\n "
- + pheno_overview
-
- + dir + "shared_kmers_between_genomes.csv\n "
- + kmer_occurance
- + highly_occuring_kmers
- + dir + "kmer_distance_tree.R (Select one of the four distances)\n\n"
- + "Files with 'nucleotide' node identifiers\n "
- + dir + "core_kmers.csv\n "
- + dir + "accessory_kmers.csv\n "
- + dir + "unique_kmers.csv\n ");
- if (PHENOTYPE != null) {
- System.out.println(dir + "phenotype_shared_kmers.csv\n "
- + dir + "phenotype_specific_kmers.csv\n "
- + dir + "phenotype_exclusive_kmers.csv\n ");
- } else {
- System.out.println("");
- }
- }*/
-
-
- /*
- public void calculate_kmer_distances_btwn_genomes(ConcurrentHashMap<String, long[]> shared_kmers_map, ConcurrentHashMap<Integer, long[]> kmer_freq_map) {
- StringBuilder header = new StringBuilder("Genomes,");
- StringBuilder all_kmers = new StringBuilder();
- StringBuilder distinct_kmers = new StringBuilder();
- StringBuilder inf_distinct_kmers = new StringBuilder();
- StringBuilder mash_distance = new StringBuilder();
-
- StringBuilder kmer_count_all_all = new StringBuilder();
- StringBuilder kmer_count_distinct_all = new StringBuilder();
- StringBuilder kmer_count_inf_distinct_all = new StringBuilder();
-
- StringBuilder kmer_count_all_sh = new StringBuilder(); // shared number of kmers
- StringBuilder kmer_count_distinct_sh = new StringBuilder(); // shared number of kmers
- StringBuilder kmer_count_inf_distinct_sh = new StringBuilder(); // shared number of kmers
- for (int i = 1; i <= total_genomes; i++) {
- if (skip_array[i-1]) {
- continue;
- }
- String phenotype = get_phenotype_for_genome(i, true);
- header.append(i).append(phenotype).append(",");
- all_kmers.append(i).append(phenotype).append(",");
- distinct_kmers.append(i).append(phenotype).append(",");
- inf_distinct_kmers.append(i).append(phenotype).append(",");
- mash_distance.append(i).append(phenotype).append(",");
-
- kmer_count_all_sh.append(i).append(phenotype).append(",");
- kmer_count_distinct_sh.append(i).append(phenotype).append(",");
- kmer_count_inf_distinct_sh.append(i).append(phenotype).append(",");
-
- kmer_count_all_all.append(i).append(phenotype).append(",");
- kmer_count_distinct_all.append(i).append(phenotype).append(",");
- kmer_count_inf_distinct_all.append(i).append(phenotype).append(",");
- for (int j = 1; j <= total_genomes; j++) {
- if (skip_array[j-1]) {
- continue;
- }
- String key = i + "_" + j;
- if (j < i) {
- key = j + "_" + i;
- }
-
- long[] shared = shared_kmers_map.get(key); //total all, total distinct, shared all, shared distinct, inf total distinct, inf shared
- double val1 = divide(shared[2], shared[0]); // all kmer distance
- double val2 = divide(shared[3], shared[1]); // distinct kmer distance
- double val3 = divide(shared[5], shared[4]); // informative distinct k-mer distance
- double mash_dist = -1.0/ K_SIZE * Math.log(val2); // 𝑑=−1/𝑘 * ln(𝑤/𝑡) where k is 17; w/t is the jaccard index.
- all_kmers.append((1-val1)).append(",");
- distinct_kmers.append((1-val2)).append(",");
- inf_distinct_kmers.append((1-val3)).append(",");
- mash_distance.append(Math.abs(mash_dist)).append(",");
-
- kmer_count_all_sh.append(shared[2]).append(",");
- kmer_count_distinct_sh.append(shared[3]).append(",");
- kmer_count_inf_distinct_sh.append(shared[5]).append(",");
-
- kmer_count_all_all.append(shared[0]).append(",");
- kmer_count_distinct_all.append(shared[1]).append(",");
- kmer_count_inf_distinct_all.append(shared[4]).append(",");
- }
- all_kmers.append("\n");
- distinct_kmers.append("\n");
- inf_distinct_kmers.append("\n");
- mash_distance.append("\n");
-
- kmer_count_all_sh.append("\n");
- kmer_count_distinct_sh.append("\n");
- kmer_count_inf_distinct_sh.append("\n");
-
- kmer_count_all_all.append("\n");
- kmer_count_distinct_all.append("\n");
- kmer_count_inf_distinct_all.append("\n");
-
- }
- String header_str = header.toString();
- header_str += "\n";
- write_string_to_file_in_DB(header_str + all_kmers.toString(), "kmer_classification/distance_all_kmers.csv");
- write_string_to_file_in_DB(header_str + distinct_kmers.toString(), "kmer_classification/distance_distinct_kmers.csv");
- write_string_to_file_in_DB(header_str + inf_distinct_kmers.toString(), "kmer_classification/distance_inf_distinct_kmers.csv");
- write_string_to_file_in_DB(header_str + mash_distance.toString(), "kmer_classification/mash_distance.csv");
- StringBuilder shared_kmer_output = new StringBuilder();
- shared_kmer_output.append("#TOTAL k-mers between two genomes\n")
- .append("#TOTAL distinct k-mers\n")
- .append(header_str).append(kmer_count_distinct_all.toString()).append("\n")
- .append("#TOTAL informative distinct k-mers\n")
- .append(header_str).append(kmer_count_inf_distinct_all.toString())
- .append("\n#TOTAL all k-mers\n")
- .append(header_str).append(kmer_count_all_all.toString()).append("\n")
- .append("#SHARED\n")
- .append("#SHARED distinct k-mers\n")
- .append(header_str).append(kmer_count_distinct_sh.toString()).append("\n")
- .append("#SHARED informative distinct k-mers\n")
- .append(header_str).append(kmer_count_inf_distinct_sh.toString()).append("\n")
- .append("#SHARED all k-mers\n")
- .append(header_str).append(kmer_count_all_sh.toString());
- write_SB_to_file_in_DB(shared_kmer_output, "kmer_classification/shared_kmers_between_genomes.csv");
- }*/
-
- /**
- * in the newest pantools version (3+), a frequency is changed from a long to an integer
- * @param nuc_node
- * @return
- */
- /*public int[] get_kmer_frequencies_property(Node nuc_node) {
- int[] freq_array;
- try {
- freq_array = (int[]) nuc_node.getProperty("frequencies");
- } catch (ClassCastException classcast) {
- long[] freq_array_long = (long[]) nuc_node.getProperty("frequencies");
- freq_array = new int [freq_array_long.length];
- for (int i=0; i < freq_array.length; i++) {
- freq_array[i] = (int) freq_array_long[i];
- }
- }
- return freq_array;
- }*/
-
/**
* in the newest pantools version, a frequency is changed from a long to an integer
* @param nuc_node
@@ -8108,7 +7744,7 @@ public class Classification {
* @param type
*/
public void core_unique_thresholds_for_classification(String type) {
- if (adj_total_genomes < 3) {
+ if (adj_total_genomes < 3 && !compare_sequences) {
System.out.println("\nThe pangenome should contain at least 3 genomes for this analysis\n");
System.exit(1);
}
@@ -8132,506 +7768,28 @@ public class Classification {
}
/**
- * Loop over all nucleotide nodes of the pangenome
- * @param kmer_occur_map
- * @param kmer_genome_presence
- * @param kmer_freq_map
- * @param pheno_kmer_map
- * @param unique_kmers
- * @param freq_per_genome
- * @param shared_kmers_map
- * @param kmer_class_count
- * @return
+ *
+ * @param kmer_occur_map
*/
- /*
- public long[] gather_kmer_information(ConcurrentHashMap<Long, ArrayList<Node>> kmer_occur_map, ConcurrentHashMap<Integer, ArrayList<Node>> kmer_genome_presence,
- ConcurrentHashMap<Integer, long[]> kmer_freq_map, ConcurrentHashMap<String, ArrayList<Node>> pheno_kmer_map,
- ConcurrentHashMap<Integer, ArrayList<Node>> unique_kmers, ConcurrentHashMap<Integer, HashMap<Long,Long>> freq_per_genome,
- ConcurrentHashMap<String, long[]> shared_kmers_map, long[] kmer_class_count) {
-
- long num_nodes = (long) graphDb.findNodes(pangenome_label).next().getProperty("num_nodes");
- distinct_node_count = new AtomicLong(0);
- total_node_count = new AtomicLong(0);
-
- loop_numbers = new LinkedBlockingQueue<>();
- if (THREADS > 1) {
- for (int n=0; n < total_genomes*100; n++) {
- loop_numbers.add(n);
- }
- } else {
- loop_numbers.add(0);
+ public synchronized void write_kmer_occurance_output(ConcurrentHashMap<Long, ArrayList<Node>> kmer_occur_map) {
+ TreeSet<Long> current_frequencies = new TreeSet<>();
+ for (Long frequency : kmer_occur_map.keySet()) {
+ current_frequencies.add(frequency);
}
-
- System.out.println("");
- atomic_counter1 = new AtomicLong(0);
- try {
- ExecutorService es = Executors.newFixedThreadPool(THREADS);
- for(int i = 1; i <= THREADS; i++) {
- es.execute(new multi_thread_find_shared_kmers(num_nodes, kmer_occur_map, kmer_genome_presence, kmer_freq_map, pheno_kmer_map,
- unique_kmers, freq_per_genome, shared_kmers_map, kmer_class_count, i));
+ StringBuilder output = new StringBuilder();
+ for (Long frequency : current_frequencies) {
+ output.append("#").append(frequency).append("#,");
+ ArrayList<Node> nodes = kmer_occur_map.get(frequency);
+ kmer_occur_map.remove(frequency);
+ for (Node nuc_node : nodes) {
+ output.append(nuc_node.getId()).append(",");
}
- System.out.print("");
- es.shutdown();
- es.awaitTermination(10, TimeUnit.DAYS);
- } catch (InterruptedException e) {
- // do nothing
- }
- long[] node_count_array = new long[2];
- node_count_array[0] = distinct_node_count.get(); // distinct
- node_count_array[1] = total_node_count.get(); // total
- return node_count_array;
- }
-
- public class multi_thread_find_shared_kmers implements Runnable {
- long num_nodes;
- ConcurrentHashMap<Long, ArrayList<Node>> kmer_occur_map;
- ConcurrentHashMap<Integer, ArrayList<Node>> kmer_genome_presence;
- ConcurrentHashMap<Integer, long[]> kmer_freq_map;
- ConcurrentHashMap<String, ArrayList<Node>> pheno_kmer_map;
- ConcurrentHashMap<Integer, ArrayList<Node>> unique_kmers;
- ConcurrentHashMap<Integer, HashMap<Long,Long>> freq_per_genome;
- ConcurrentHashMap<String, long[]> shared_kmers_map;
- long[] kmer_class_count;
- int thread_nr;
-
- public multi_thread_find_shared_kmers(long num_nodes, ConcurrentHashMap<Long, ArrayList<Node>> kmer_occur_map, ConcurrentHashMap<Integer,
- ArrayList<Node>> kmer_genome_presence, ConcurrentHashMap<Integer, long[]> kmer_freq_map, ConcurrentHashMap<String, ArrayList<Node>> pheno_kmer_map,
- ConcurrentHashMap<Integer, ArrayList<Node>> unique_kmers,
- ConcurrentHashMap<Integer, HashMap<Long,Long>> freq_per_genome, ConcurrentHashMap<String, long[]> shared_kmers_map,
- long[] kmer_class_count, int thread_nr) {
- this.num_nodes = num_nodes;
- this.kmer_occur_map = kmer_occur_map;
- this.kmer_genome_presence = kmer_genome_presence;
- this.kmer_freq_map = kmer_freq_map;
- this.pheno_kmer_map = pheno_kmer_map;
- this.unique_kmers = unique_kmers;
- this.freq_per_genome = freq_per_genome;
- this.shared_kmers_map = shared_kmers_map;
- this.kmer_class_count = kmer_class_count;
- this.thread_nr = thread_nr;
- }
-
- public void run() {
- long one_procent = (num_nodes+100)/100;
- try (Transaction tx = graphDb.beginTx()) {
- while (!loop_numbers.isEmpty()) {
- int freq ;
- try {
- freq = loop_numbers.take();
- } catch (InterruptedException e) { // this will never happen
- freq = -1;
- continue;
- }
-
- if (atomic_counter1.get() == num_nodes) {
- continue;
- }
- keys.put("" + freq, "");
- ResourceIterator<Node> nuc_nodes;
- if (freq == 0 && THREADS > 1) {
- nuc_nodes = graphDb.findNodes(nucleotide_label, "high_frequency", true);
- } else if (THREADS == 1) { // get all nodes at the same time when using only 1 thread
- nuc_nodes = graphDb.findNodes(nucleotide_label);
- } else {
- nuc_nodes = graphDb.findNodes(nucleotide_label, "frequency", freq);
- }
-
- System.out.print("\rGathering k-mer nodes: " + atomic_counter1.get() + "/" + num_nodes + " (" + percentage_counter + "%)");
- while (nuc_nodes.hasNext()) {
- atomic_counter1.getAndIncrement();
- if (thread_nr == 1) {
- long nodes = atomic_counter1.get();
- double nodes_d = (double) nodes;
- percentage_counter = String.format("%.2f", nodes_d/one_procent);
- }
- if (atomic_counter1.get() % 5001 == 0 || atomic_counter1.get() == num_nodes) {
- System.out.print("\rGathering k-mer nodes: "
- + atomic_counter1.get() + "/" + num_nodes + " (" + percentage_counter + "%) "); // spaces are intentional
- }
- Node nuc_node = nuc_nodes.next();
- HashMap<String, Integer> pheno_count_map = new HashMap<>();
- if (nuc_node.hasLabel(degenerate_label)) {
- continue;
- }
- //long[] freq_array = (long[]) nuc_node.getProperty("frequencies");
- int[] freq_array = get_kmer_frequencies_property(nuc_node);
- int kmer_frequency = get_kmer_frequency(nuc_node);
- int kmer_size = (int) nuc_node.getProperty("length");
- int actual_kmers = kmer_size - KMinOne;
- //System.out.println(nuc_node + " " + kmer_size + " " + actual_kmers + Arrays.toString(freq_array));
-
- if (Mode.contains("COMPRESSED")) {
- distinct_node_count.getAndIncrement(); // node_count1 is distinct
- } else {
- distinct_node_count.addAndGet(actual_kmers);
- }
- increase_kmer_occur_map(kmer_occur_map, kmer_frequency, nuc_node, thread_nr);
- boolean core = true, accessory = false, unique = false;
- int counter = 0;
- for (int i=1; i <= freq_array.length-1; i++) {
- if (skip_array[i-1]) {
- continue;
- }
-
- long frequency = freq_array[i];
- if (Mode.contains("COMPRESSED")) {
- total_node_count.getAndIncrement(); // node_count2 is total
- } else {
- total_node_count.addAndGet((frequency * actual_kmers));
- }
-
- if (frequency == 0) {
- core = false;
- continue;
- }
- increase_freq_per_genome_map(freq_per_genome, i, frequency);
- counter ++;
- if (PHENOTYPE != null) {
- String pheno = geno_pheno_map.get(i);
- if (pheno != null) {
- try_incr_hashmap(pheno_count_map, pheno, 1); // pheno_count_map is not shared by other threads
- }
- }
- }
-
- try_incr_AL_chashmap(kmer_genome_presence, counter, nuc_node);
-
- if (counter >= core_threshold) { // core
- if (Mode.contains("COMPRESSED")) {
- kmer_class_count[0] ++; // kmer_count is distinct
- } else {
- kmer_class_count[0] += actual_kmers;
- }
- } else if (counter <= unique_threshold) { // unique
- unique = true;
- if (Mode.contains("COMPRESSED")) {
- kmer_class_count[2] ++;
- } else {
- kmer_class_count[2] += actual_kmers;
- }
- } else { // accessory
- if (Mode.contains("COMPRESSED")) {
- kmer_class_count[1] ++;
- } else {
- kmer_class_count[1] += actual_kmers;
- }
- accessory = true;
- }
-
- determine_kmer_pheno_shared_specific(nuc_node, pheno_count_map, pheno_kmer_map);
- for (int i = 1; i <= freq_array.length-1; i++) {
- if (skip_array[i-1]) {
- continue;
- }
- increase_shared_kmers_map(freq_array, i, shared_kmers_map, actual_kmers, unique); // synchronized function
- if (freq_array[i] == 0) {
- continue;
- }
- increase_kmer_freq_map(kmer_freq_map, i, core, accessory, freq_array, nuc_node, actual_kmers, unique_kmers);
- }
- }
- keys.remove("" + freq);
- }
- long nodes = atomic_counter1.get();
- double nodes_d = (double) nodes;
- percentage_counter = String.format("%.2f", nodes_d/one_procent);
- System.out.print("\rGathering k-mer nodes: " + atomic_counter1.get() + "/" + num_nodes + " (" + percentage_counter + "%)");
- tx.success();
- }
- }
- }*/
-
- /**
- * Shared kmers between two genomes
- * @param freq_array
- * @param i
- * @param shared_kmers_map
- * @param actual_kmers
- * @param unique
- */
- /*
- public synchronized void increase_shared_kmers_map(int[] freq_array, int i, ConcurrentHashMap<String, long[]> shared_kmers_map, int actual_kmers, boolean unique) {
- for (int j = 1; j < freq_array.length; j ++) {
- if (i > j) {
- continue;
- }
- if (skip_array[j-1] || (freq_array[i] == 0 && freq_array[j] == 0)) {
- continue;
- }
-
- String key = i + "_" + j;
- long[] shared_kmers = shared_kmers_map.get(key); //total all, total distinct, shared all, shared distinct, inf distinct all, inf distinct shared
- if (Mode.contains("COMPRESSED")) {
- shared_kmers[1] += 1;
- if (!unique) {
- shared_kmers[4] += 1;
- }
- } else {
- shared_kmers[1] += actual_kmers;
- if (!unique) {
- shared_kmers[4] += actual_kmers;
- }
- }
-
- if (freq_array[i] >= freq_array[j]) { // compressed kmers
- if (Mode.contains("COMPRESSED")) {
- shared_kmers[0] += freq_array[i];
- if (freq_array[j] != 0) {
- shared_kmers[2] += freq_array[j];
- shared_kmers[3] += 1;
- if (!unique) {
- shared_kmers[5] += 1;
- }
- }
- } else {
- shared_kmers[0] += freq_array[i]*actual_kmers;
- if (freq_array[j] != 0) {
- shared_kmers[2] += freq_array[j]*actual_kmers;
- shared_kmers[3] += actual_kmers;
- if (!unique) {
- shared_kmers[5] += actual_kmers;
- }
- }
- }
- } else { // frequency i is smaller than the value of j
- if (Mode.contains("COMPRESSED")) { // compressed kmers
- shared_kmers[0] += freq_array[j];
- if (freq_array[i] != 0) {
- shared_kmers[2] += freq_array[i];
- shared_kmers[3] += 1;
- if (!unique) {
- shared_kmers[5] += 1;
- }
- }
- } else {
- shared_kmers[0] += freq_array[j]*actual_kmers;
- if (freq_array[i] != 0) {
- shared_kmers[2] += freq_array[i]*actual_kmers;
- shared_kmers[3] += actual_kmers;
- if (!unique) {
- shared_kmers[5] += actual_kmers;
- }
- }
- }
- }
- shared_kmers_map.put(key, shared_kmers);
- }
- }*/
-
- /**
- *
- * @param kmer_freq_map
- * @param i
- * @param core
- * @param accessory
- * @param freq_array
- * @param nuc_node
- * @param actual_kmers
- * @param unique_kmers
- */
- /*
- public synchronized void increase_kmer_freq_map(ConcurrentHashMap<Integer, long[]> kmer_freq_map, int i, boolean core, boolean accessory,
- int[] freq_array, Node nuc_node, int actual_kmers, ConcurrentHashMap<Integer, ArrayList<Node>> unique_kmers) {
-
- long[] current_freq = kmer_freq_map.get(i); // total, core, access, unique, distinct total, distinct core, distinct access, distinct uni
- int pos1 = 3, pos2 = 7; // unique positions in array
- if (core) {
- pos1 = 1;
- pos2 = 5;
- } else if (accessory) {
- pos1 = 2;
- pos2 = 6;
- } else {
- try_incr_AL_chashmap(unique_kmers, i, nuc_node);
- }
- if (Mode.contains("COMPRESSED")) {
- current_freq[0] += freq_array[i];
- current_freq[4] += 1;
- current_freq[pos1] += freq_array[i];
- current_freq[pos2] += 1;
- } else {
- current_freq[0] += freq_array[i] * actual_kmers;
- current_freq[4] += actual_kmers;
- current_freq[pos1] += (freq_array[i] * actual_kmers);
- current_freq[pos2] += actual_kmers;
- }
- kmer_freq_map.put(i, current_freq);
- }*/
-
- /**
- * Count the distinct and total degenerate nucleotide nodes for all genomes
- * @param degenerate_kmer_count
- * @return
- */
- /*
- public int[] sum_degenerate_nodes(int[] degenerate_kmer_count) {
- int [] sum = new int[2]; // [total, distinct]
- for (int i = 0; i < degenerate_kmer_count.length; i++) {
- if (i % 2 == 0 ) { // total counts
- sum[0] += degenerate_kmer_count[i];
- } else { // distinct
- sum[1] += degenerate_kmer_count[i];
- }
- }
- return sum;
- }*/
-
- /**
- * Creates kmer_classification_overview.txt
- *
- * @param kmer_freq_map
- * @param node_count
- * @param kmer_class_count
- * @param degenerate_count
- */
- /*
- public void create_kmer_classification_overview(ConcurrentHashMap<Integer, long[]> kmer_freq_map, long[] node_count,
- long[] kmer_class_count, int[] degenerate_count) {
-
- StringBuilder output_builder = new StringBuilder();
- long total_kmers = kmer_class_count[0] + kmer_class_count[1] + kmer_class_count[2];
- String core_pc = get_percentage_str(kmer_class_count[0], total_kmers, 2);
- String accessory_pc = get_percentage_str(kmer_class_count[1], total_kmers, 2);
- String unique_pc = get_percentage_str(kmer_class_count[2], total_kmers, 2);
- int[] sum_degenerate_kmers = sum_degenerate_nodes(degenerate_count); // total & distinct
- if (!Mode.contains("COMPRESSED")) {
- output_builder.append("Uncompressed the k-mers. K-mer size is ").append(K_SIZE).append(", extracting ").append(KMinOne)
- .append(" of every compressed k-mer\n");
- } else {
- output_builder.append("Counted compressed k-mers. Each k-mer node is counted once\n");
- }
- output_builder.append("To obtain the distinct k-mer counts, the frequency of k-mers was ignored\n\n");
- output_builder.append("Total k-mers: ").append(node_count[1])
- .append("\nTotal degenerate k-mers: ").append(sum_degenerate_kmers[0])
- .append("\n\nDistinct k-mers: ").append(node_count[0])
- .append("\nDistinct degenerate k-mers: ").append(sum_degenerate_kmers[1])
- .append("\nCore: ").append(kmer_class_count[0]).append(" (").append(core_pc).append("%)")
- .append("\nAccessory: ").append(kmer_class_count[1]).append(" (").append(accessory_pc).append("%)")
- .append("\nUnique: ").append(kmer_class_count[2]).append(" (").append(unique_pc).append("%)").append("\n\n");
-
- long[] kmer_class_count2 = new long[6];
- for (int i=1; i <= total_genomes; i++) {
- if (skip_array[i-1]) {
- continue;
- }
- long[] value_array = kmer_freq_map.get(i);
- String percentage1 = get_percentage_str(value_array[1], value_array[0], 2);
- String percentage2 = get_percentage_str(value_array[2], value_array[0], 2);
- String percentage3 = get_percentage_str(value_array[3], value_array[0], 2);
- String percentage5 = get_percentage_str(value_array[5], value_array[4], 2);
- String percentage6 = get_percentage_str(value_array[6], value_array[4], 2);
- String percentage7 = get_percentage_str(value_array[7], value_array[4], 2);
- output_builder.append("Genome ").append(i)
- .append("\nAll k-mers: ").append(value_array[0])
- .append("\nDegenerate k-mers: ").append(degenerate_count[(i*2)-1])
- .append("\nCore: ").append(value_array[1]).append(", ").append(percentage1)
- .append("%\nAccessory: ").append(value_array[2]).append(", ").append(percentage2)
- .append("%\nUnique: ").append(value_array[3]).append(", ").append(percentage3).append("%\n\n")
- .append("Distinct k-mers: ").append(value_array[4])
- .append("\nDistinct degenerate k-mers: ").append(degenerate_count[(i*2)-2])
- .append("\nCore: ").append(value_array[5]).append(", ").append(percentage5)
- .append("%\nAccessory: ").append(value_array[6]).append(", ").append(percentage6)
- .append("%\nUnique: ").append(value_array[7]).append(", ").append(percentage7).append("%\n\n");
- kmer_class_count2[0] += value_array[1];
- kmer_class_count2[1] += value_array[5];
- }
- write_SB_to_file_in_DB(output_builder, "kmer_classification/kmer_classification_overview.txt");
- }*/
-
- /**
- * Creates accessory_kmers.csv & core_kmers.csv
- * @param kmer_genome_presence
- */
- /*
- public void create_kmer_core_accessory_output(ConcurrentHashMap<Integer, ArrayList<Node>> kmer_genome_presence) {
- try (BufferedWriter out = new BufferedWriter(new FileWriter(WORKING_DIRECTORY + "kmer_classification/accessory_kmers.csv"))) {
- for (int i= total_genomes; i > 1; i--) {
- if (!kmer_genome_presence.containsKey(i)) {
- continue;
- }
- System.out.print("\rWriting core & accessory nodes: Genome " + i + " "); // spaces are intentional
- ArrayList<Node> nodes = kmer_genome_presence.get(i);
- StringBuilder node_builder = new StringBuilder();
- for (Node node1 : nodes) {
- long node_id = node1.getId();
- node_builder.append(node_id).append(",");
- }
- if (i == adj_total_genomes) { // core
- write_string_to_file_in_DB(node_builder.toString().replaceFirst(".$",""), "kmer_classification/core_kmers.csv");
- } else { // accessory
- String percentage = get_percentage_str(i, adj_total_genomes, 1);
- out.write(i + " genomes " + percentage + "%\n" + node_builder.toString().replaceFirst(".$","") + "\n");
- }
- }
- out.close();
- } catch (IOException ioe) {
- System.out.println("\nUnable to create: " + WORKING_DIRECTORY + "kmer_classification/accessory_kmers.csv\n");
- System.exit(1);
- }
- System.out.print("\r "); // spaces are intentional
- }*/
-
- /**
- * the node identifiers of unique k-mers ordered by genome.
- * @param unique_kmers
- * @return
- */
- /*
- public long create_kmer_unique_output(ConcurrentHashMap<Integer, ArrayList<Node>> unique_kmers) {
- long total_unique_kmers = 0;
- try (BufferedWriter out = new BufferedWriter(new FileWriter(WORKING_DIRECTORY + "kmer_classification/unique_kmers.csv"))) {
- for (int i=1; i <= total_genomes; i++) {
- System.out.print("\rWriting unique k-mers: genome " + i);
- if (skip_array[i-1]) {
- continue;
- }
- out.write("Genome " + i + "\n");
- if (!unique_kmers.containsKey(i)) {
- continue;
- }
- ArrayList<Node> nodes = unique_kmers.get(i);
- StringBuilder node_builder = new StringBuilder();
- for (Node node1 : nodes) {
- long node_id = node1.getId();
- node_builder.append(node_id).append(",");
- }
- String node_str = node_builder.toString().replaceFirst(".$","");
- String[] unique_array1 = node_str.split(",");
- total_unique_kmers += unique_array1.length;
- out.write(node_str + "\n");
- }
- out.close();
- } catch (IOException ioe) {
- System.out.println("\nUnable to create: " + WORKING_DIRECTORY + "kmer_classification/unique_kmers.csv\n");
- System.exit(1);
- }
- System.out.println("\r "); // spaces are intentional
- return total_unique_kmers;
- }*/
-
- /**
- *
- * @param kmer_occur_map
- */
- public synchronized void write_kmer_occurance_output(ConcurrentHashMap<Long, ArrayList<Node>> kmer_occur_map) {
- TreeSet<Long> current_frequencies = new TreeSet<>();
- for (Long frequency : kmer_occur_map.keySet()) {
- current_frequencies.add(frequency);
- }
- StringBuilder output = new StringBuilder();
- for (Long frequency : current_frequencies) {
- output.append("#").append(frequency).append("#,");
- ArrayList<Node> nodes = kmer_occur_map.get(frequency);
- kmer_occur_map.remove(frequency);
- for (Node nuc_node : nodes) {
- output.append(nuc_node.getId()).append(",");
- }
- output.append("\n");
- }
- if (!check_if_file_exists(WORKING_DIRECTORY + "kmer_classification/kmer.log")) {
- write_SB_to_file_full_path(output, WORKING_DIRECTORY + "kmer_/kmer.log");
- } else {
- append_SB_to_file_full_path(output, WORKING_DIRECTORY + "kmer_classification/kmer.log");
+ output.append("\n");
+ }
+ if (!check_if_file_exists(WORKING_DIRECTORY + "kmer_classification/kmer.log")) {
+ write_SB_to_file_full_path(output, WORKING_DIRECTORY + "kmer_/kmer.log");
+ } else {
+ append_SB_to_file_full_path(output, WORKING_DIRECTORY + "kmer_classification/kmer.log");
}
}
@@ -8882,20 +8040,73 @@ public class Classification {
Reports all phenotype nodes and their properties
*/
public void phenotype_overview() {
- System.out.println("\nReporting all phenotypes stored in the pangenome database\n");
-
+ //System.out.println("\nReporting all phenotypes stored in the pangenome database\n");
HashMap<String, Integer> count_phenotype = new HashMap<>();
HashMap<String, ArrayList<Integer>> genomes_per_phenotype = new HashMap<>();
- Set<String> phenotype_set = new HashSet<>();
+ Set<String> phenotype_set = new HashSet<>(); // phenotype properties
String phenos_per_genomes = retrieve_phenotypes_for_overview(count_phenotype, genomes_per_phenotype, phenotype_set);
String phenotype_occurance = count_phenotype_occurance(phenotype_set, count_phenotype);
String genomes_per_pheno = print_genomes_per_phenotype(phenotype_set, genomes_per_phenotype);
write_string_to_file_in_DB(genomes_per_pheno + phenotype_occurance + phenos_per_genomes, "phenotype_overview.txt");
- System.out.println("Overview written to:\n "
+ System.out.println("\nOverview written to:\n "
+ WORKING_DIRECTORY + "phenotype_overview.txt\n");
}
+ /**
+ * Get all available phenotypes from 'phenotype' nodes
+ * @return Arraylist with all phenotype properties (no values)
+ */
+ public ArrayList<String> retrieve_phenotypes_properties() {
+ HashSet<String> phenotype_properties_set = new HashSet<>();
+ try (Transaction tx = graphDb.beginTx()) { // start database transaction
+ ResourceIterator<Node> pheno_nodes = graphDb.findNodes(phenotype_label);
+ while (pheno_nodes.hasNext()) {
+ Node pheno_node = pheno_nodes.next();
+ Iterable<String> properties = pheno_node.getPropertyKeys();
+ for (String property : properties) {
+ if (property.equals("genome")) {
+ continue;
+ }
+ phenotype_properties_set.add(property);
+ }
+ }
+ tx.success();
+ }
+ //converting set to a list to make sure the order is always the same
+ ArrayList<String> phenotype_properties_list = new ArrayList<>(phenotype_properties_set);
+ return phenotype_properties_list;
+ }
+
+ /**
+ *
+ * @return
+ */
+ public HashMap<String, String> retrieve_phenotypes_for_metrics() {
+ HashMap<String, String> all_phenotypes_map = new HashMap<>(); // key is genome nr with phenotype property, value is the phenotype value
+ try (Transaction tx = graphDb.beginTx()) { // start database transaction
+ ResourceIterator<Node> pheno_nodes = graphDb.findNodes(phenotype_label);
+ while (pheno_nodes.hasNext()) {
+ Node pheno_node = pheno_nodes.next();
+
+ Iterable<String> properties = pheno_node.getPropertyKeys();
+ int genome_nr = (int) pheno_node.getProperty("genome");
+
+ for (String property : properties) {
+ if (property.equals("genome")) {
+ continue;
+ }
+ Object phenotype_value = pheno_node.getProperty(property); // print a value from node without converting?!
+ // value is only used for printing, therefore can always be converted to a string
+ String phenotype_str_value = String.valueOf(phenotype_value);
+ all_phenotypes_map.put(genome_nr + "#" + property, phenotype_str_value);
+ }
+ }
+ tx.success(); // transaction successful, commit changes
+ }
+ return all_phenotypes_map;
+ }
+
/**
*
* @param count_phenotype
@@ -9034,7 +8245,7 @@ public class Classification {
.append("\n")
.append("df = read.csv(\"").append(WD_full_path).append("pangenome_size/gene/gains_losses/average_all.csv\", sep=\",\",header = TRUE)\n")
.append("plot1 = ggplot(df, aes(x=x, y=y, color=Category)) +\n")
- .append(" scale_color_manual(values=c(\"Accessory\" = \"#0066CC\", \"Core\" = \"#009900\", \"Unique\" = \"#990000\")) +\n")
+ .append(" scale_color_manual(values=c(\"Accessory\" = \"#0072B2\", \"Core\" = \"#009E73\", \"Unique\" = \"#D55E00\")) +\n")
.append(" geom_line(size = 1.5) +\n")
.append(" theme(text = element_text(size=12)) +\n")
.append(" labs(x = \"Number of genomes\") +\n")
@@ -9087,7 +8298,7 @@ public class Classification {
public void append_common_part_gains_losses_rscript(StringBuilder rscript) {
rscript.append("plot1 = ggplot(df_average, aes(x=x, y=y, color=Category, linetype=Metric)) +\n")
.append(" geom_line(size = 1.0, data = df_median, aes(x =x, y =y, color=Category)) +\n")
- .append(" scale_color_manual(values=c(\"Accessory\" = \"#0066CC\", \"Core\" = \"#009900\", \"Unique\" = \"#990000\")) +\n")
+ .append(" scale_color_manual(values=c(\"Accessory\" = \"#0072B2\", \"Core\" = \"#009E73\", \"Unique\" = \"#D55E00\")) +\n")
.append(" scale_linetype_manual(values=c(\"Average\" = \"dotted\", \"Median\" = \"solid\")) +\n")
.append(" geom_line(size = 1.7) +\n")
.append(" labs(x = \"Number of genomes\") +\n")
@@ -9125,14 +8336,16 @@ public class Classification {
if (unique.equals("")) {
rscript.append("#! /usr/bin/env RScript\n")
.append("#Assuming the R libraries were installed via Conda, the next lines can be ignored. If not, use them to manually install the required packages\n")
- .append("#install.packages(\"ggplot2\", \"").append(R_LIB).append("\", \"https://cran.us.r-project.org\")\n");
+ .append("#install.packages(\"ggplot2\", \"").append(R_LIB).append("\", \"https://cran.us.r-project.org\")\n")
+ .append("#install.packages(\"svglite\", \"").append(R_LIB).append("\", \"https://cran.us.r-project.org\")\n");
if (type.equals("K-mers")) {
rscript.append("#install.packages(\"dplyr\", \"").append(R_LIB).append("\", \"https://cloud.r-project.org\")\n")
.append("#install.packages(\"scales\", \"").append(R_LIB).append("\", \"https://cran.us.r-project.org\")\n\n");
} else {
rscript.append("\n");
}
- rscript.append("library(ggplot2)\n");
+ rscript.append("library(ggplot2)\n")
+ .append("#library(svglite) #required to save plot as SVG\n");
if (type.equals("K-mers")) {
rscript.append("#library(scales) #uncomment when you want to show the total number of k-mers in millions instead of a scientific number\n")
.append("#library(dplyr) #uncomment when you want to show the total number of k-mers in millions instead of a scientific number\n\n");
@@ -9153,7 +8366,7 @@ public class Classification {
transform_y = " #scale_y_continuous(labels = unit_format(unit = \"M\")) + # convert scientific number to millions (requires scales library)\n";
}
rscript.append("plot1 = ggplot(df, aes(x=x, y=y, color=Category, size=Category)) +\n")
- .append(" scale_color_manual(values=c(\"Median\" = \"#000000\", \"Accessory\" = \"#0066CC\", \"Core\" = \"#009900\", \"Unique\" = \"#990000\")) +\n")
+ .append(" scale_color_manual(values=c(\"Median\" = \"#000000\", \"Accessory\" = \"#0072B2\", \"Core\" = \"#009E73\", \"Unique\" = \"#D55E00\")) +\n")
.append(" scale_size_manual(values=c(\"Median\" = 0.2, \"Accessory\" = 0.8, \"Core\" = 0.8, \"Unique\" = 0.8)) +\n")
.append(" geom_point() + \n")
.append(" theme(text = element_text(size=12)) + \n")
@@ -9173,6 +8386,7 @@ public class Classification {
.append(" theme_bw(base_size = 18) # increase this number of have larger text and numbers\n\n");
rscript.append("pdf(NULL)\n")
+ .append("#ggsave(\"").append(path).append("core_accessory").append(unique).append("_growth.svg\", plot= plot1, height = 10, width = 10)\n")
.append("ggsave(\"").append(path).append("core_accessory").append(unique).append("_growth.png\", plot= plot1, height = 10, width = 10)\n")
.append("cat(\"\\nPangenome growth written to: ").append(path).append("core_accessory").append(unique).append("_growth.png\\n\\n\")\n");
@@ -9182,36 +8396,6 @@ public class Classification {
write_string_to_file_in_DB(rscript.toString() + "\n", "pangenome_size/" + gene_or_kmer + "/pangenome_growth.R");
}
}
-
- /**
- * k-mer distance NJ tree
- * @param output_path
- */
- /*
- public static void create_kmer_distance_rscript(String output_path) {
- String R_LIB = check_r_libraries_environment();
- StringBuilder rscript = new StringBuilder ();
- rscript.append("#! /usr/bin/env RScript\n\n")
- .append("# Use one of the following files\n")
- .append("# ").append(WD_full_path).append("kmer_classification/mash_distance.csv\n")
- .append("# ").append(WD_full_path).append("kmer_classification/distance_distinct_kmers.csv\n")
- .append("# ").append(WD_full_path).append("kmer_classification/distance_inf_distinct_kmers.csv\n")
- .append("# ").append(WD_full_path).append("kmer_classification/distance_all_kmers.csv\n\n")
- .append("#Assuming the R libraries were installed via Conda, the next line can be ignored. If not, use it to manually install the required package\n")
- .append("#install.packages(\"ape\", \"").append(R_LIB).append("\", \"https://cran.us.r-project.org\")\n")
- .append("library(ape)\n\n")
- .append("input = read.csv(\"").append(WD_full_path).append("kmer_classification/mash_distance.csv\", sep=\",\", header = TRUE)\n")
- .append("input[").append((adj_total_genomes + 2)).append("] <- NULL\n") // when having 204 genomes, remove column 206
- .append("df2 = subset(input, select = -c(Genomes))\n")
- .append("df.dist2 =as.matrix(df2, labels=TRUE)\n")
- .append("colnames(df.dist2) <- rownames(df.dist2) <- input[['Genomes']]\n")
- .append("NJ_tree <- nj(df.dist2)\n")
- .append("pdf(NULL)\n")
- .append("plot(NJ_tree, main = \"Neighbor Joining\")\n")
- .append("write.tree(NJ_tree, tree.names = TRUE, file=\"").append(output_path).append("kmer_distance.tree\")\n")
- .append("cat(\"\\nK-mer distance tree written to: ").append(output_path).append("kmer_distance.tree\\n\\n\")");
- write_SB_to_file_full_path(rscript, output_path + "kmer_distance_tree.R");
- }*/
/**
* Gene distance NJ tree
@@ -9271,20 +8455,6 @@ public class Classification {
System.out.println("--gap-open was set. " + GAP_OPEN + " mismatches allowed (per cluster) during cluster construction");
}
}
-
- /**
- *
- * @param hm_nodes_list
- * @return
- */
- public static String[] convert_new_node_list_to_old_str_array(ArrayList<Node> hm_nodes_list) {
- String[] hmgroup_array = new String[hm_nodes_list.size()];
- for (int i=0; i < hm_nodes_list.size(); i++) {
- Node hm_node = hm_nodes_list.get(i);
- hmgroup_array[i] = hm_node.getId() + "";
- }
- return hmgroup_array;
- }
/**
*
@@ -9478,7 +8648,6 @@ public class Classification {
*/
public static void check_which_hmgroup_of_gene(ArrayList<Node> gene_nodes_list, HashMap<Node, ArrayList<Node>> mrnas_for_genes_at_same_pos) {
for (Node gene_node : gene_nodes_list) {
- //System.out.println(gene_node);
Iterable<Relationship> gene_rels = gene_node.getRelationships(RelTypes.codes_for);
for (Relationship rel : gene_rels) {
Node mrna_node = rel.getEndNode();
@@ -9801,8 +8970,8 @@ public class Classification {
found_mrnas.add(mrna_node);
if (standalone) {
//System.out.println(info);
- nuc_sequence = split_seq_in_parts_of_60bp(nuc_sequence);
- prot_sequence = split_seq_in_parts_of_60bp(prot_sequence);
+ nuc_sequence = split_seq_in_parts_of_80bp(nuc_sequence);
+ prot_sequence = split_seq_in_parts_of_80bp(prot_sequence);
output_builder.append(info).append("\n");
nuc_seq_builder.append(">").append(protein_id).append(" ").append(name).append(" ").append(address[0]).append("\n")
.append(nuc_sequence).append("\n");
@@ -9914,7 +9083,7 @@ public class Classification {
tx.success(); // transaction successful, commit changes
} catch (NotFoundException nfe ) {
System.out.println("Unable to start the database");
- return;
+ System.exit(1);
}
long node_id = 0;
@@ -9933,324 +9102,14 @@ public class Classification {
System.out.println("\nUse -node OR -name\n");
System.exit(1);
}
- annotation_get_connected_genes(function_node_list);
- tx.success(); // transaction successful, commit changes
- }
- graphDb.shutdown();
- System.out.println("Output written to:\n "
- + WORKING_DIRECTORY + "find_genes/by_annotation/find_genes_by_annotation.log\n "
- + WORKING_DIRECTORY + "find_genes/by_annotation/nucleotide_sequences\n "
- + WORKING_DIRECTORY + "find_genes/by_annotation/protein_sequences\n");
- }
-
- /**
- * Requires
- * -dp
- * -rf
- *
- * Optional
- * -phenotype
- * -tn
- * --core-threshold
- */
- public void msa_of_regions() {
- System.out.println("\nAligning selected regions with MAFFT\n");
- check_if_program_exists_stderr("mafft -h", 100, "MAFFT", true); // check if program is set to $PATH
- check_if_program_exists_stderr("FastTree -h", 100, "Fasttree", true); // check if program is set to $PATH
- report_number_of_threads(true, true); // prints how many threads were selected by user
- check_if_graphDb_is_available(); // starts up the graph database if needed
- create_directory_in_DB("alignments/regions/var_inf_positions");
- if (target_genome != null || skip_genomes != null) {
- System.out.println("\r'msa_of_regions' is unable to use --reference/-ref or --skip. You should exclude these genomes from your --regions-file\n");
- }
- try (Transaction tx = graphDb.beginTx()) { // start database transaction
- Node pangenome_node = graphDb.findNodes(pangenome_label).next();
- stop_if_panproteome(pangenome_node, "msa_of_regions"); // stops the progam when run on a panproteome, retrieves K_size & total_genomes
- create_skip_arrays(false, true); // create skip array if -skip/-ref is provided by user
- if (PHENOTYPE == null) {
- System.out.println("\rNo --phenotype was provided, unable to find phenotype specific SNPs");
- } else {
- retrieve_phenotypes(); // Creates and fills geno_pheno_map and phenotype_map when a phenotype was provided by the user
- }
- tx.success(); // transaction successful, commit changes
- } catch (NotFoundException nfe) {
- System.out.println("\nUnable to start the pangenome database\n");
- System.exit(1);
- }
- graphDb.shutdown();
- connect_pangenome();
- indexSc = new IndexScanner(indexDb);
- genomeSc = new SequenceScanner(genomeDb, 1, 1, K_SIZE, indexSc.get_pre_len());
- regions_to_search = read_regions_file();
- prepare_region_msa_input();
- System.out.println("\nStep 1/3. Performing the alignment");
- String[] msa_command = {"mafft", "--auto", "--anysymbol", "--thread", THREADS + "", "--clustalout",
- WORKING_DIRECTORY + "/alignments/regions/nuc_input.fasta"};
- boolean pass = false;
- while (!pass) {
- String msa_output = ExecCommand.ExecCommand(msa_command);
- if (!msa_output.equals("")) {
- write_string_to_file_full_path(msa_output, WORKING_DIRECTORY + "/alignments/regions/nuc.afa");
- pass = true;
- }
- }
- convert_afa_to_aligned_fasta(WORKING_DIRECTORY + "/alignments/regions/nuc_input.fasta",
- WORKING_DIRECTORY + "/alignments/regions/nuc.afa");
-
- System.out.println("Step 2/3. Inferring phylogeny");
- String[] run_fasttree = {"FastTree","-out", WORKING_DIRECTORY + "alignments/regions/nuc.newick",
- WORKING_DIRECTORY + "alignments/regions/nuc.fasta"};
- ExecCommand.ExecCommand(run_fasttree);
-
- System.out.println("Step 3/3. Reading the alignment");
- HashMap<String, Integer> shared_snps_map = new HashMap<>();
- StringBuilder pheno_specific_output = new StringBuilder("# Each row contains: position in the alignment, reference allele,other alleles, "
- + "phenotype, number of sequences with the phenotype and letter/total sequences with phenotype\n");
- HashMap<String, Integer> pheno_specific_group_sites = new HashMap<>();
- String output_path = WORKING_DIRECTORY + "alignments/regions/";
- String genome_order_file = output_path + "nuc_input_genomes.txt";
- int[] var_inf_sites = count_var_inf_sites_in_msa(shared_snps_map, pheno_specific_output, pheno_specific_group_sites,
- output_path + "nuc.afa", "MSA", "nucleotide", genome_order_file); // variable, informative, conserved sites
- create_shared_site_matrices(shared_snps_map, output_path +"var_inf_positions/", var_inf_sites[0], "", "nucleotide", genome_order_file);
- create_shared_site_matrices(shared_snps_map, output_path +"var_inf_positions/", var_inf_sites[1], "#inf", "nucleotide", genome_order_file);
- create_identity_matrices(shared_snps_map, var_inf_sites[0], var_inf_sites[2], "nucleotide",
- output_path + "nuc_identity.csv", output_path + "nuc_input_genomes.txt");
-
- System.out.print("\nNucleotide variable/informative sites: " + var_inf_sites[0] + "/" + var_inf_sites[1] + "\n"
- + "\n"
- + "Output written to:\n "
- + output_path + "nuc_input.fasta\n "
- + output_path + "nuc.fasta\n "
- + output_path + "nuc.afa\n "
- + output_path + "nuc.newick\n "
- + output_path + "nuc_identity.csv\n "
- + output_path + "nuc_alignment.info\n ");
-
- if (PHENOTYPE != null) {
- System.out.print(output_path + "nuc_phenotype_specific_changes.info\n ");
- }
- System.out.println(output_path + "var_inf_positions/\n ");
- }
-
- /**
- * One alignment on the sequences of multiple homology groups
- *
- * Requires
- * -dp
- * -hm
- */
- public void msa_of_multiple_groups() {
- System.out.println("\nPerforming one alignment on the sequences of multiple groups\n");
- check_if_program_exists_stderr("FastTree -h", 100, "Fasttree", true); // check if program is set to the $PATH
- check_if_program_exists_stderr("mafft -h", 100, "MAFFT", true); // check if program is set to the $PATH
- report_number_of_threads(true, true); // prints how many threads were selected by user
- check_if_graphDb_is_available(); // starts up the graph database if needed
- ArrayList<Node> hm_nodes_list;
- try (Transaction tx = graphDb.beginTx()) { // start database transaction
- Node pangenome_node = graphDb.findNodes(pangenome_label).next();
- check_if_panproteome(pangenome_node); // sets PROTEOME boolean that controls functions, retrieves K_size & total_genomes
- check_current_grouping_version(); // check which version of homology grouping is active
- hm_nodes_list = retrieve_hmgroups(true);
- create_skip_arrays(false, true); // create skip array if -skip/-ref is provided by user
- if (PHENOTYPE == null) {
- System.out.println("No --phenotype was provided, unable to find phenotype specific SNPs\n");
- }
- retrieve_phenotypes(); // Creates and fills geno_pheno_map and phenotype_map when a phenotype was provided by the user
- tx.success(); // transaction successful, commit changes
- } catch (NotFoundException nfe) {
- System.out.println("Unable to start the database\n");
- return;
- }
-
- String hm_identifiers_str = "";
- for (Node hm_node : hm_nodes_list) {
- hm_identifiers_str += hm_node.getId() + ",";
- }
-
- check_mode_for_msa();
- create_msa_multi_input(hm_nodes_list);
- run_multi_group_msa(); // run mafft and fasttree
-
- String output_path = WORKING_DIRECTORY + "alignments/grouping_v" + grouping_version + "/multiple_groups/";
-
- initialize_BLOSUM();
- String similarity_dir = output_path + "similarity_identity/";
- String var_inf_dir = output_path + "var_inf_positions/";
- String genome_order_file = output_path + "genome_order.info";
- ArrayList<String> nuc_or_prot_list = prepare_type_list_for_msa(); // list can contain "protein", "nucleotide" or both
- for (String nuc_or_prot : nuc_or_prot_list) {
- String nuc_or_prot_short = "nuc";
- if (nuc_or_prot.equals("protein")) {
- nuc_or_prot_short = "prot";
- }
- String input_file = WD_full_path + "/alignments/grouping_v" + grouping_version + "/multiple_groups/";
- StringBuilder pheno_disrupt = new StringBuilder("#Use this file to see why a position is phenotype specific or not. "
- + "The overview shows the number of phenotype members with a specific letter on variable positions in the alignment"
- + " followed by the required threshold to be phenotype specific\n");
- StringBuilder pheno_specific_output = new StringBuilder("# Each row contains: position in the alignment, "
- + "reference letter/other letters found, phenotype, number of sequences with the phenotype and letter/total sequences with phenotype\n");
- if (nuc_or_prot.equals("protein")) {
- input_file += "prot.afa";
- } else {
- input_file += "nuc.afa";
- }
- HashMap<String, Integer> pheno_specific_group_sites = new HashMap<>();
- System.out.print("\rReading " + nuc_or_prot + " alignment");
- HashMap<String, Integer> shared_snps_map = new HashMap<>();
- int[] var_inf_sites = count_var_inf_sites_in_msa(shared_snps_map, pheno_specific_output, pheno_specific_group_sites,
- input_file, hm_identifiers_str, nuc_or_prot, genome_order_file); // variable, informative, conserved sites
-
- create_shared_site_matrices(shared_snps_map, var_inf_dir, var_inf_sites[0], "", nuc_or_prot, genome_order_file);
- create_shared_site_matrices(shared_snps_map, var_inf_dir, var_inf_sites[1], "#inf", nuc_or_prot, genome_order_file);
- create_identity_matrices(shared_snps_map, var_inf_sites[0], var_inf_sites[2], nuc_or_prot,
- similarity_dir + nuc_or_prot_short + "_identity.csv", genome_order_file);
- if (nuc_or_prot.equals("protein")) {
- create_similarity_matrices(shared_snps_map, similarity_dir + nuc_or_prot_short + "_similarity.csv", var_inf_sites[0],
- var_inf_sites[2], genome_order_file);
- }
- nuc_or_prot = nuc_or_prot.substring(0,1).toUpperCase() + nuc_or_prot.substring(1);
- System.out.println("\r" + nuc_or_prot + " variable/informative sites: " + var_inf_sites[0] + "/" + var_inf_sites[1]);
- prepare_phenotype_results_msa_of_many_groups(pheno_specific_group_sites, output_path, pheno_specific_output, pheno_disrupt, nuc_or_prot);
- }
- delete_file_full_path(genome_order_file);
-
- System.out.print("\nOutput written to:\n "
- + output_path + "\n "
- + output_path + "similarity_identity/\n "
- + output_path + "var_inf_positions/\n\n");
- if (PHENOTYPE != null) {
- System.out.print("Phenotype output written to:\n");
- if (Mode.equals("BOTH") || Mode.equals("NUCLEOTIDE")) {
- System.out.print(" " + output_path + "phenotype_specific_changes_nuc.txt\n "
- + output_path + "phenotype_disrupted_nuc.txt\n");
- }
- if (Mode.equals("BOTH") || Mode.equals("PROTEIN")) {
- System.out.print(" " + output_path + "phenotype_specific_changes_nuc.txt\n "
- + output_path + "phenotype_disrupted_nuc.txt\n");
- }
- System.out.println("");
- } else {
- //System.out.println("");
- }
- }
-
- /**
- * Run mafft and fasttree against nucleotide and protein sequences of mulitple homology groups
- */
- public void run_multi_group_msa() {
- String output_path = WORKING_DIRECTORY + "alignments/grouping_v" + grouping_version + "/multiple_groups/";
- ArrayList<String> nuc_or_prot_list = prepare_type_list_for_msa(); // list can contain "protein", "nucleotide" or both
- for (String nuc_or_prot : nuc_or_prot_list) { // align nucleotide and protein sequences
- int try_counter = 0;
- String nuc_or_prot_short = "nuc";
- if (nuc_or_prot.equals("protein")) {
- nuc_or_prot_short = "prot";
- }
- System.out.print("\rRunning MAFFT against " + nuc_or_prot + " sequences");
- String[] mafft_command = {"mafft", "--auto", "--anysymbol", "--thread", THREADS + "", "--clustalout",
- output_path + nuc_or_prot_short + "_input.fasta"};
- boolean pass = false;
- while (!pass) {
- String mafft_output = ExecCommand.ExecCommand(mafft_command);
- try_counter ++;
- if (try_counter > 1) {
- System.out.print("\rRunning MAFFT against " + nuc_or_prot + " sequences. Attempt " + try_counter);
- }
- if (!mafft_output.equals("")) {
- write_string_to_file_full_path(mafft_output, output_path + nuc_or_prot_short + ".afa");
- convert_afa_to_aligned_fasta(output_path + nuc_or_prot_short + "_input.fasta", output_path + nuc_or_prot_short + ".afa");
- pass = true;
- }
- }
- }
- System.out.println("");
-
- boolean incorrect_identifiers = check_if_file_exists(output_path + "identifiers_incorrect_for_fasttree");
- for (String nuc_or_prot : nuc_or_prot_list) {
- System.out.print("\rInferring phylogeny on " + nuc_or_prot + " alignment");
- String nuc_or_prot_short = "nuc";
- if (nuc_or_prot.equals("protein")) {
- nuc_or_prot_short = "prot";
- }
- if (incorrect_identifiers) {
- run_fasttree_on_renamed_identifiers(output_path + "identifiers_incorrect_for_fasttree",
- output_path + nuc_or_prot_short + ".fasta", nuc_or_prot);
- } else {
- String[] fasttree;
- if (nuc_or_prot.equals("protein")) {
- fasttree = new String[]{"FastTree","-out", output_path + "prot" + ".newick", output_path + "prot" + ".fasta"};
- } else {
- fasttree = new String[]{"FastTree","-out", output_path + "nuc" + ".newick", "-nt", output_path + "nuc" + ".fasta"};
- }
- ExecCommand.ExecCommand(fasttree);
- include_genome_number_in_fasttree(output_path + "genome_order.info", output_path + nuc_or_prot_short + ".newick");
- }
- }
- System.out.println("\n");
- }
-
- /**
- *
- * @param genome_order
- * @param tree_file
- */
- public static void include_genome_number_in_fasttree(String genome_order, String tree_file) {
- ArrayList<Integer> genome_order_list = read_genome_order_file(genome_order, false);
- ArrayList<String> protein_id_list = get_full_protein_identifiers(genome_order, false);
- String tree = retrieve_tree_file(tree_file);
- for (int i=0; i < protein_id_list.size(); i++) {
- tree = tree.replace(protein_id_list.get(i), genome_order_list.get(i) + "_" + protein_id_list.get(i));
- }
- write_string_to_file_full_path(tree, tree_file);
- }
-
- /**
- *
- * @param tree_file
- * @return
- */
- public static String retrieve_tree_file(String tree_file) {
- String tree = "";
- try (BufferedReader in = new BufferedReader(new FileReader(tree_file))) { // read original fasta files
- for (int c = 0; in.ready();) { // has only 1 line
- tree = in.readLine().trim();
- }
- in.close();
- } catch (IOException ioe) {
- System.out.println("\nUnable to read: " + tree_file + "\n");
- System.exit(1);
- }
- return tree;
- }
-
- /**
- *
- * @param pheno_specific_group_sites
- * @param output_path
- * @param pheno_specific_output
- * @param pheno_disrupt
- * @param nuc_or_prot
- */
- public static void prepare_phenotype_results_msa_of_many_groups(HashMap<String, Integer> pheno_specific_group_sites, String output_path,
- StringBuilder pheno_specific_output, StringBuilder pheno_disrupt, String nuc_or_prot) {
- if (PHENOTYPE == null) {
- return;
- }
- String nuc_or_prot_short = "nuc";
- if (nuc_or_prot.equals("protein")) {
- nuc_or_prot_short = "prot";
- }
- write_SB_to_file_full_path(pheno_disrupt, output_path + "phenotype_disrupted_" + nuc_or_prot_short + ".txt");
- StringBuilder pheno_spec_builder = new StringBuilder("# Total phenotype specific SNPs\n");
- for (String key : pheno_specific_group_sites.keySet()) {
- if (key.endsWith("_groups")) {
- continue;
- }
- int value = pheno_specific_group_sites.get(key);
- pheno_spec_builder.append("# ").append(key).append(": ").append(value).append("\n");
+ annotation_get_connected_genes(function_node_list);
+ tx.success(); // transaction successful, commit changes
}
- write_string_to_file_full_path(pheno_spec_builder.toString() + pheno_specific_output.toString(),
- output_path + "phenotype_specific_changes_" + nuc_or_prot_short + ".txt");
+ graphDb.shutdown();
+ System.out.println("Output written to:\n "
+ + WORKING_DIRECTORY + "find_genes/by_annotation/find_genes_by_annotation.log\n "
+ + WORKING_DIRECTORY + "find_genes/by_annotation/nucleotide_sequences\n "
+ + WORKING_DIRECTORY + "find_genes/by_annotation/protein_sequences\n");
}
/**
@@ -10262,8 +9121,8 @@ public class Classification {
* @param output_file
* @param genome_order_file
*/
- public void create_identity_matrices(HashMap<String, Integer> shared_snps_map, int variable_positions, int conserved_positions, String prot_or_nuc,
- String output_file, String genome_order_file) {
+ public static void create_identity_matrices(HashMap<String, Integer> shared_snps_map, int variable_positions, int conserved_positions, String prot_or_nuc,
+ String output_file, String genome_order_file) {
ArrayList<String> protein_id_list = get_full_protein_identifiers(genome_order_file, false);
ArrayList<Integer> genome_order_list = read_genome_order_file(genome_order_file, false);
@@ -10327,391 +9186,18 @@ public class Classification {
}
write_string_to_file_full_path(header_builder.toString() + "\n" + output_builder.toString(), output_file);
}
-
- /*
- Prepares nucleotde and protein input sequences for the muliple homology group alignment
- Prepares two itol templates for the fasttree phylogeny
- */
- public int create_msa_multi_input(ArrayList<Node> hm_nodes_list) {
- StringBuilder prot_fasta = new StringBuilder();
- StringBuilder nuc_fasta = new StringBuilder();
- StringBuilder genome_order = new StringBuilder();
- StringBuilder itol_hm_template = new StringBuilder("DATASET_COLORSTRIP\nSEPARATOR COMMA\nDATASET_LABEL,label1\nCOLOR,#ff0000\n"
- + "STRIP_WIDTH,40\nSHOW_INTERNAL,1\n\nDATA\n");
- StringBuilder itol_pheno_template = new StringBuilder("DATASET_COLORSTRIP\nSEPARATOR COMMA\nDATASET_LABEL,label1\nCOLOR,#ff0000\n"
- + "STRIP_WIDTH,40\nSHOW_INTERNAL,1\n\nDATA\n");
- StringBuilder info_builder = new StringBuilder("#Information about sequences in homology group\n#Occurance in genomes\n");
- StringBuilder info_builder_part2 = new StringBuilder("##genome, mRNA name, mRNA id, node id, address, gene length, gene copy number within the group\n");
- if (PROTEOME) {
- info_builder_part2 = new StringBuilder("##genome, protein id, node id, protein length, protein copy number within the group\n");
- }
- StringBuilder incorrect_identifiers = new StringBuilder("#the original identifers are not unique or contain a column or semicolon\n"
- + "#old identifier, new identifier\n");
- ArrayList<Integer> prot_lengths = new ArrayList<>();
- ArrayList<Integer> nuc_lengths = new ArrayList<>();
- HashMap<String, Integer> pheno_counter_map = new HashMap<>();
- ArrayList<String> phenotypes_list = new ArrayList<>();
- int total_sequences = 0, total_groups = 0;
- AtomicInteger phenotype_counter = new AtomicInteger(0);
- StringBuilder hm_color_info = new StringBuilder("#Colors used for homology groups\n\n");
- boolean use_different_identifiers = false; // the current protein identifers cannot be used by fasttree
- HashSet<String> proper_identifiers_set = new HashSet<>();
- try (Transaction tx = graphDb.beginTx()) { // start database transaction
- for (Node hm_node : hm_nodes_list) {
- check_if_hm_is_correct_grouping(hm_node);
- long hm_node_id = hm_node.getId();
- String color = COLOR_CODES[total_groups];
- hm_color_info.append("#").append(hm_node_id).append(" ").append(color).append(" ").append(COLOR_NAMES[total_groups]).append("\n");
- total_groups ++;
- ArrayList<Integer> present_genomes = new ArrayList<>();
- Iterable<Relationship> all_rels = hm_node.getRelationships();
- info_builder_part2.append("#").append(hm_node_id).append("\n");
- int[] genome_counts = new int[total_genomes];
- for (Relationship rel : all_rels) {
- Node mrna_node = rel.getEndNode();
- int genome_nr = (int) mrna_node.getProperty("genome");
- String protein_ID = (String) mrna_node.getProperty("protein_ID");
- if (skip_array[genome_nr-1]) {
- continue;
- }
- genome_counts[genome_nr-1] += 1;
- int copy_nr = genome_counts[genome_nr-1];
- total_sequences ++;
- System.out.print("\rGathering sequences: " + total_groups + "/" + hm_nodes_list.size() + " homology groups. " + total_sequences + " sequences");
- long mrna_node_id = mrna_node.getId();
- if (protein_ID.contains(":") || protein_ID.contains(";")) { // not allowed in newick format
- String clean_id = protein_ID.replace(":",".").replace(";",".");
- proper_identifiers_set.add(clean_id);
- use_different_identifiers = true;
- incorrect_identifiers.append(protein_ID).append(",").append(genome_nr).append("_").append(copy_nr).append("_").append(clean_id).append("\n");
- } else {
- proper_identifiers_set.add(protein_ID);
- incorrect_identifiers.append(protein_ID).append(",").append(genome_nr).append("_").append(copy_nr).append("_").append(protein_ID).append("\n");
- }
- String mrna_protein = get_protein_sequence(mrna_node);
- prot_lengths.add(mrna_protein.length());
- present_genomes.add(genome_nr);
- if (PROTEOME) {
- info_builder_part2.append(genome_nr).append(", ").append(protein_ID).append(", ").append(mrna_node_id).append(", ")
- .append(mrna_protein.length()).append(", ").append(copy_nr).append("\n");
- } else {
- String mrna_name = (String) mrna_node.getProperty("name");
- if (mrna_name.equals("-")) {
- mrna_name = hm_node_id + "";
- }
- int[] address = (int[]) mrna_node.getProperty("address");
- String mrna_sequence = get_nucleotide_sequence(mrna_node);
- nuc_lengths.add(mrna_sequence.length());
- nuc_fasta.append(">").append(protein_ID).append("\n").append(mrna_sequence).append("\n");
- info_builder_part2.append(genome_nr).append(", ").append(mrna_name).append(", ").append(protein_ID).append(", ").append(mrna_node_id)
- .append(", ").append(genome_nr).append(" ").append(address[1]).append(" ").append(address[2]).append(" ").append(address[3]).append(", ")
- .append(mrna_sequence.length()).append(", ").append(copy_nr).append("\n");
-
- }
- prot_fasta.append(">").append(protein_ID).append("\n").append(mrna_protein).append("\n");
- genome_order.append(genome_nr).append(",").append(protein_ID).append("\n");
- itol_hm_template.append(genome_nr).append("_").append(protein_ID).append(",").append(color).append("\n");
- append_msa_multi_pheno_template(genome_nr, pheno_counter_map,phenotype_counter, phenotypes_list, itol_pheno_template, protein_ID);
- }
- String genome_freqs = determine_frequency_list_int(present_genomes);
- TreeSet<Integer> absent = get_missing_genomes_in_arraylist(present_genomes);
- info_builder.append("#").append(hm_node_id).append("\nPresent: ").append(genome_freqs)
- .append("\nAbsent: ").append(absent).append("\n\n");
- info_builder_part2.append("\n");
- }
- tx.success(); // transaction successful, commit changes
- }
- System.out.println("\n");
- String output_path = "alignments/grouping_v" + grouping_version + "/multiple_groups/";
- delete_directory_in_DB(output_path); // delete files from a previous run
- create_directory_in_DB("alignments/grouping_v" + grouping_version);
- create_directory_in_DB(output_path + "similarity_identity");
- create_directory_in_DB(output_path + "var_inf_positions");
- String prot_lengths_str = determine_frequency_list_int(prot_lengths);
- write_SB_to_file_in_DB(prot_fasta, output_path + "prot_input.fasta");
- write_SB_to_file_in_DB(genome_order, output_path + "genome_order.info");
- write_string_to_file_in_DB(hm_color_info.toString() + itol_hm_template.toString(), output_path + "itol_tree_template_groups.txt");
- create_msa_multi_pheno_template(phenotypes_list, itol_pheno_template, output_path);
- String add_incorrect_ids = "";
- if (use_different_identifiers || proper_identifiers_set.size() < total_sequences) {
- write_SB_to_file_in_DB(incorrect_identifiers, output_path + "identifiers_incorrect_for_fasttree");
- replace_ids_in_itol_templates(incorrect_identifiers, WORKING_DIRECTORY + output_path);
- add_incorrect_ids = incorrect_identifiers.toString();
- }
-
- if (PROTEOME) {
- write_string_to_file_in_DB("Protein lengths: " + prot_lengths_str + "\n\n"
- + info_builder.toString() + info_builder_part2.toString() + add_incorrect_ids, output_path + "sequences.info");
- } else {
- String nuc_lengths_str = determine_frequency_list_int(nuc_lengths);
- write_string_to_file_in_DB("Protein lengths: " + prot_lengths_str
- + "\nNucleotide lengths: " + nuc_lengths_str + "\n\n"
- + info_builder.toString() + info_builder_part2.toString() + add_incorrect_ids, output_path + "sequences.info");
- write_SB_to_file_in_DB(nuc_fasta, output_path + "nuc_input.fasta");
- }
-
- return total_sequences;
- }
-
- /**
- *
- * @param incorrect_identifiers
- * @param path
- */
- public void replace_ids_in_itol_templates(StringBuilder incorrect_identifiers, String path) {
- String[] incorrect_identifiers_array = incorrect_identifiers.toString().split("\n");
- ArrayList<String> new_identifiers = new ArrayList<>();
- for (String line : incorrect_identifiers_array) {
- if (!line.startsWith("#")) {
- String[] line_array = line.split(",");
- new_identifiers.add(line_array[line_array.length-1]);
- }
- }
- replace_itol_template(path + "itol_tree_template_groups.txt", new_identifiers);
- if (check_if_file_exists(path + "itol_tree_template_phenotype.txt")) {
- replace_itol_template(path + "itol_tree_template_phenotype.txt", new_identifiers);
- }
- }
-
- /**
- *
- * @param itol_template
- * @param new_identifiers
- */
- public void replace_itol_template(String itol_template, ArrayList<String> new_identifiers) {
- StringBuilder new_template = new StringBuilder();
- try (BufferedReader in = new BufferedReader(new FileReader(itol_template))) {
- boolean print = false;
- int counter = 0;
- for (int c = 0; in.ready();) {
- String line = in.readLine().trim();
- if (line.equals("DATA")) {
- print = true;
- new_template.append(line).append("\n");
- continue;
- }
- if (print) {
- String[] line_array = line.split(",");
- new_template.append(new_identifiers.get(counter)).append(",").append(line_array[line_array.length-1]).append("\n");
- counter ++ ;
- } else {
- new_template.append(line).append("\n");
- }
- }
- in.close();
- } catch (IOException ioe) {
- System.out.println("\nUnable to read: " + itol_template + "\n");
- System.exit(1);
- }
- write_SB_to_file_full_path(new_template, itol_template);
- }
-
- /**
- *
- * @param genome_nr
- * @param pheno_counter_map
- * @param phenotype_counter
- * @param phenotypes_list
- * @param itol_pheno_template
- * @param protein_id
- */
- public void append_msa_multi_pheno_template(int genome_nr, HashMap<String, Integer> pheno_counter_map, AtomicInteger phenotype_counter,
- ArrayList<String> phenotypes_list, StringBuilder itol_pheno_template, String protein_id) {
-
- if (PHENOTYPE == null) {
- return;
- }
- String current_pheno = geno_pheno_map.get(genome_nr);
- if (current_pheno.equals("?")) {
- return;
- }
- String color;
- if (pheno_counter_map.containsKey(current_pheno)) {
- int pheno_count = pheno_counter_map.get(current_pheno);
- color = COLOR_CODES[pheno_count];
- } else {
- color = COLOR_CODES[phenotype_counter.get()];
- phenotypes_list.add(current_pheno);
- pheno_counter_map.put(current_pheno, phenotype_counter.get());
- phenotype_counter.getAndIncrement();
- }
- itol_pheno_template.append(genome_nr).append("_").append(protein_id).append(",").append(color).append("\n");
- }
-
- /**
- *
- * @param phenotypes_list
- * @param itol_pheno_template
- * @param output_path
- */
- public void create_msa_multi_pheno_template(ArrayList<String> phenotypes_list, StringBuilder itol_pheno_template, String output_path) {
- if (PHENOTYPE == null) {
- return;
- }
- int sequence_nr = 0;
- StringBuilder pheno_color_info = new StringBuilder("Colors used for '" + PHENOTYPE +"' phenotype\n\n");
- for (String pheno : phenotypes_list) {
- pheno_color_info.append("#").append(pheno).append(" ").append(COLOR_CODES[sequence_nr]).append(" ").append(COLOR_NAMES[sequence_nr]).append("\n");
- sequence_nr ++;
- }
- write_string_to_file_in_DB(pheno_color_info + "\n" + itol_pheno_template.toString(), output_path + "itol_tree_template_phenotype.txt");
- }
-
- /**
- *
- * @param present_genomes
- * @return
- */
- public TreeSet<Integer> get_missing_genomes_in_arraylist(ArrayList<Integer> present_genomes) {
- TreeSet<Integer> absent = new TreeSet<>();
- for (int i = 1; i <= total_genomes; ++i) {
- if (skip_array[i-1]) {
- continue;
- }
- if (!present_genomes.contains(i)) {
- absent.add(i);
- }
- }
- return absent;
- }
-
- /**
- * Three options
- * 1. Read the input file given through -hm
- * 2. Read homology group identifiers from the 'SELECTED_HMGROUPS' string
- * 3. Retrieve all homology groups with more than 1 sequence
- *
- * @param standalone
- * @return
- */
- public static ArrayList<Node> retrieve_hmgroups(boolean standalone) {
- ArrayList<Node> hm_node_list = new ArrayList<>();
- if (SELECTED_HMGROUPS != null && standalone) { // 1. read input file
- hm_node_list = read_hmgroup_input_file();
- } else if (SELECTED_HMGROUPS != null && !standalone) { // 2. hmgroup ids are placed in the SELECTED_HMGROUPS string, not in a file
- hm_node_list = retrieve_hmgroups_of_matching_input_string();
- } else { // 3. if no --homology-groups are given, retrieve all of them
- hm_node_list = retrieve_all_hmgroups();
- }
- return hm_node_list;
- }
-
- /**
- msa_of_group()
-
- Requires
- -dp
- -hm
-
- *
- @param standalone
- @param trim
- @param read_alignments
- */
- public void msa_of_group(boolean standalone, boolean trim, boolean read_alignments) {
- if (standalone) {
- System.out.println("\nMultiple sequence alignment on homology groups\n");
- report_number_of_threads(true, true); // prints how many threads were selected by user
- }
- check_if_graphDb_is_available(); // starts up the graph database if needed
- check_if_program_exists_stderr("FastTree -h", 100, "Fasttree", true); // check if program is set to the $PATH
- check_if_program_exists_stderr("mafft -h", 100, "MAFFT", true); // check if program is set to the $PATH
- try (Transaction tx = graphDb.beginTx()) { // start database transaction
- Node pangenome_node = graphDb.findNodes(pangenome_label).next();
- check_if_panproteome(pangenome_node); // sets PROTEOME boolean that controls functions, retrieves K_size & total_genomes
- if (standalone) {
- create_skip_arrays(false, true); // create skip array if --skip/-ref is provided by user
- check_mode_for_msa();
- }
- check_current_grouping_version(); // check which version of homology grouping is active
- retrieve_phenotypes(); // Creates and fills geno_pheno_map and phenotype_map when a phenotype was provided by the user
- if (grouping_version < 1) {
- System.out.println("\nNo homology grouping is active\n");
- System.exit(1);
- }
- tx.success(); // transaction successful, commit changes
- } catch (NotFoundException nfe) {
- System.out.println("Unable to start the pangenome database\n");
- return;
- }
- if (PHENOTYPE == null && standalone) {
- System.out.println("No --phenotype was provided, unable to find phenotype specific SNPs\n");
- }
-
- create_directory_in_DB("alignments/grouping_v" + grouping_version);
- create_directory_in_DB("alignments/grouping_v" + grouping_version + "/groups/");
- ArrayList<Node> hm_node_list = new ArrayList<>();
- String output_path = WORKING_DIRECTORY + "alignments/grouping_v" + grouping_version + "/";
- try (Transaction tx = graphDb.beginTx()) { // start database transaction
- hm_node_list = retrieve_hmgroups(standalone);
- if (!trim) {
- hm_node_list = prepare_msa_sequences(hm_node_list, false);
- System.out.println("Aligning " + hm_node_list.size() + " sequences");
- } else {
- System.out.println("Aligning " + hm_node_list.size() + " trimmed sequences");
- }
- tx.success(); // transaction successful, commit changes
- }
-
-
- write_log = true;
- run_msa(hm_node_list, trim);
- if (standalone) { // when run from commandline: trim and restart to align the trimmed sequences
- hm_node_list = trim_prealigned_proteins(hm_node_list);
- SELECTED_HMGROUPS = ""; // SELECTED_HMGROUPS will be read by the function after restarting
- for (Node hm_node : hm_node_list) { // add groups that remain after trimming
- SELECTED_HMGROUPS += hm_node.getId() + ",";
- }
- if (hm_node_list.isEmpty()) {
- System.out.println("\n\nNone of the trimmed alignments can be used for the second alignment round. "
- + "Use '--mode no-trimming' to further analyze them\n");
- return;
- } else {
- System.out.println("\nRestarting this function to align " + hm_node_list.size() + " trimmed sequences");
- }
- msa_of_group(false, true, true); // restarting this function to align the trimmed sequences
- } else if (!standalone && read_alignments) { // this only happens when this function calls itself
- rscript_for_group_var_inf_site_distances();
- create_write_msa_trimmed_output(hm_node_list);
- include_identity_similarity_to_relations(hm_node_list, trim); // this function is currently disabled, do not remove
- print_results_msa(output_path);
- }
- }
-
+
/**
- * @param output_path
+ *
+ * @param msaNames
*/
- public static void print_results_msa(String output_path) {
- if (PHENOTYPE == null) {
- System.out.println("\nOutput written to:\n "
- + output_path + "groups/\n\n"
- + "Provide a phenotype to find phenotype specific variants! (--phenotype)\n");
- } else {
- System.out.println("\nAlignments written to:\n "
- + output_path + "groups/"
- + "\n\nPhenotype output written to:\n"
- + " " + output_path + "groups_with_phenotype_specific_changes.txt");
-
- if ((Mode.startsWith("BOTH") || Mode.startsWith("NUCLEOTIDE"))) { // nucleotide sequences
- System.out.print(" " + output_path + "phenotype_specific_changes_nuc.txt\n");
- }
- if ((Mode.startsWith("BOTH") || Mode.startsWith("PROTEIN"))) { // protein sequences
- System.out.print(" " + output_path + "phenotype_specific_changes_prot.txt\n");
- }
- System.out.println("");
- }
- }
-
- /**
- @param hm_node_list
- */
- public void create_write_msa_trimmed_output(ArrayList<Node> hm_node_list) {
- String partial_output_path = WORKING_DIRECTORY + "alignments/grouping_v" + grouping_version + "/";
+ public static void create_write_msa_trimmed_output(ArrayList<String> msaNames, String outdirMsa) {
System.out.println("");
System.out.println("\rReading alignments");
ArrayList<String> nuc_or_prot_list = prepare_type_list_for_msa(); // list can contain "protein", "nucleotide" or both
initialize_BLOSUM();
- delete_file_full_path(partial_output_path + "/groups_with_phenotype_specific_changes.txt");
+ delete_file_full_path(outdirMsa + "/groups_with_phenotype_specific_changes.txt");
+
for (String nuc_or_prot : nuc_or_prot_list) {
ArrayList<String> groups_with_inf_sites = new ArrayList<>();
ArrayList<String> groups_with_var_sites = new ArrayList<>();
@@ -10721,106 +9207,71 @@ public class Classification {
nuc_or_prot_short = "nuc";
nuc_or_prot_cap = "Nucleotide";
}
-
+
StringBuilder pheno_specific_output = new StringBuilder("# Each row contains: position in the alignment, "
+ "reference letter/other letters found, phenotype, number of sequences with the phenotype and letter/total sequences with phenotype\n");
HashMap<String, Integer> pheno_specific_group_sites = new HashMap<>();
int group_counter = 1;
- for (Node hm_node : hm_node_list) {
- String group_id = hm_node.getId() +"";
+ for (String group_id : msaNames) {
//System.out.println(" -> " + hmgroup);
- String output_path = partial_output_path + "groups/" + group_id + "/";
+ String output_path = outdirMsa + group_id + "/";
new File(output_path + "output/var_inf_positions/").mkdir(); // create directory
new File(output_path + "output/similarity_identity/").mkdir();// create directory
HashMap<String, Integer> shared_snps_map = new HashMap<>();
- System.out.print("\r Reading " + nuc_or_prot + " alignments: " + group_counter + "/" + hm_node_list.size() +
+ System.out.print("\r Reading " + nuc_or_prot + " alignments: " + group_counter + "/" + msaNames.size() +
". variable/informative sites: " + total_var_inf_sites[0] + "/" + total_var_inf_sites[1]);
group_counter ++;
-
+
String genome_order = output_path + "/input/genome_order.info";
String input_file = output_path + "output/" + nuc_or_prot_short + "_trimmed.afa";
- int[] var_inf_sites = count_var_inf_sites_in_msa(shared_snps_map, pheno_specific_output, pheno_specific_group_sites,
- input_file, group_id, nuc_or_prot + "trimmed", genome_order); // variable, informative, conserved sites
-
- if (var_inf_sites[0] > 0) { // // when variable sites are found
+ int[] var_inf_sites = count_var_inf_sites_in_msa(shared_snps_map, pheno_specific_output, pheno_specific_group_sites,
+ input_file, group_id, nuc_or_prot + "trimmed", genome_order); // variable, informative, conserved sites
+
+ if (var_inf_sites[0] > 0) { // when variable sites are found
groups_with_var_sites.add(group_id);
total_var_inf_sites[0] += var_inf_sites[0];
- }
- if (var_inf_sites[1] > 0) { // when parsimony informative sites are present
+ }
+ if (var_inf_sites[1] > 0) { // when parsimony informative sites are present
groups_with_inf_sites.add(group_id);
total_var_inf_sites[1] += var_inf_sites[1];
- }
+ }
create_new_newick_file_for_phenotype(input_file, true, genome_order); // rename labels in phylogeny
- create_shared_site_matrices(shared_snps_map, output_path + "output/var_inf_positions/", var_inf_sites[0],
+ create_shared_site_matrices(shared_snps_map, output_path + "output/var_inf_positions/", var_inf_sites[0],
"", nuc_or_prot_short + "_trimmed", genome_order);
- create_shared_site_matrices(shared_snps_map, output_path + "output/var_inf_positions/", var_inf_sites[1],
+ create_shared_site_matrices(shared_snps_map, output_path + "output/var_inf_positions/", var_inf_sites[1],
"#inf", nuc_or_prot_short + "_trimmed", genome_order);
if (nuc_or_prot.equals("protein")) {
- create_similarity_matrices(shared_snps_map, output_path + "output/similarity_identity/" + nuc_or_prot_short + "_trimmed_similarity.csv",
- var_inf_sites[0], var_inf_sites[2], genome_order);
+ create_similarity_matrices(shared_snps_map, output_path + "output/similarity_identity/" + nuc_or_prot_short + "_trimmed_similarity.csv",
+ var_inf_sites[0], var_inf_sites[2], genome_order);
}
- create_identity_matrices(shared_snps_map, var_inf_sites[0], var_inf_sites[2],
+ create_identity_matrices(shared_snps_map, var_inf_sites[0], var_inf_sites[2],
nuc_or_prot, output_path + "output/similarity_identity/" + nuc_or_prot_short + "_trimmed_identity.csv", genome_order);
}
-
- System.out.print("\r " + nuc_or_prot_cap + " variable/informative positions: " + total_var_inf_sites[0] + "/" + total_var_inf_sites[1] +
- " (" + groups_with_var_sites.size() + "/" + groups_with_inf_sites.size() + " groups) \n"); // spaces are intentional
- prepare_phenotype_results_msa(nuc_or_prot, hm_node_list, pheno_specific_group_sites, partial_output_path, pheno_specific_output.toString());
- String output = "# " + groups_with_var_sites.size() + " groups with variable sites:\n"
+
+ prepare_phenotype_results_msa(nuc_or_prot, msaNames, pheno_specific_group_sites, outdirMsa, pheno_specific_output.toString());
+ String output = "# " + groups_with_var_sites.size() + " groups with variable sites:\n"
+ groups_with_var_sites.toString().replace("[","").replace(" ","").replace("]","") + "\n\n" +
- "# " + groups_with_inf_sites.size() + " groups with parsimony informative positions:\n"
+ "# " + groups_with_inf_sites.size() + " groups with parsimony informative positions:\n"
+ groups_with_inf_sites.toString().replace("[","").replace(" ","").replace("]","");
-
- write_string_to_file_full_path(output, partial_output_path + "groups_with_var_inf_positions_" + nuc_or_prot_short + ".txt");
- }
- }
-
- /**
- * Try to align the sequences 3 times before shutting down the function
- * @param hm_node_list
- * @param trim
- */
- public void run_msa(ArrayList<Node> hm_node_list, boolean trim) {
- boolean pass = false; // pass when all alignment (& phylogeny) files exists
- int loop_counter = 0;
- while (!pass) {
- ArrayList<Node> to_be_aligned_list = check_if_msa_is_complete(hm_node_list, trim);
- if (to_be_aligned_list.isEmpty()) {
- pass = true;
- continue;
- }
- if (THREADS == 1) {
- int hm_counter = 1;
- for (Node hm_node : hm_node_list) {
- System.out.print("\r Aligning homology groups: " + hm_counter + "/" + hm_node_list.size() + " groups");
- run_msa_commands_mafft(hm_node.getId()+"", trim);
- hm_counter ++;
- }
- } else { // more than 1 thread selected
- LOG = true; // to print the status of the shell script
- shell_script_for_parralel_mafft(hm_node_list, trim);
- shell_script_for_parralel_fasttree(hm_node_list, trim);
- LOG = false;
- }
- System.out.println("");
- loop_counter ++;
- if (loop_counter == 3) {
- System.out.print("\nFailed to align " + to_be_aligned_list.size() + " groups: ");
- for (Node group_node : to_be_aligned_list) {
- System.out.print(group_node.getId() + ", ");
- }
- System.out.println("");
- System.exit(1);
+
+ write_string_to_file_full_path(output, outdirMsa + "groups_with_var_inf_positions_" + nuc_or_prot_short + ".txt");
+
+ String additional_spaces = "";
+ if (nuc_or_prot_cap.equals("Protein")) {
+ additional_spaces = " ";
}
+ System.out.println("\r " + nuc_or_prot_cap + " variable sites " + additional_spaces + ": " + total_var_inf_sites[0] + " (" + groups_with_var_sites.size() + " alignments)"
+ + " \n" // spaces are intentional
+ + " " + nuc_or_prot_cap + " informative sites" + additional_spaces +": " + total_var_inf_sites[1] + " (" + groups_with_inf_sites.size() + " alignments)");
}
}
-
+
/**
- * Currently not used.
- * @param hm_node_list
- * @param trimmed
+ * Currently not used
+ * @param msaNames
+ * @param trimmed
*/
- public static void include_identity_similarity_to_relations(ArrayList<Node> hm_node_list, boolean trimmed) {
+ public static void include_identity_similarity_to_relations(ArrayList<String> msaNames, boolean trimmed) {
boolean test = true;
if (test) {
return; // this function is currently disabled. do not remove
@@ -10837,16 +9288,15 @@ public class Classification {
file_name += "_trimmed";
}
int hm_counter = 0;
- for (Node hm_node : hm_node_list) {
- String group_id = hm_node.getId() + "";
+ for (String group_id : msaNames) {
hm_counter ++;
System.out.print("\rUpdating identity and similarity scores on 'is_similar_to' relationships: "
- + nuc_or_prot + ", " + hm_counter + "/" + hm_node_list.size());
+ + nuc_or_prot + ", " + hm_counter + "/" + msaNames.size());
HashMap<String, Relationship> is_similar_rels_map = create_protein_id_hashmap_of_group(group_id);
if (is_similar_rels_map.isEmpty()) {
continue;
}
- String input_file = WD_full_path + "alignments/grouping_v" + grouping_version + "/groups/" +
+ String input_file = WD_full_path + "alignments/grouping_v" + grouping_version + "/" +
group_id + "/output/similarity_identity/" + file_name;
HashMap<String, Double> identity_score_map = read_identity_similarity_matrix(input_file + "_identity.csv");
include_identity_similarity(identity_score_map, is_similar_rels_map, "identity", trimmed, nuc_or_prot);
@@ -10973,16 +9423,16 @@ public class Classification {
}
return score_map;
}
-
+
/**
- *
+ *
* @param nuc_or_prot
- * @param hm_node_list
+ * @param msaNames
* @param pheno_specific_group_sites
* @param output_path
- * @param pheno_specific_output
+ * @param pheno_specific_output
*/
- public static void prepare_phenotype_results_msa(String nuc_or_prot, ArrayList<Node> hm_node_list,
+ public static void prepare_phenotype_results_msa(String nuc_or_prot, ArrayList<String> msaNames,
HashMap<String, Integer> pheno_specific_group_sites, String output_path, String pheno_specific_output) {
if (PHENOTYPE == null) {
@@ -10997,7 +9447,7 @@ public class Classification {
boolean snps_found = false;
StringBuilder pheno_specific_header = new StringBuilder("# Selected phenotype: " + PHENOTYPE
- + "\n# Phenotype specific " + snp_or_substi1 + "s in " + nuc_or_prot + " sequences of " + hm_node_list.size() + " homology groups\n");
+ + "\n# Phenotype specific " + snp_or_substi1 + "s in " + nuc_or_prot + " sequences of " + msaNames.size() + " homology groups\n");
for (Map.Entry<String, Integer> entry : pheno_specific_group_sites.entrySet()) {
String phenotype = entry.getKey();
if (phenotype.endsWith("_groups")) {
@@ -11089,61 +9539,6 @@ public class Classification {
write_string_to_file_full_path(nuc_or_prot_cap + output_str, output_path + "/groups_with_phenotype_specific_changes.txt");
}
}
-
- /**
- * Homology group identifiers are given in the SELECTED_HMGROUP string, not in a file
- * @return
- */
- public static ArrayList<Node> retrieve_hmgroups_of_matching_input_string() {
- ArrayList<Node> all_hm_list = new ArrayList<>();
- String[] groups_array = SELECTED_HMGROUPS.split(",");
- for (String group_id_str : groups_array) {
- long group_id = Long.parseLong(group_id_str);
- Node hm_node = graphDb.getNodeById(group_id);
- test_if_correct_label(hm_node, homology_group_label, true);
- all_hm_list.add(hm_node);
- }
- return all_hm_list;
- }
-
- public static int count_not_unique_hmgroups() {
- int counter = 0;
- ResourceIterator<Node> hm_nodes = graphDb.findNodes(homology_group_label);
- while (hm_nodes.hasNext()) {
- Node hm_node = hm_nodes.next();
- int num_members = (int) hm_node.getProperty("num_members");
- if (num_members == 1) {
- continue;
- }
- counter++;
- }
- return counter;
- }
-
- /**
- * Store all homology groups nodes with more than 1 member in an arraylist
- * @return
- */
- public static ArrayList<Node> retrieve_all_hmgroups() {
- ArrayList<Node> hm_list = new ArrayList<>();
- System.out.print("\rNo homology groups were provided via --homology-groups or -hm, using all ");
- ResourceIterator<Node> hm_nodes = graphDb.findNodes(homology_group_label);
- int counter = 0;
- while (hm_nodes.hasNext()) {
- Node hm_node = hm_nodes.next();
- if (counter > 5) {
- //continue;
- }
- int num_members = (int) hm_node.getProperty("num_members");
- if (num_members == 1) {
- continue;
- }
- hm_list.add(hm_node);
- counter ++;
- }
- System.out.println("Aligning (all) " + hm_list.size() + " groups with more than one sequence");
- return hm_list;
- }
/**
* Requires original fasta input file and aligned output from mafft
@@ -11219,23 +9614,6 @@ public class Classification {
}
}
-
- public void convert_afa_to_aligned_fasta_loop(ArrayList<Node> hm_nodes, boolean trim, String dot) {
- //int group_counter;
- for (Node hm_node2 : hm_nodes) {
- //group_counter ++;
- String path2 = WORKING_DIRECTORY + "/alignments/grouping_v" + grouping_version + "/groups/" + hm_node2.getId() + "/";
- String in_path2 = path2 + "input/";
- String out_path2 = path2 + "output/";
- if (Mode.startsWith("BOTH") || Mode.startsWith("PROTEIN") || !trim) {
- convert_afa_to_aligned_fasta(in_path2 + "prot.fasta", out_path2 + "prot" + dot + "afa");
- }
- if (Mode.startsWith("BOTH") || Mode.startsWith("NUCLEOTIDE")) { //
- convert_afa_to_aligned_fasta(in_path2 + "nuc.fasta", out_path2 + "nuc" + dot + "afa");
- }
- }
- }
-
/*
Returned list can contain "protein", "nucleotide" or both.
*/
@@ -11243,7 +9621,7 @@ public class Classification {
ArrayList<String> type_list = new ArrayList<>();
if (PROTEOME) {
type_list.add("protein");
- } else if (Mode.startsWith("BOTH")) {
+ } else if (Mode.startsWith("BOTH") || Mode.equals("0")) {
type_list.add("protein");
type_list.add("nucleotide");
} else if (Mode.startsWith("PROTEIN")) {
@@ -11309,43 +9687,22 @@ public class Classification {
if (!overwrite && present) {
return;
}
-
- String identifiers_file = input_array[0] + "input/identifiers_incorrect_for_fasttree";
- boolean incorrect_identifiers = check_if_file_exists(identifiers_file);
+
HashMap<String, String> sequence_phenotype = new HashMap<>();
- if (incorrect_identifiers) { // some of the identifiers are identical
- try (BufferedReader in = new BufferedReader(new FileReader(identifiers_file))) {
- for (int c = 0; in.ready();) {
- String line = in.readLine(); //important that read is not trimmed
- if (line.startsWith("#")) {
- continue;
- }
- String[] line_array = line.split(",");
- String[] line_array2 = line_array[1].split("_");
- String pheno = geno_pheno_map.get(Integer.parseInt(line_array2[0]));
- sequence_phenotype.put(line_array[1], line_array2[0] + "_" + line_array2[1] + "_" + pheno + "_" + line_array2[2]);
- }
- } catch (IOException ioe) {
- System.out.println("\nUnable to read: " + identifiers_file + "\n");
- System.exit(1);
- }
- } else {
- int sequence_counter = 0;
- try (BufferedReader in = new BufferedReader(new FileReader(input_fasta))) {
- for (int c = 0; in.ready();) {
- String line = in.readLine();
- if (line.startsWith(">")) {
- int genome_nr = genome_order_list.get(sequence_counter);
- String pheno = geno_pheno_map.get(genome_nr);
- String[] line_array = line.split(" ");
- sequence_phenotype.put(line_array[0].replace(">",""), genome_nr + " " + pheno);
- }
+ int sequence_counter = 0;
+ try (BufferedReader in = new BufferedReader(new FileReader(input_fasta))) {
+ for (int c = 0; in.ready();) {
+ String line = in.readLine();
+ if (line.startsWith(">")) {
+ int genome_nr = genome_order_list.get(sequence_counter);
+ String pheno = geno_pheno_map.get(genome_nr);
+ String[] line_array = line.split(" ");
+ sequence_phenotype.put(line_array[0].replace(">",""), genome_nr + " " + pheno);
}
- in.close();
- } catch (IOException ioe) {
- System.out.println("Unable to read: " + input_fasta + "\n");
- System.exit(1);
- }
+ }
+ } catch (IOException ioe) {
+ System.out.println("Unable to read: " + input_fasta + "\n");
+ System.exit(1);
}
try (BufferedReader in = new BufferedReader(new FileReader(input_newick))) {
@@ -11354,309 +9711,36 @@ public class Classification {
for (String key : sequence_phenotype.keySet()) { //for (String key : position_map.keySet()) {
String value = sequence_phenotype.get(key);
String[] value_array = value.split(" ");
- if (incorrect_identifiers) {
- line = line.replace(key, value);
- } else {
- line = line.replace(key, value_array[1] + "_" + key);
- }
-
+ line = line.replace(key, value_array[1] + "_" + key);
}
write_string_to_file_full_path(line, output_newick);
}
- in.close();
} catch (IOException ioe) {
System.out.println("Unable to read: " + input_newick + "\n");
System.exit(1);
}
}
-
- /**
- * Check if the required output files of a multiple sequence alignment exist.
- * Mode combinations 0,1,2 with FAST
- * @param hm_node_list array with strings of homology group node (identifiers) that still need to be aligned
- * @param trim
- * @return
- */
- public static ArrayList<Node> check_if_msa_is_complete(ArrayList<Node> hm_node_list, boolean trim) {
- ArrayList<Node> to_be_aligned_list = new ArrayList<>();
- String dot = ".";
- if (trim) {
- dot = dot.replace(".","_trimmed.");
- }
-
- int done_count = 0, not_done_count = 0;
- for (Node hm_node : hm_node_list) {
- String hmgroup = hm_node.getId() +"";
- String path = WORKING_DIRECTORY + "/alignments/grouping_v" + grouping_version + "/groups/" + hmgroup + "/output/";
- boolean pass1, pass2;//, pass3, pass4;
- if (FAST) {
- pass1 = check_if_file_exists(path + "nuc" + dot + "fasta");
- pass2 = check_if_file_exists(path + "prot" + dot + "fasta");
- } else {
- pass1 = check_if_file_exists(path + "nuc" + dot + "newick");
- pass2 = check_if_file_exists(path + "prot" + dot + "newick");
- }
- if (Mode.startsWith("PROTEIN")) { // only protein sequences
- pass1 = true;
- } else if (Mode.startsWith("NUCLEOTIDE") && trim) { // only nucleotide sequences, proteins are still used in first round to trim sequences
- pass2 = true;
- }
-
- if (!pass1 || !pass2) {
- to_be_aligned_list.add(hm_node);
- not_done_count ++;
- } else {
- done_count ++;
- }
-
- if ((not_done_count + done_count) % 100 == 0 || (not_done_count + done_count) == hm_node_list.size()) {
- System.out.print("\r Checking MSA completeness -> " + not_done_count + " not done, " + done_count + " done ");
- }
- }
-
- System.out.print("\r "); // spaces are intentional
- return to_be_aligned_list;
- }
-
- /**
- *
- * @param script
- * @param process_counter
- * @param group_counter
- * @param total_groups
- * @param message
- */
- public static void add_wait_for_alignment_shell(StringBuilder script, int process_counter, int group_counter, int total_groups, String message) {
- if (process_counter % THREADS == 0) {
- script.append("printf \"\\r").append(message).append(group_counter).append("/").append(total_groups).append(" groups\"\nwait\n");
- }
- }
-
- /**
- * MAFFT is run in parralel using a shell script
- * Why? running multiple threads that mafft with ExecCommand.ExecCommand(); caused an issues where threads got stuck.
- * (Can still be written, each thread should have its own buffered reader/writer)
- * @param hm_node_list
- * @param trim
- */
- public void shell_script_for_parralel_mafft(ArrayList<Node> hm_node_list, boolean trim) {
- int group_counter = 0, process_counter = 0;
- String dot = ".";
- if (trim) {
- dot = dot.replace(".","_trimmed.");
- }
- StringBuilder script = new StringBuilder();
- System.out.print("\r");
- String[] run_shell_cmd = new String[]{"/bin/sh", "script.sh"};
- ArrayList<Node> current_group_selection = new ArrayList<>();
- for (Node hm_node : hm_node_list) {
- group_counter ++;
- create_directory_in_DB("alignments/grouping_v" + grouping_version + "/groups/" + hm_node.getId() + "/output/");
- String path = WORKING_DIRECTORY + "alignments/grouping_v" + grouping_version + "/groups/" + hm_node.getId() + "/";
- String in_path = path + "input/";
- String out_path = path + "output/";
- current_group_selection.add(hm_node);
- if ((Mode.startsWith("BOTH") || Mode.startsWith("PROTEIN") || !trim)) { // protein alignment is required for trimming
- if (!check_if_file_exists(out_path + "prot" + dot + "afa")) {
- script.append("mafft --auto --anysymbol --quiet --thread 1 --clustalout ").append(in_path).append("prot").append(dot).append("fasta > ")
- .append(out_path).append("prot").append(dot).append("afa &\n");
- process_counter ++;
- add_wait_for_alignment_shell(script, process_counter, group_counter, hm_node_list.size(), "Aligning homology groups: ");
- }
- }
-
- if ((Mode.startsWith("BOTH") || Mode.startsWith("NUCLEOTIDE"))) { //
- if (!check_if_file_exists(out_path + "nuc" + dot + "afa")) {
- script.append("mafft --auto --anysymbol --quiet --thread 1 --clustalout ").append(in_path).append("nuc").append(dot).append("fasta > ")
- .append(out_path).append("nuc").append(dot).append("afa &\n");
- process_counter ++;
- add_wait_for_alignment_shell(script, process_counter, group_counter, hm_node_list.size(), "Aligning homology groups: ");
- }
- }
- if (process_counter % 100 == 0 && process_counter > 0) {
- // convert afa file to fasta. do this after every 100 alignments. the fasta file is checked by tools checking the progress
- script.append("printf \"\\rAligning homology groups ").append(group_counter).append("/").append(hm_node_list.size()).append(" groups\"\nwait\n");
- write_SB_to_file_full_path(script, "script.sh");
- ExecCommand.ExecCommand(run_shell_cmd);
- script = new StringBuilder();
- convert_afa_to_aligned_fasta_loop(current_group_selection, trim, dot);
- }
- }
- script.append("printf \"\\rAligning homology groups ").append(group_counter).append("/").append(hm_node_list.size()).append(" groups\"\nwait\n");
- write_SB_to_file_full_path(script, "script.sh");
- ExecCommand.ExecCommand(run_shell_cmd);
- convert_afa_to_aligned_fasta_loop(current_group_selection, trim, dot);
- System.out.println("\r "); // spaces are intentional
- delete_file_full_path("log");
- delete_file_full_path("script.sh");
- }
-
- /**
- *
- * @param hm_node_list
- * @param trim
- */
- public void shell_script_for_parralel_fasttree(ArrayList<Node> hm_node_list, boolean trim) {
- String[] cmd = new String[]{"/bin/sh", "script.sh"};
- int group_counter = 0, process_counter = 0;
- String dot = ".";
- if (trim) {
- dot = dot.replace(".","_trimmed.");
- }
- StringBuilder script = new StringBuilder();
- if (FAST) { // no phylogenies are created when the --fast argument was included
- return;
- }
-
- ArrayList<String> groups_with_incorrect_ids = new ArrayList<>();
- ArrayList<String> groups_with_correct_ids = new ArrayList<>();
- for (Node hm_node : hm_node_list) {
- String add = ""; // this string becomes '_temp' for groups with non unique identifiers
- String group_id = hm_node.getId() +"";
- group_counter ++;
- String path = WORKING_DIRECTORY + "/alignments/grouping_v" + grouping_version + "/groups/" + group_id + "/";
- String out_path = path + "output/";
-
- if (check_if_file_exists(path + "input/identifiers_incorrect_for_fasttree")) { // new files need to be created for this
- groups_with_incorrect_ids.add(group_id);
- add = "_temp";
- } else {
- groups_with_correct_ids.add(group_id);
- }
-
- if (Mode.startsWith("BOTH") || Mode.startsWith("PROTEIN") || !trim) { // protein alignment is required for trimming
- if (!check_if_file_exists(out_path + "prot" + dot + "newick")) {
- script.append("FastTree -out ").append(out_path).append("prot").append(dot).append("newick ")
- .append(out_path).append("prot").append(add).append(dot).append("fasta &\n");
- process_counter ++;
- add_wait_for_alignment_shell(script, process_counter, group_counter, hm_node_list.size(), "Phylogeny inference: ");
- }
- }
-
- if (Mode.startsWith("BOTH") || Mode.startsWith("NUCLEOTIDE")) { //
- if (!check_if_file_exists(out_path + "nuc" + dot + "newick")) {
- script.append("FastTree -out ").append(out_path).append("nuc").append(dot).append("newick ")
- .append(out_path).append("nuc").append(add).append(dot).append("fasta &\n");
- process_counter ++;
- add_wait_for_alignment_shell(script, process_counter, group_counter, hm_node_list.size(), "Phylogeny inference: ");
- }
- }
- }
-
- // create new identifiers for the non unique ones before starting fasttree in parralel
- StringBuilder remove_files = new StringBuilder("echo 'Removing temp files'\n");
- for (String group_id : groups_with_incorrect_ids) {
- String path = WORKING_DIRECTORY + "/alignments/grouping_v" + grouping_version + "/groups/" + group_id + "/";
- String new_ids_file = path + "input/identifiers_incorrect_for_fasttree";
- if (Mode.startsWith("BOTH") || Mode.startsWith("PROTEIN") || !trim) { // protein alignment is required for trimming
- ArrayList<String> new_identifiers = retrieve_new_identifiers_for_fasttree(new_ids_file);
- create_renamed_fasta_for_fasttree(path + "output/prot" + dot + "fasta", new_identifiers, path + "output/prot_temp" + dot + "fasta" );
- remove_files.append("rm ").append(path).append("output/prot_temp").append(dot).append("fasta\n");
- }
- if (Mode.startsWith("BOTH") || Mode.startsWith("NUCLEOTIDE")) { // nucleotide sequences
- ArrayList<String> new_identifiers = retrieve_new_identifiers_for_fasttree(new_ids_file);
- create_renamed_fasta_for_fasttree(path + "output/nuc" + dot + "fasta", new_identifiers, path + "output/nuc_temp" + dot + "fasta");
- remove_files.append("rm ").append(path).append("output/nuc_temp").append(dot).append("fasta\n");
- }
- }
-
- script.append("echo 'Phylogeny inference: ").append(group_counter).append("/")
- .append(hm_node_list.size()).append(" groups'\nwait\n").append(remove_files.toString()).append("\n");
- write_SB_to_file_full_path(script, "script.sh");
- ExecCommand.ExecCommand(cmd);
-
- // loop to add genome numbers to phylogenetic trees
- group_counter = 0;
- for (String group_id : groups_with_correct_ids) {
- System.out.print("\rFinalising phylogenies " + group_counter + "/" + groups_with_correct_ids.size());
- String path = WORKING_DIRECTORY + "/alignments/grouping_v" + grouping_version + "/groups/" + group_id + "/";
- String in_path = path + "input/";
- String out_path = path + "output/";
- if (Mode.startsWith("BOTH") || Mode.startsWith("PROTEIN")) { // protein alignment is required for trimming
- include_genome_number_in_fasttree(in_path + "genome_order.info", out_path + "prot" + dot + "newick");
- }
- if (Mode.startsWith("BOTH") || Mode.startsWith("NUCLEOTIDE")) { //
- include_genome_number_in_fasttree(in_path + "genome_order.info", out_path + "nuc" + dot + "newick");
- }
- group_counter ++;
- }
- System.out.print("\r "); // spaces are intentional
- delete_file_full_path("script.sh");
- }
public static void initialize_BLOSUM() {
if (BLOSUM != 45 && BLOSUM != 62 && BLOSUM != 80) {
System.out.println("BLOSUM value must be 45, 62 or 80. Using BLOSUM62");
BLOSUM = 62;
}
- initialize_BLOSUM_matrix(BLOSUM);
- }
-
- /*
- How to use?
- msa_of_group -dp DATABASE --mode no-trimming
- */
- public void msa_of_group_no_trimming() {
- System.out.println("\nMultiple sequence alignment on homology groups (without trimming)\n");
- check_if_program_exists_stderr("FastTree -h", 100, "Fasttree", true); // check if program is set to $PATH
- check_if_program_exists_stderr("mafft -h", 100, "MAFFT", true); // check if program is set to $PATH
- check_if_graphDb_is_available(); // starts up the graph database if needed
- try (Transaction tx = graphDb.beginTx()) { // start database transaction
- Node pangenome_node = graphDb.findNodes(pangenome_label).next();
- check_if_panproteome(pangenome_node); // sets PROTEOME boolean that controls functions, retrieves K_size & total_genomes
- check_current_grouping_version(); // check which version of homology grouping is active
- create_skip_arrays(false, true); // create skip arrays for sequences and genomes if -skip/-ref is provided by user
- tx.success(); // transaction successful, commit changes
- } catch (NotFoundException nfe) {
- System.out.println("Unable to start the database\n");
- return;
- }
-
- check_mode_for_msa();
- if (PHENOTYPE == null) {
- System.out.println("No --phenotype was provided, unable to find phenotype specific SNPs\n");
- }
-
- initialize_BLOSUM();
- create_directory_in_DB("alignments/grouping_v" + grouping_version);
- create_directory_in_DB("alignments/grouping_v" + grouping_version + "/groups/");
- String output_dir = WORKING_DIRECTORY + "alignments/grouping_v" + grouping_version + "/";
- ArrayList<Node> hm_nodes_list = new ArrayList<>();
- try (Transaction tx = graphDb.beginTx()) { // start database transaction
- retrieve_phenotypes(); // Creates and fills geno_pheno_map and phenotype_map when a phenotype was provided by the user
- hm_nodes_list = read_hmgroup_input_file();
- hm_nodes_list = prepare_msa_sequences(hm_nodes_list, false);
- run_msa_without_trimming(hm_nodes_list);
- tx.success(); // transaction successful, commit changes
- }
- graphDb.shutdown();
- rscript_for_group_var_inf_site_distances();
- create_write_msa_no_trimming_output(hm_nodes_list);
- //include_identity_similarity_to_relations(hmgroup_array, false); // this function is currently disabled, do not remove!
- System.out.println("\nAlignments written to: \n "
- + WORKING_DIRECTORY + "alignments/grouping_v" + grouping_version + "/groups/");
- if (PHENOTYPE != null) {
- System.out.println("\nPhenotype output written to:\n "
- + output_dir + "groups_with_phenotype_specific_changes.txt");
- if ((Mode.startsWith("BOTH") || Mode.startsWith("NUCLEOTIDE"))) { // nucleotide sequences
- System.out.print(" " + output_dir + "phenotype_specific_changes_nuc.txt\n");
- }
- if ((Mode.startsWith("BOTH") || Mode.startsWith("PROTEIN"))) { // protein sequences
- System.out.print(" " + output_dir + "phenotype_specific_changes_prot.txt\n");
- }
- System.out.println("");
- }
+ initialize_BLOSUM_matrix(BLOSUM);
}
-
+
/**
- *
- * @param hm_nodes_list
+ *
+ * @param msaNames
+ * @param outdirMsa
*/
- public void create_write_msa_no_trimming_output(ArrayList<Node> hm_nodes_list) {
+ public static void create_write_msa_no_trimming_output(ArrayList<String> msaNames, String outdirMsa) {
+ System.out.println("");
System.out.println("\nReading alignments");
- String output_dir = WORKING_DIRECTORY + "alignments/grouping_v" + grouping_version + "/";
- delete_file_full_path(output_dir + "/groups_with_phenotype_specific_changes.txt");
ArrayList<String> nuc_or_prot_list = prepare_type_list_for_msa(); // list can contain "protein", "nucleotide" or both
+ initialize_BLOSUM();
+ delete_file_full_path(outdirMsa + "/groups_with_phenotype_specific_changes.txt");
+
for (String nuc_or_prot : nuc_or_prot_list) {
StringBuilder groups_with_inf_pos = new StringBuilder("#groups with parsimony informative sites:\n");
StringBuilder groups_with_var_pos = new StringBuilder("#groups with variables sites:\n");
@@ -11672,17 +9756,16 @@ public class Classification {
HashMap<String, Integer> pheno_specific_group_sites = new HashMap<>();
int group_counter = 1;
- for (Node hm_node : hm_nodes_list) {
- String group_id = hm_node.getId() + "";
- new File(output_dir + "groups/" + group_id + "/output/similarity_identity/").mkdir(); // create directory
- new File(output_dir + "groups/" + group_id + "/output/var_inf_positions/").mkdir(); // create directory
+ for (String group_id : msaNames) {
+ new File(outdirMsa + group_id + "/output/similarity_identity/").mkdir(); // create directory
+ new File(outdirMsa + group_id + "/output/var_inf_positions/").mkdir(); // create directory
HashMap<String, Integer> shared_snps_map = new HashMap<>();
- System.out.print("\r Reading " + nuc_or_prot + " alignments: " + group_counter + "/" + hm_nodes_list.size() + ". variable/informative: "
+ System.out.print("\r Reading " + nuc_or_prot + " alignments: " + group_counter + "/" + msaNames.size() + ". variable/informative: "
+ total_var_inf_sites[0] + "/" + total_var_inf_sites[1]);
group_counter ++;
- String output_dir1 = output_dir + "groups/" + group_id + "/output/";
+ String output_dir1 = outdirMsa + group_id + "/output/";
String input_file = output_dir1 + nuc_or_prot_short + ".afa";
- String genome_order = output_dir + "groups/" + group_id + "/input/genome_order.info";
+ String genome_order = outdirMsa + group_id + "/input/genome_order.info";
int[] var_inf_sites = count_var_inf_sites_in_msa(shared_snps_map, pheno_specific_output,
pheno_specific_group_sites, input_file, group_id, nuc_or_prot, genome_order); // variable, informative, conserved sites
total_var_inf_sites[0] += var_inf_sites[0];
@@ -11703,9 +9786,9 @@ public class Classification {
var_inf_sites[0], var_inf_sites[2], genome_order);
}
}
- write_string_to_file_full_path(groups_with_var_pos.toString() + "\n\n" + groups_with_inf_pos.toString(),
- output_dir + "groups_with_var_inf_positions_" + nuc_or_prot_short + ".txt");
- prepare_phenotype_results_msa(nuc_or_prot, hm_nodes_list, pheno_specific_group_sites, output_dir, pheno_specific_output.toString());
+ write_string_to_file_full_path(groups_with_var_pos.toString() + "\n\n" + groups_with_inf_pos.toString(),
+ outdirMsa + "groups_with_var_inf_positions_" + nuc_or_prot_short + ".txt");
+ prepare_phenotype_results_msa(nuc_or_prot, msaNames, pheno_specific_group_sites, outdirMsa, pheno_specific_output.toString());
String nuc_or_prot_cap = nuc_or_prot.substring(0, 1).toUpperCase() + nuc_or_prot.substring(1);
int total_var_groups = groups_with_var_pos.toString().split(",").length;
int total_inf_groups = groups_with_inf_pos.toString().split(",").length;
@@ -11715,48 +9798,21 @@ public class Classification {
if (total_var_inf_sites[0] == 0) {
total_var_groups = 0;
}
- System.out.print("\r " + nuc_or_prot_cap + " variable/informative positions: " + total_var_inf_sites[0] + "/" + total_var_inf_sites[1]
- + " (" + total_var_groups + "/" + total_inf_groups + " groups) \n"); // spaces are intentional
- }
- }
-
- /*
-
- */
- public void run_msa_without_trimming(ArrayList<Node> hm_node_list) {
- boolean pass = false; // pass when all alignment (& phylogeny) files exists
- int loop_counter = 0;
- while (!pass) {
- ArrayList<Node> to_be_aligned = check_if_msa_is_complete(hm_node_list, false);
- if (to_be_aligned.isEmpty()) {
- pass = true;
- } else {
- int hm_counter = 1;
- for (Node hm_node : to_be_aligned) {
- System.out.print("\rAligning homology groups: " + hm_counter + "/" + to_be_aligned.size() + " groups");
- run_msa_commands_mafft(hm_node.getId()+"", false);
- hm_counter ++;
- }
- System.out.println("");
- loop_counter ++;
- if (loop_counter == 3) {
- System.out.print("\nFailed to align " + to_be_aligned.size() + " groups: ");
- for (Node group_node : to_be_aligned) {
- System.out.print(group_node.getId() + ", ");
- }
- System.out.println("");
- System.exit(1);
- }
+ String additional_spaces = "";
+ if (nuc_or_prot_cap.equals("Protein")) {
+ additional_spaces = " ";
}
+ System.out.println("\r " + nuc_or_prot_cap + " variable sites " + additional_spaces + ": " + total_var_inf_sites[0] + " (" + total_var_groups + " alignments)"
+ + " \n" // spaces are intentional
+ + " " + nuc_or_prot_cap + " informative sites" + additional_spaces +": " + total_var_inf_sites[1] + " (" + total_inf_groups + " alignments)");
}
}
/**
* Threshold is dependent on genomes found in the alignment, and --core-threshold
- * @param position_map // this function assumes the position map does NOT have genome numbers
* @param genome_order, path to txt file
*/
- public static void prepare_phenotype_threshold_msa_no_genome_nrs(HashMap<String, ArrayList<Integer>> position_map, String genome_order) {
+ public static void prepare_phenotype_threshold_msa_no_genome_nrs(String genome_order) {
if (PHENOTYPE == null) {
return;
}
@@ -11795,16 +9851,18 @@ public class Classification {
* @param trim can be "trimmed" or ""
* @param output_path
*/
- public static void find_pheno_specific_sites(HashMap<String, ArrayList<Integer>> position_map, StringBuilder pheno_specific_output,
- String nuc_or_prot, HashMap<String, Integer> pheno_specific_group_sites, StringBuilder alignment_info, String genome_order_file, String trim,
- String output_path) {
+ public static void find_pheno_specific_sites(HashMap<String, ArrayList<Integer>> position_map,
+ StringBuilder pheno_specific_output,
+ String nuc_or_prot, HashMap<String, Integer> pheno_specific_group_sites,
+ StringBuilder alignment_info,
+ String genome_order_file, String trim, String output_path) {
if (pheno_specific_output == null || PHENOTYPE == null) {
return;
}
StringBuilder pheno_log_builder = new StringBuilder("\n#All variable positions of the alignment");
- String pheno_log_header = "#Use this file to see why a position is phenotype specific or not. The overview shows the number of phenotype "
- + "members with a specific letter on variable positions in the alignment followed by the required threshold to be phenotype specific\n";
+ StringBuilder pheno_log_header = new StringBuilder("#Use this file to see why a position is phenotype specific or not. The overview shows the number of phenotype "
+ + "members with a specific letter on variable positions in the alignment followed by the required threshold to be phenotype specific\n");
String SNP_or_substi = "SNPs", nuc_or_prot_cap = "Nucleotide";
String nuc_or_prot_short = "nuc";
if (nuc_or_prot.equals("protein")) {
@@ -11812,13 +9870,32 @@ public class Classification {
nuc_or_prot_cap = "Amino acid";
nuc_or_prot_short = "prot";
}
- prepare_phenotype_threshold_msa_no_genome_nrs(position_map, genome_order_file);
+ prepare_phenotype_threshold_msa_no_genome_nrs(genome_order_file);
ArrayList<Integer> genome_order_list = read_genome_order_file(genome_order_file, false);
HashMap<String, Integer> pheno_specific_counter = new HashMap<>(); // the number of phenotype specific variations for this alignment
StringBuilder pheno_specific_sites = new StringBuilder("Phenotype specific " + SNP_or_substi + " per position in the alignment."
+ " Each row contains: position in the alignment, reference allele/other alleles, phenotype,"
+ " number of sequences with the phenotype and letter/total sequences with phenotype\n");
-
+
+ pheno_log_header.append("Number of sequences per phenotype and required threshold\n");
+ HashMap<String, Integer> phenotypeCounts = new HashMap<>();
+ for (int genome_nr : genome_order_list) {
+ String pheno = geno_pheno_map.get(genome_nr);
+ try_incr_hashmap(phenotypeCounts, pheno, 1);
+
+ }
+
+
+ for (String phenotype: phenotypeCounts.keySet()){
+ int count = phenotypeCounts.get(phenotype);
+ int threshold = phenotype_threshold_map.get(phenotype);
+ pheno_log_header.append(phenotype + ": " + count + "," + threshold + "\n");
+ }
+ pheno_log_header.append("\n");
+
+
+
+
TreeSet<Integer> positions_set = new TreeSet<>();
HashMap<Integer, ArrayList<String>> found_pos_map = new HashMap<>(); // key is position, value is list with
for (String key : position_map.keySet()) {
@@ -11846,7 +9923,7 @@ public class Classification {
ArrayList<Integer> present_genomes = new ArrayList<>();
HashMap<String, Integer> phenotype_occurance = create_phenotype_occurance_map_msa(present_genomes, genome_order_list, sequence_numbers);
Collections.sort(present_genomes); // ascending
- pheno_log_builder.append("\n").append(nuc_or_prot_cap).append(" ").append(actual_position).append(character).append(": ")
+ pheno_log_builder.append("\n").append(nuc_or_prot_cap).append(" ").append(actual_position).append(character).append(". genomes: ")
.append(present_genomes.toString().replace("[","").replace(" ","").replace("]","")).append("\n");
determine_pheno_specific_sites_msa(phenotype_occurance, pheno_log_builder, position, character, other_characters, pheno_specific_sites,
pheno_specific_output, pheno_specific_counter);
@@ -11901,7 +9978,6 @@ public class Classification {
* @param other_characters
* @param pheno_specific_sites
* @param pheno_specific_output
- * @param added_phenotypes
* @param pheno_specific_counter
*/
public static void determine_pheno_specific_sites_msa(HashMap<String, Integer> phenotype_occurance, StringBuilder pheno_log_builder, int position, String character,
@@ -11982,188 +10058,17 @@ public class Classification {
}
/**
- * Prepare several input files for the input homology groups
- * prot.fasta, protein sequences
- * nuc.fasta, nucleotide sequences
- * genome_order.info, list of genome number and identifiers
- * identifiers_incorrect_for_fasttree, created when the identifers are not unique
- * sequences.info, relevant information for user
- *
- *
- * @param hm_node_list
- * @param ignore_unique_limit, still write unique sequences when true'
- * @return updated list where groups with 1 member are removed
- */
- public ArrayList<Node> prepare_msa_sequences(ArrayList<Node> hm_node_list, boolean ignore_unique_limit) {
- ArrayList<Node> updated_hm_node_list = new ArrayList<>(); // exclude homology groups with only 1 sequence
- long total_hmgroups = hm_node_list.size();
- int group_counter = 0, not_unique_counter = 0;
- System.out.println("");
- int print_threshold = 100;
- if (total_hmgroups < 500) {
- print_threshold = 10;
- }
-
- for (Node hm_node : hm_node_list) {
- group_counter ++;
- if (group_counter % print_threshold == 0 || group_counter == total_hmgroups || group_counter < 50) {
- System.out.print("\rPreparing sequences: " + group_counter + "/" + total_hmgroups + " homology groups");
- }
- String path = WORKING_DIRECTORY + "/alignments/grouping_v" + grouping_version + "/groups/" + hm_node.getId();
- String input_path = path + "/input/";
- String output_path = path + "/output/";
- boolean pass3 = check_if_file_exists(input_path + "prot.fasta");
- boolean pass4 = check_if_file_exists(input_path + "nuc.fasta");
- if (PROTEOME) {
- pass4 = true;
- }
- if (pass3 && pass4) {
- updated_hm_node_list.add(hm_node);
- continue;
- }
-
- check_if_hm_is_correct_grouping(hm_node);
- int num_members = (int) hm_node.getProperty("num_members"); // number of sequences in group
- if (num_members == 1 && !ignore_unique_limit) { // do not create files for groups with 1 sequence
- SELECTED_HMGROUPS = SELECTED_HMGROUPS.replace(hm_node.getId() +",", "");
- continue;
- }
- updated_hm_node_list.add(hm_node);
- not_unique_counter ++;
- new File(input_path).mkdirs(); // create directory
- new File(output_path).mkdirs(); // create directory
- write_msa_input_files(hm_node, input_path);
- }
-
- int total_non_uni_hms = count_not_unique_hmgroups();
- if (total_non_uni_hms <= not_unique_counter && Mode.startsWith("BOTH")) {
- // this file is used to skip this function completely
- write_string_to_file_in_DB("all sequences were extracted", "/alignments/grouping_v" + grouping_version + "/groups/extract_sequences_done");
- }
-
- if (updated_hm_node_list.size() < hm_node_list.size()) {
- System.out.println("\rNumber of selected groups lowered from " + hm_node_list.size() + " to " + updated_hm_node_list.size() +
- " due having only 1 sequence in the group");
- } else {
- System.out.println("");
- }
- return updated_hm_node_list;
- }
-
- /**
- * Check if node has 'homology_group' label
- * @param hm_node
- */
- public static void check_if_hm_is_correct_grouping(Node hm_node) {
- boolean correct = test_if_correct_label(hm_node, homology_group_label, false);
- if (!correct) {
- correct = test_if_correct_label(hm_node, inactive_homology_group_label, false);
- if (!correct) {
- System.out.println(hm_node + " is not an homology group");
- } else {
- int group_version = (int) hm_node.getProperty("group_version");
- System.out.println("\n" + hm_node + " is an inactive homology group! Grouping " + grouping_version + " is active while this homology group is version " + group_version);
- }
- System.exit(1);
- }
- }
-
- /**
- * Creates several input files for the input homology groups
- * prot.fasta, protein sequences
- * nuc.fasta, nucleotide sequences
- * genome_order.info, list of genome number and identifiers
- * identifiers_incorrect_for_fasttree, created when the identifers are not unique
- * sequences.info, relevant information for user
- *
- * @param hm_node
- * @param input_path
- */
- public void write_msa_input_files(Node hm_node, String input_path) {
- Iterable<Relationship> all_relations = hm_node.getRelationships(RelTypes.has_homolog);
- StringBuilder protein_fasta_file = new StringBuilder();
- StringBuilder nucleotide_fasta_file = new StringBuilder();
- StringBuilder genome_nrs_builder = new StringBuilder();
- ArrayList<Integer> present_genomes = new ArrayList<>();
- StringBuilder info_builder_header = new StringBuilder("#Information about sequences in homology group\n#Occurance in genomes\n");
- StringBuilder info_builder = new StringBuilder("#genome, gene/mRNA name, mRNA identifier, node identifier, address, strand\n");
- if (PROTEOME) {
- info_builder = new StringBuilder("#genome, protein identifier, protein node id\n");
- }
- int num_members = (int) hm_node.getProperty("num_members"); // number of sequences in group
- HashSet<String> proper_identifiers_set = new HashSet<>();
- StringBuilder incorrect_identifiers = new StringBuilder("#The original identifers are not unique or these contain a column or semicolon. "
- + "Therefore, new identifiers are created."
- + "\n#old identifier, new identifier\n");
- boolean use_different_identifiers = false; // the current protein identifers cannot be used by fasttree
- int[] copies = new int[total_genomes];
- for (Relationship rel : all_relations) {
- Node mrna_node = rel.getEndNode();
- String mrna_protein = get_protein_sequence(mrna_node);
- mrna_protein = split_seq_in_parts_of_60bp(mrna_protein);
- int genome_nr = (int) mrna_node.getProperty("genome");
- copies[genome_nr-1] += 1;
- int copy_nr = copies[genome_nr-1];
- present_genomes.add(genome_nr);
- String protein_id = (String) mrna_node.getProperty("protein_ID");
- if (protein_id.contains(":") || protein_id.contains(";")) { // not allowed in newick format
- String clean_id = protein_id.replace(":",".").replace(";",".");
- proper_identifiers_set.add(clean_id);
- use_different_identifiers = true;
- incorrect_identifiers.append(protein_id).append(",").append(genome_nr).append("_").append(copy_nr).append("_").append(clean_id).append("\n");
- } else {
- proper_identifiers_set.add(protein_id);
- incorrect_identifiers.append(protein_id).append(",").append(genome_nr).append("_").append(copy_nr).append("_").append(protein_id).append("\n");
- }
-
- long mrna_node_id = mrna_node.getId();
- genome_nrs_builder.append(genome_nr).append(",").append(protein_id).append("\n");
- if (!PROTEOME) {
- int[] address = (int[]) mrna_node.getProperty("address");
- String strand = (String) mrna_node.getProperty("strand");
- String name = (String) mrna_node.getProperty("name");
- if (name.equals("")) {
- name = "-";
- }
- String nuc_sequence = get_nucleotide_sequence(mrna_node);
- nuc_sequence = split_seq_in_parts_of_60bp(nuc_sequence);
- protein_fasta_file.append(">").append(protein_id).append(" ").append(address[0]).append("_").append(address[1]).append("_").append(address[2]).append("_").append(address[3]).append("\n")
- .append(mrna_protein).append("\n");
- nucleotide_fasta_file.append(">").append(protein_id).append(" ").append(address[0]).append("_").append(address[1]).append("_").append(address[2]).append("_").append(address[3]).append("\n")
- .append(nuc_sequence).append("\n");
- info_builder.append(genome_nr).append(", ").append(name).append(", ").append(protein_id).append(", ").append(mrna_node_id).append(", ")
- .append(address[0]).append(" ").append(address[1]).append(" ").append(address[2]).append(" ").append(address[3]).append(", ").append(strand).append("\n");
- } else {
- protein_fasta_file.append(">").append(protein_id).append("\n").append(mrna_protein).append("\n");
- info_builder.append(genome_nr).append(", ").append(protein_id).append(mrna_node_id).append(", ").append("\n");
- }
- }
- TreeSet<Integer> absent = get_missing_genomes_in_arraylist(present_genomes);
- String genome_freqs = determine_frequency_list_int(present_genomes);
- info_builder_header.append("Present: ").append(genome_freqs)
- .append("\nAbsent: ").append(absent.toString().replace("[","").replace("]","").replace(",","")).append("\n\n");
- if (use_different_identifiers || proper_identifiers_set.size() < num_members) {
- write_SB_to_file_full_path(incorrect_identifiers, input_path + "identifiers_incorrect_for_fasttree");
- }
- write_string_to_file_full_path(info_builder_header.toString() + info_builder.toString(), input_path + "sequences.info");
- write_SB_to_file_full_path(protein_fasta_file, input_path + "prot.fasta");
- write_SB_to_file_full_path(genome_nrs_builder, input_path + "genome_order.info");
- if (!PROTEOME) {
- write_SB_to_file_full_path(nucleotide_fasta_file, input_path + "nuc.fasta");
- }
- }
-
- /**
- * Put a newline character after every 60 characters
+ * The default width of the FASTA format is 80
+ * Put a newline character after every 80 characters
* @param sequence
* @return
*/
- public static String split_seq_in_parts_of_60bp(String sequence) {
+ public static String split_seq_in_parts_of_80bp(String sequence) {
String new_string = "";
for (int i = 0; i < sequence.length(); i++) {
char c = sequence.charAt(i);
new_string += c;
- if ((i+1) % 60 == 0) {
+ if ((i+1) % 80 == 0) {
new_string += "\n";
}
}
@@ -12173,127 +10078,6 @@ public class Classification {
}
return new_string;
}
-
- /*
- Gives multiple threads to a single Mafft execution
- */
- public void run_msa_commands_mafft(String hmgroup, boolean trim) {
- boolean exists;
- String mafft_output;
- String threads_str = report_number_of_threads(false, true); // prints how many threads were selected by user
- create_directory_in_DB("alignments/grouping_v" + grouping_version + "/groups/" + hmgroup + "/output/" );
- String dot = ".";
- if (trim) {
- dot = dot.replace(".", "_trimmed.");
- }
- hmgroup += "/";
- String path = WORKING_DIRECTORY + "/alignments/grouping_v" + grouping_version + "/groups/" + hmgroup + "/";
- String in_path = path + "input/";
- String out_path = path + "output/";
- boolean incorrect_identifiers = check_if_file_exists(in_path + "/identifiers_incorrect_for_fasttree");
- String[] prot_command = {"mafft","--auto", "--anysymbol", "--thread", threads_str, "--clustalout", in_path + "prot" + dot + "fasta"};
- if (Mode.startsWith("BOTH") || Mode.startsWith("PROTEIN") || !trim) { // protein alignment is required for trimming
- exists = check_if_file_exists(out_path + "/prot" + dot + "afa");
- while (!exists) {
- mafft_output = ExecCommand.ExecCommand(prot_command);
- if (!mafft_output.equals("")) {
- exists = true;
- }
- write_string_to_file_full_path(mafft_output, out_path + "prot" + dot + "afa");
- convert_afa_to_aligned_fasta(in_path + "prot.fasta", out_path + "prot" + dot + "afa");
- }
-
- if (!FAST && !incorrect_identifiers) {
- String[] prottree = {"FastTree","-out", out_path + "prot" + dot + "newick", out_path + "prot" + dot + "fasta"};
- ExecCommand.ExecCommand(prottree);
- include_genome_number_in_fasttree(in_path + "genome_order.info" , out_path + "prot" + dot + "newick");
- } else if (!FAST && incorrect_identifiers) {
- run_fasttree_on_renamed_identifiers(in_path + "/identifiers_incorrect_for_fasttree", out_path + "prot" + dot + "fasta", "protein");
- }
- }
-
- String[] nuc_command = new String[] {"mafft", "--auto", "--anysymbol", "--thread", threads_str, "--clustalout", in_path + "nuc" + dot + "fasta" };
- if (Mode.startsWith("BOTH") || Mode.startsWith("NUCLEOTIDE")) { // nucleotide sequences
- exists = check_if_file_exists(out_path + "nuc" + dot + "afa");
- while (!exists) {
- mafft_output = ExecCommand.ExecCommand(nuc_command);
- if (!mafft_output.equals("")) {
- exists = true;
- }
- write_string_to_file_full_path(mafft_output, out_path + "nuc" + dot + "afa");
- convert_afa_to_aligned_fasta(in_path + "nuc.fasta", out_path + "nuc" + dot + "afa");
- }
- if (!FAST && !incorrect_identifiers) {
- String[] nuctree = {"FastTree", "-out", out_path + "nuc" + dot + "newick", "-nt", out_path + "nuc" + dot + "fasta"};
- ExecCommand.ExecCommand(nuctree);
- include_genome_number_in_fasttree(in_path + "genome_order.info", out_path + "nuc" + dot + "newick");
- } else if (!FAST && incorrect_identifiers) {
- run_fasttree_on_renamed_identifiers(in_path + "/identifiers_incorrect_for_fasttree", out_path + "nuc" + dot + "fasta", "nucleotide");
- }
- }
- }
-
- public static void run_fasttree_on_renamed_identifiers(String identifiers_file, String original_fasta, String nucleotide_or_protein) {
- ArrayList<String> new_identifiers = retrieve_new_identifiers_for_fasttree(identifiers_file);
- create_renamed_fasta_for_fasttree(original_fasta, new_identifiers, "temp.fasta");
- String[] tree;
- String tree_output = original_fasta.replace("fasta","newick");
- if (nucleotide_or_protein.equals("nucleotide")) {
- tree = new String[]{"FastTree", "-out", tree_output, "-nt", "temp.fasta"};
- } else {
- tree = new String[]{"FastTree", "-out", tree_output, "temp.fasta"};
- }
- ExecCommand.ExecCommand(tree);
- }
-
- /**
- *
- * @param identifiers_file
- * @return
- */
- public static ArrayList<String> retrieve_new_identifiers_for_fasttree(String identifiers_file) {
- ArrayList<String> new_identifiers = new ArrayList<>();
- try (BufferedReader in = new BufferedReader(new FileReader(identifiers_file))) {
- for (int c = 0; in.ready();) {
- String line = in.readLine(); //important that read is not trimmed
- if (line.startsWith("#")) {
- continue;
- }
- String[] line_array = line.split(",");
- new_identifiers.add(line_array[1]);
- }
- } catch (IOException ioe) {
- System.out.println("\nUnable to read: " + identifiers_file + "\n");
- System.exit(1);
- }
- return new_identifiers;
- }
-
- /**
- *
- * @param original_fasta
- * @param new_identifiers
- * @param output_file
- */
- public static void create_renamed_fasta_for_fasttree(String original_fasta, ArrayList<String> new_identifiers, String output_file) {
- StringBuilder new_fasta = new StringBuilder();
- int sequence_counter = 0;
- try (BufferedReader in = new BufferedReader(new FileReader(original_fasta))) {
- for (int c = 0; in.ready();) {
- String line = in.readLine(); //important that read is not trimmed
- if (line.startsWith(">")) {
- new_fasta.append(">").append(new_identifiers.get(sequence_counter)).append("\n");
- sequence_counter ++;
- } else {
- new_fasta.append(line).append("\n");
- }
- }
- } catch (IOException ioe) {
- System.out.println("\nUnable to read: " + original_fasta + "\n");
- System.exit(1);
- }
- write_SB_to_file_full_path(new_fasta, output_file);
- }
/**
*
@@ -12721,6 +10505,7 @@ public class Classification {
} else { // no variable positions
matrix_builder = new StringBuilder("Alignment does not contain variable positions");
}
+ new File(output_path + "var_inf_positions/").mkdirs(); // create directory
write_SB_to_file_full_path(matrix_builder, output_path + "var_inf_positions/" + nuc_or_prot_short + trim + "_variable_positions.csv");
}
@@ -12804,8 +10589,11 @@ public class Classification {
* @param pheno_specific_output
* @return
*/
- public static StringBuilder prepare_alignment_info(String hmgroup, int total_sequences, int skipped_sequences, int ali_length, HashSet<Integer> genome_set, String input_file,
- int conserved_sites, String informative_sites_overview, ArrayList<String> variable_positions, ArrayList<String> skip_positions, StringBuilder pheno_specific_output) {
+ public static StringBuilder prepare_alignment_info(String hmgroup, int total_sequences, int skipped_sequences,
+ int ali_length, HashSet<Integer> genome_set, String input_file,
+ int conserved_sites, String informative_sites_overview,
+ ArrayList<String> variable_positions,
+ ArrayList<String> skip_positions, StringBuilder pheno_specific_output) {
String info;
if (!hmgroup.equals("MSA")) { // hmgroup is a node identifier
info = "\nHomology group " + hmgroup + ", members: " + total_sequences + "\n#" + input_file + "\n";
@@ -12853,7 +10641,8 @@ public class Classification {
* @param shared_snps_map
*/
public static void calculate_sequence_similarity(int i, int sequence_counter, String[][] all_positions, int snp_pos, char char1,
- ArrayList<Integer> genome_order_list, HashMap<String, Integer> shared_snps_map) {
+ ArrayList<Integer> genome_order_list, HashMap<String, Integer> shared_snps_map) {
+
for (int j = i+1; j < sequence_counter; j++) { // j = i + 1 to prevent comparison against itself
int genome_nr2 = genome_order_list.get(j);
if (skip_array[genome_nr2-1]) {
@@ -12861,125 +10650,13 @@ public class Classification {
}
String character2 = all_positions[j][snp_pos];
char char2 = character2.charAt(0);
+
int score = match[char1][char2];
if (score > 0) {
try_incr_hashmap(shared_snps_map, i + "#" + j + "#similar", 1);
}
}
}
-
- /**
- * Trim nucleotide and protein input sequences based on the first PROTEIN alignment.
- *
- * 1. Read the protein alignment, find the longest gap at the end and start (count_aa_to_trim)
- * 2
- *
- * @param original_hm_node_list
- * @return
- */
- public static ArrayList<Node> trim_prealigned_proteins(ArrayList<Node> original_hm_node_list) {
- int group_counter = 0;
- ArrayList<Node> suitable_groups = new ArrayList<>();
- ArrayList<String> excluded_groups = new ArrayList<>();
- for (Node hm_node : original_hm_node_list) {
- String group_id = hm_node.getId() +"";
- group_counter ++;
- String path = WORKING_DIRECTORY + "alignments/grouping_v" + grouping_version + "/groups/" + group_id + "/";
- String in_path = path + "input/";
- String out_path = path + "output/" ;
- if (group_counter % 10 == 0 || group_counter == original_hm_node_list.size()) {
- System.out.print("\rTrimming sequences: " + group_counter + "/" + original_hm_node_list.size() + " homology groups ");
- }
- boolean pass = check_if_group_is_trimmed(hm_node, in_path, suitable_groups, excluded_groups);
- if (pass) { // group is already trimmed
- continue;
- }
-
- HashMap<String, int[]> seq_trim_map = new HashMap<>();
- // key is the fasta header, value is array with number of aa at the start and end of the sequence that need to be trimmed
- int[] longest_start_end_gap = count_aa_to_trim(out_path + "/prot.fasta", seq_trim_map); // gaps at start, gaps at end, alignment length
- if (longest_start_end_gap[0] + longest_start_end_gap[1] < longest_start_end_gap[2]) {
- suitable_groups.add(hm_node);
- if (Mode.startsWith("BOTH") || Mode.startsWith("NUCLEOTIDE")) {
- trim_sequences(seq_trim_map, group_id, in_path + "/nuc.fasta", true);
- }
- if (Mode.startsWith("BOTH") || Mode.startsWith("PROTEIN")) {
- trim_sequences(seq_trim_map, group_id, in_path + "/prot.fasta", false);
- }
- } else {
- excluded_groups.add(group_id);
- }
- create_trimmed_info_file(longest_start_end_gap, group_id, seq_trim_map, in_path);
- }
-
- if (excluded_groups.size() > 0) { // one ore multiple groups were excluded due to trimmed edges overlapping
- write_string_to_file_in_DB(excluded_groups.toString().replace("[","").replace("]","").replace(" ",""),
- "alignments/grouping_v" + grouping_version + "/groups_excluded_based_on_trimming.txt");
- System.out.print("\rTrimming sequences: " + group_counter + "/" + original_hm_node_list.size() + " homology groups. "
- + "Excluded " + excluded_groups.size() + " groups. "
- + "See " + WORKING_DIRECTORY + "alignments/grouping_v" + grouping_version + "/groups_excluded_based_on_trimming.txt");
- } else {
- System.out.print("\rTrimming sequences: " + group_counter + "/" + original_hm_node_list.size() + " homology groups. Excluded 0 groups");
- }
- return suitable_groups; // convert arraylist to array
- }
-
- /**
- * Creates 'trimmed.info' and 'not_trimmed' when the group must be excluded
- *
- * @param longest_start_end_gap
- * @param hmgroup
- * @param seq_trim_map
- * @param in_path
- */
- public static void create_trimmed_info_file(int[] longest_start_end_gap, String hmgroup, HashMap<String, int[]> seq_trim_map, String in_path) {
- String trimmed = "Protein alignment length: " + longest_start_end_gap[2]
- + "\nLongest start gap: " + longest_start_end_gap[0]
- + "\nLongest end gap: " + longest_start_end_gap[1];
-
- if (longest_start_end_gap[0] + longest_start_end_gap[1] < longest_start_end_gap[2]) {
- trimmed += "\n\nTotal number of trimmed positions at the start and end of each protein sequence."
- + " Multiply the number by three to obtain the number of positions in for the nucleotide sequences.\n";
- for (String sequence_name : seq_trim_map.keySet()) {
- int[] trimmed_prot_positions = seq_trim_map.get(sequence_name);
- String[] seq_array = sequence_name.split(" ");
- trimmed += seq_array[0].replace(">","") + ": " + trimmed_prot_positions[0] + ", " + trimmed_prot_positions[1] + "\n";
- }
- } else {
- write_string_to_file_full_path("sequences to short", in_path + "/not_trimmed");
- trimmed += "\nNo trimmed sequence could be created";
- }
- write_string_to_file_full_path(trimmed, in_path + "/trimmed.info");
- }
-
- /**
- *
- * @param hm_node
- * @param in_path
- * @param suitable_groups
- * @param excluded_groups
- * @return
- */
- public static boolean check_if_group_is_trimmed(Node hm_node, String in_path, ArrayList<Node> suitable_groups, ArrayList<String> excluded_groups) {
- boolean pass1 = false;
- if (Mode.startsWith("BOTH")) { // both nucleotide and protein sequences
- pass1 = check_if_file_exists(in_path + "/trimmed.info");
- boolean pass2 = check_if_file_exists(in_path + "/not_trimmed");
- if (pass2) {
- excluded_groups.add(hm_node.getId()+""); // long + str to convert to a string
- return true;
- }
- } else if (Mode.startsWith("PROTEIN")) { // proteins only
- pass1 = check_if_file_exists(in_path + "/prot_trimmed.fasta");
- } else if (Mode.startsWith("NUCLEOTIDE")) { // nucleotides only
- pass1 = check_if_file_exists(in_path + "/nuc_trimmed.fasta");
- }
-
- if (pass1) {
- suitable_groups.add(hm_node);
- }
- return pass1;
- }
/**
*
@@ -13073,7 +10750,7 @@ public class Classification {
nuc_count_loop = 0;
}
}
- trimmed_seq = split_seq_in_parts_of_60bp(trimmed_seq);
+ trimmed_seq = split_seq_in_parts_of_80bp(trimmed_seq);
output_builder.append(trimmed_seq).append("\n");
}
@@ -13716,112 +11393,6 @@ public class Classification {
return included_phenotype;
}
-
- /**
- * test if its actually phenotype or header contains spaces
- * @return
- */
- public static HashMap retrieve_phenotypes_per_genome() {
- HashMap<Integer, String> geno_pheno_map = new HashMap<>();
- ResourceIterator<Node> all_pheno_nodes = graphDb.findNodes(phenotype_label);
- boolean first = true;
- while (all_pheno_nodes.hasNext()) {
- if (first) {
- System.out.println("All phenotypes:");
- first = false;
- }
- Node pheno_node = all_pheno_nodes.next();
- Iterable<String> propkeys = pheno_node.getPropertyKeys();
- String phenotypes_str = "";
- int genome = (int) pheno_node.getProperty("genome");
- for (String property: propkeys) {
- Object value = pheno_node.getProperty(property);
- if (property.equals("genome")) {
- continue;
- }
- //System.out.println(property);
- if (value instanceof String) {
- String part_info = (String) value;
- phenotypes_str += property + ": " + part_info + ", ";
- } else if (value instanceof Integer) {
- int part_info = (int) value;
- phenotypes_str += property + ": " + part_info + ", ";
- } else if (value instanceof Boolean) {
- boolean part_info = (boolean) value;
- phenotypes_str += property + ": " + part_info + ", ";
- } else {
- System.out.println("something else.. finish function");
- System.exit(1);
- }
- }
- phenotypes_str = phenotypes_str.replaceFirst(".$","").replaceFirst(".$","");
- System.out.println("Genome " + genome + ": " + phenotypes_str);
- geno_pheno_map.put(genome, phenotypes_str);
- }
- if (first) {
- System.out.println("No phenotypes in pangenome");
- } else {
- System.out.println("");
- }
- return geno_pheno_map;
- }
-
- /**
- *
- * @param shared_genes_map
- * @param unique_genes_map
- */
- public static void find_shared_genes_no_ref(HashMap<String, Integer> shared_genes_map, HashMap<Integer, Integer> unique_genes_map) {
- ResourceIterator<Node> homology_groups = graphDb.findNodes(homology_group_label);
- HashMap<Integer, Integer> copy_number_map = new HashMap<>();
- while (homology_groups.hasNext()) {
- Node hm_group = homology_groups.next();
- int[] fields = (int[]) hm_group.getProperty("copy_number");
- int position = 0;
- for (int cn : fields) {
- if (position == 0) { // first value is empty
- position ++;
- continue;
- }
- copy_number_map.put(position, cn);
- position ++;
- }
-
- for (Map.Entry<Integer, Integer> entry : copy_number_map.entrySet()) {
- int key = entry.getKey();
- int value = entry.getValue();
- boolean unique_bool = true;
- for (Map.Entry<Integer, Integer> entry2 : copy_number_map.entrySet()) {
- int key2 = entry2.getKey();
- int value2 = entry2.getValue();
- if (key == key2) {
- continue;
- }
- if (value2 > 0) {
- unique_bool = false;
- }
- if (key >= key2) {
- continue;
- }
- String key_str = String.valueOf(key);
- String key2_str = String.valueOf(key2);
- String combined_key = key_str + "_" + key2_str;
- int shared_genes = shared_genes_map.get(combined_key);
- if (value > value2) {
- shared_genes += value2;
- } else {
- shared_genes += value;
- }
- shared_genes_map.put(combined_key, shared_genes);
- }
- if (unique_bool == true) {
- int unique_genes = unique_genes_map.get(key);
- unique_genes += value;
- unique_genes_map.put(key, unique_genes);
- }
- }
- }
- }
/**
* Is able to count all types of 'feature' nodes from GFF files.
@@ -14029,8 +11600,8 @@ public class Classification {
log_builder.append(protein_id).append(", ").append(gene_name).append(", ").append(address[0]).append(", ").append(mrna_node_id).append(", ")
.append(nuc_sequence.length()).append(", ").append(prot_sequence.length()).append(", ").append(address_str).append("\n");
present_genomes.add(address[0]);
- nuc_sequence = split_seq_in_parts_of_60bp(nuc_sequence);
- prot_sequence = split_seq_in_parts_of_60bp(prot_sequence);
+ nuc_sequence = split_seq_in_parts_of_80bp(nuc_sequence);
+ prot_sequence = split_seq_in_parts_of_80bp(prot_sequence);
nuc_seq_builder.append(">").append(protein_id).append(" ").append(gene_name).append(" ").append(address[0]).append("\n").append(nuc_sequence).append("\n");
prot_seq_builder.append(">").append(protein_id).append(" ").append(gene_name).append(" ").append(address[0]).append("\n").append(prot_sequence).append("\n");
}
@@ -15168,27 +12739,6 @@ public class Classification {
return add_str;
}
- /**
- *
- * @param mrna_list
- * @param mrna_gene_position_map
- * @param position_map
- * @return
- */
- public int[] create_array_with_mrna_positions(ArrayList<Node> mrna_list, HashMap<Node, int[]> mrna_gene_position_map, HashMap<Integer, Node> position_map) {
- int[] all_poss_array_int = new int[mrna_list.size()];
- int counter = 0;
- for (Node mrna_node : mrna_list) { // checking the position of the user mrna's in the complete genome
- int[] array_position = mrna_gene_position_map.get(mrna_node);
- all_poss_array_int[counter] = array_position[0];
- position_map.put(array_position[0], mrna_node);
- System.out.println(mrna_node + " " + array_position[0] + " " + array_position[1]);
- counter ++;
- }
- Arrays.sort(all_poss_array_int);
- return all_poss_array_int;
- }
-
/**
*
* @param hm_node_list
@@ -15264,75 +12814,6 @@ public class Classification {
}
return mrnas_per_position;
}
-
- /**
- * First step of msa_of_regions. Retrieval of regions from the pangenome
- */
- public static void prepare_region_msa_input() {
- StringBuilder fasta_builder = new StringBuilder();
- StringBuilder genome_nrs_builder = new StringBuilder();
-
- int counter = 1;
- if (regions_to_search.length > 100) {
- System.out.println("\nRetrieving regions");
- }
- for (String region_str : regions_to_search) {
- if (regions_to_search.length > 100) {
- printProgressBar(regions_to_search.length, counter, "regions", false);
- }
-
- String[] region_array = region_str.split(" ");
- int genome_nr;
- int sequence_nr;
- int start_pos;
- int end_pos;
- try {
- genome_nr = Integer.parseInt(region_array[0]);
- sequence_nr = Integer.parseInt(region_array[1]);
- start_pos = Integer.parseInt(region_array[2]);
- end_pos = Integer.parseInt(region_array[3]);
- } catch (NumberFormatException nfe) {
- System.out.println("Unable to correctly retrieve four numbers in: " + region_str);
- continue;
- }
-
- boolean reverse = false;
- String rev_complement = "";
- if (region_str.endsWith("-")) {
- reverse = true;
- region_str = region_str.replace(" -","");
- rev_complement = "_rvComplement";
- }
-
- if (genome_nr > total_genomes) {
- System.out.println("A genome with number " + genome_nr + " does not exists! Only " + total_genomes + " genomes in pangenome\n");
- System.exit(1);
- }
- if (end_pos < start_pos) {
- System.out.println("The start position is lower as the end position. " + region_str + "\n");
- System.exit(1);
- }
-
- region_str = region_str.replace(" ","_"); // 1 1 1 1000 becomes 1_1_1_1000
- String region;
- if (!reverse) {
- region = get_region(genome_nr, sequence_nr, start_pos-1, end_pos-1, true);
- } else {
- region = get_region(genome_nr, sequence_nr, start_pos-1, end_pos-1, false);
- }
- fasta_builder.append(">").append(region_str).append(rev_complement).append("\n")
- .append(region).append("\n");
-
- genome_nrs_builder.append(genome_nr).append(",").append(region_str).append(rev_complement).append("\n");
- if (region.length() < 10) {
- System.out.println("The length of " + region_str + " is below 10 characters.");
- System.exit(1);
- }
- counter ++;
- }
- write_SB_to_file_in_DB(fasta_builder, "/alignments/regions/nuc_input.fasta");
- write_SB_to_file_in_DB(genome_nrs_builder, "/alignments/regions/nuc_input_genomes.txt");
- }
/**
* Create two files
@@ -15412,16 +12893,17 @@ public class Classification {
}
/**
- *
- * @return
+ * Count all functional annotations in the pangenome and put the counts in function_count_map
+ * @return function_count_map
*/
public HashMap<String, int[]> count_functions_for_metrics() {
HashMap<String, HashSet<Node>> mrnas_with_function_set = new HashMap<>();
+ // key is genome nr or sequence id. value are mrna's with at least one function
HashMap<String, int[]> function_count_map = new HashMap<>(); // key is genome or sequence id + type of function or "ALL"
count_phobius_signalp_for_metrics(mrnas_with_function_set, function_count_map);
count_cog_for_metrics(mrnas_with_function_set, function_count_map);
- get_BGCs_per_sequence2(function_count_map);
+ get_BGCs_per_sequence(mrnas_with_function_set, function_count_map);
Label[] labels = new Label[]{go_label, pfam_label, interpro_label, tigrfam_label};
RelationshipType[] reltypes = new RelationshipType[]{RelTypes.has_go, RelTypes.has_pfam, RelTypes.has_interpro, RelTypes.has_tigrfam};
@@ -15453,9 +12935,10 @@ public class Classification {
if (!annotation_identifiers.contains(annotation_id)) {
continue;
}
- } else if (PROTEOME && skip_array[genome_nr-1]) {
+ } else if (skip_array[genome_nr-1]) { // proteome is true
continue;
}
+
if (!PROTEOME && !mrna_node.hasProperty("longest_transcript")) {
continue; // will only be counted if they are part of the longest transcript
}
@@ -15524,14 +13007,15 @@ public class Classification {
/**
* Count phobius secreted, receptor and transmembrane nodes
- * @param mrnas_with_function_set
- * @param mrnas_with_functions
+ * @param mrnas_with_function_set key is genome nr or sequence id. value are mrna's with at least one function
+ * @param function_count_map
*/
- public void count_phobius_signalp_for_metrics(HashMap<String, HashSet<Node>> mrnas_with_function_set, HashMap<String, int[]> mrnas_with_functions) {
- HashMap<String, Integer> temp_mrnas_with_function = new HashMap<>(); // key is genome or sequence number with "#ph_secreted" or "ph_transmembrane"
-
- // count signalp nodes
- ResourceIterator<Node> signalp_nodes = graphDb.findNodes(signalp_label);
+ public void count_phobius_signalp_for_metrics(HashMap<String, HashSet<Node>> mrnas_with_function_set,
+ HashMap<String, int[]> function_count_map) {
+
+ HashMap<String, Integer> temp_mrnas_with_function = new HashMap<>();
+ // key is genome or sequence number with "#ph_secreted" or "ph_transmembrane"
+ ResourceIterator<Node> signalp_nodes = graphDb.findNodes(signalp_label); // count signalp nodes
int total_signalp = (int) count_nodes(signalp_label);
long node_counter = 0;
int signalp = 0;
@@ -15629,7 +13113,7 @@ public class Classification {
for (String key : temp_mrnas_with_function.keySet()) {
int nr_of_mrnas = temp_mrnas_with_function.get(key);
String[] key_array = key.split("#");
- int[] phobius_signalp_nodes = mrnas_with_functions.get(key_array[0] + "#phobius_signalp");
+ int[] phobius_signalp_nodes = function_count_map.get(key_array[0] + "#phobius_signalp");
if (phobius_signalp_nodes == null) {
phobius_signalp_nodes = new int[3];
}
@@ -15640,24 +13124,27 @@ public class Classification {
} else { // signalp
phobius_signalp_nodes[2] += nr_of_mrnas;
}
- mrnas_with_functions.put(key_array[0] + "#phobius_signalp", phobius_signalp_nodes);
+ function_count_map.put(key_array[0] + "#phobius_signalp", phobius_signalp_nodes);
}
for (int i=1; i <= total_genomes; i++) {
if (skip_array[i-1]) {
continue;
}
- if (!mrnas_with_functions.containsKey(i + "#phobius_signalp")) {
+ if (!function_count_map.containsKey(i + "#phobius_signalp")) {
int[] phobius_signalp_nodes = new int[3];
- mrnas_with_functions.put(i + "#phobius_signalp", phobius_signalp_nodes);
+ function_count_map.put(i + "#phobius_signalp", phobius_signalp_nodes);
}
}
- mrnas_with_functions.put("pangenome#phobius_signalp", new int[]{total_secreted, total_transmembranes, signalp});
+ function_count_map.put("pangenome#phobius_signalp", new int[]{total_secreted, total_transmembranes, signalp});
}
/**
- *
- * @return
+ * SELECTED_HMGROUPS must be set: the input file to a 'homology_group' node identifiers file
+ * The variable can be set by the user with --homology-groups
+ *
+ * Homology group identifiers files have different formats for the core, accessory, unique and phenotype groups
+ * @return list with 'homology_group' node identifiers
*/
public static ArrayList<Node> read_hmgroup_input_file() {
String hmgroups_str = "";
@@ -15668,21 +13155,18 @@ public class Classification {
}
try (BufferedReader in = new BufferedReader(new FileReader(SELECTED_HMGROUPS))) {
- int line_count = 0;
- String temp_hmgroup_str = "";
+ StringBuilder temp_hmgroup_str = new StringBuilder();
for (int c = 0; in.ready();) {
hmgroups_str = in.readLine().trim();
- if (hmgroups_str.equals("")) {
- continue;
- } else if (hmgroups_str.startsWith("Genome")) {
+ if (hmgroups_str.equals("") || hmgroups_str.startsWith("Genome")) {
// do nothing
- } else if (!hmgroups_str.contains(" genomes") && !hmgroups_str.contains("Phenotype") && !hmgroups_str.contains("#")) { // accessory hmgroups were provided
- temp_hmgroup_str += hmgroups_str + ", ";
+ } else if (!hmgroups_str.contains(" genomes") && !hmgroups_str.contains("Phenotype")
+ && !hmgroups_str.contains("#")) { // accessory hmgroups were provided
+ temp_hmgroup_str.append(hmgroups_str).append(", ");
}
- line_count ++;
}
- temp_hmgroup_str = temp_hmgroup_str.replaceFirst(".$","").replaceFirst(".$","");
- hmgroups_str = temp_hmgroup_str;
+ temp_hmgroup_str = new StringBuilder(temp_hmgroup_str.toString().replaceFirst(".$", "").replaceFirst(".$", ""));
+ hmgroups_str = temp_hmgroup_str.toString();
if (hmgroups_str.contains("/")) {
System.out.println("Homology group input not correctly formatted");
System.exit(1);
@@ -15934,23 +13418,6 @@ public class Classification {
APPEND = false;
}
}
-
- /**
- *
- * @param values
- * @return
- */
- public static String parenthesis_around_values(String values) {
- String parenthesis_str = "", temp;
- String[] valueArray = values.split(", ");
- for (String value: valueArray) {
- temp = "\"" + value + "\"";
- parenthesis_str += temp + ", ";
- }
- parenthesis_str = parenthesis_str.replaceFirst(".$","");
- parenthesis_str = parenthesis_str.replaceFirst(".$","");
- return parenthesis_str;
- }
/**
*
@@ -16113,84 +13580,6 @@ public class Classification {
}
}
- /**
- * Returns a pangenome pointer pointing to the specified genomic position.
- *
- * @param addr An integer array lile {genome_number, sequence_number, begin_position, end_position}
- * @return A pointer to the genomic position in the pangenome
- */
- public static IndexPointer locate(int[] addr) {
- int node_start_pos, low, high, mid , node_len, genomic_pos;
- boolean forward;
- Node node, neighbor, seq_node;
- Relationship rel;
- String anchor_sides, origin = "G" + addr[0] + "S" + addr[1];
- long[] anchor_nodes;
- int[] anchor_positions;
- int[] address = Arrays.copyOf(addr,addr.length);
- genomic_pos = address[2] - 1;
- seq_node = graphDb.findNode(sequence_label, "identifier", address[0]+"_"+address[1]);
- anchor_nodes = (long[]) seq_node.getProperty("anchor_nodes");
- anchor_positions = (int[]) seq_node.getProperty("anchor_positions");
- anchor_sides = (String) seq_node.getProperty("anchor_sides");
- // Find the immediate preceding anchor_node, searching in the sorted array of anchor positions.
- for (low = 0, high = anchor_sides.length() - 1, mid = (low + high) / 2; low <= high; mid = (low + high) / 2) {
- if (genomic_pos < anchor_positions[mid]) {
- high = mid - 1;
- } else if (genomic_pos > anchor_positions[mid]) {
- low = mid + 1;
- } else {
- break;
- }
- }
- if (genomic_pos < anchor_positions[mid]) {
- --mid;
- }
- forward = anchor_sides.charAt(mid) == 'F';
- try (Transaction tx = graphDb.beginTx()) { // start database transaction
- node = graphDb.getNodeById(anchor_nodes[mid]);
- node_start_pos = anchor_positions[mid];
- node_len = (int) node.getProperty("length");
- // Traverse the pangenome from the anchor node until reach to the target
- while (node_start_pos + node_len <= genomic_pos)
- {
- address[2] = node_start_pos + node_len - K_SIZE + 1;
- rel = seqLayer.get_outgoing_edge(node, origin, address[2]);
- if (rel == null) {
- System.out.println("Failed to locate address : " + address[0] + " " + address[1] + " " + address[2]);
- break;
- }
- neighbor = rel.getEndNode();
- forward = rel.getType().name().charAt(1) == 'F';
- node_start_pos += node_len - K_SIZE + 1;
- node = neighbor;
- node_len = (int) node.getProperty("length");
- }
- tx.success(); // transaction successful, commit changes
- }
- return new IndexPointer(node.getId(), forward, forward ? genomic_pos - node_start_pos : node_len - 1 - (genomic_pos - node_start_pos), -1l);
- }
-
- /**
- * Gives the outgoing relationship to take based on the query coordinate.
- *
- * @param current_node The current node to go out from.
- * @param origin The string determining query genome and sequence, e.g. "G2S3"
- * @param pos The query position.
- * @return The proper outgoing edge.
- */
- public static Relationship get_outgoing_edge(Node current_node, String origin, int pos) {
- int[] occurrence;
- for (Relationship r_out : current_node.getRelationships(Direction.OUTGOING)) {
- occurrence = (int[])r_out.getProperty(origin, null);
- if (occurrence != null) {
- if (Arrays.binarySearch(occurrence, pos) >= 0)
- return r_out;
- }
- }
- return null;
- }
-
/**
* Calculate the GC content per sequence
* GC ratio per block (of 1000bp) is currently disabled. This is used for CIRCOS plots and the ability to do this should not be removed
@@ -16242,174 +13631,62 @@ public class Classification {
nucleotide_count[4] += nuc_counts_sequence[4];
nucleotide_count[5] += nuc_counts_sequence[5];
out.write("#sequence " + sequence_id + "\nA: " + nuc_counts_sequence[0] + " T: " + nuc_counts_sequence[1] +
- " C: " + nuc_counts_sequence[2] + " G: " + nuc_counts_sequence[3] + " N: " + nuc_counts_sequence[4] +
- " other: " + nuc_counts_sequence[5] + "\n");
- }
- out.close();
- } catch (IOException e) {
- System.out.println("Unable to read: " + WORKING_DIRECTORY + "metrics/GC/" + genome_nr + "/nucleotide_count.txt");
- System.exit(1);
- }
- return nucleotide_count;
- }
-
- /**
- * Read the file with nucleotide counts that was created in a previous run
- * @param genome_nr
- * @param nuc_count_per_seq
- */
- public static void read_nucleotide_count(int genome_nr, HashMap<String, long[]> nuc_count_per_seq) {
- long[] total_count = {0,0,0,0,0,0}; // nucleotide counts for the entire genome, [A, T, C, G, N, other]
- try (BufferedReader in = new BufferedReader(new FileReader(WORKING_DIRECTORY + "metrics/GC/" + genome_nr + "/nucleotide_count.txt"))) { // read the GFF file
- String identifier = "";
- for (int c = 0; in.ready();) {
- String line = in.readLine().trim();
- String[] line_array = line.split(" ");
- if (line.startsWith("#")) {
- identifier = line_array[1];
- continue;
- }
- int position = 0;
- long[] sequence_counts = {0,0,0,0,0,0}; // nucleotide counts for a sequence, [A, T, C, G, N, other]
- for (int i=1; i<= line_array.length-1; i += 2) {
- sequence_counts[position] = Long.parseLong(line_array[i]);
- total_count[position] += Long.parseLong(line_array[i]);
- position ++;
- }
- nuc_count_per_seq.put(identifier, sequence_counts);
- }
- } catch (IOException ioe) {
- System.out.println("Failed to read info file");
- System.exit(1);
- }
- nuc_count_per_seq.put(genome_nr + "", total_count);
- }
-
- /**
- * Retrieve the genomic region from the genome database
- * @param genome
- * @param sequence
- * @param begin
- * @param end
- * @param forward
- * @return
- */
- public static String get_region(int genome, int sequence, int begin, int end, boolean forward) {
- if (begin > end) {
- System.out.println("\nStart location of this region is higher than its end location -> " + genome + " " + sequence + " " + begin + " " +end );
- System.exit(1);
- }
- StringBuilder seq = new StringBuilder();
- genomeSc.get_sub_sequence(seq, genome, sequence, begin, end - begin + 1, forward);
- String region = seq.toString();
- return region;
- }
-
- /**
- *
- * @param genomes_array
- * @return
- */
- public static String[] sort_str_array(String[] genomes_array) {
- int[] int_array = Arrays.stream(genomes_array).mapToInt(Integer::parseInt).toArray(); //string to int string_to_int
- Arrays.sort(int_array);
- String strArray[] = Arrays.stream(int_array).mapToObj(String::valueOf).toArray(String[]::new);
- return strArray;
- }
-
- /**
- *
- * @param genomes_array
- * @return
- */
- public static int[] sort_str_array_return_int(String[] genomes_array) {
- int[] int_array = Arrays.stream(genomes_array).mapToInt(Integer::parseInt).toArray(); //string to int
- Arrays.sort(int_array);
- return int_array;
- }
-
- /**
- *
- * @param genomes_array
- * @return
- */
- public static long[] convert_str_array_to_long(String[] genomes_array) {
- long[] int_array = Arrays.stream(genomes_array).mapToLong(Long::parseLong).toArray(); //string to int
- return int_array;
- }
-
- /**
- *
- * @param genome1
- * @param genome2
- * @return
- */
- public static String create_combi_key_str(String genome1, String genome2) {
- String combi_key = genome1 + "_" + genome2;
- int genome1_int = Integer.valueOf(genome1);
- int genome2_int = Integer.valueOf(genome2);
- if (genome1_int > genome2_int) {
- combi_key = genome2 + "_" + genome1;
- }
- return combi_key;
- }
-
- // universal function
- /**
- * String and Integer
- * @param hashmap
- * @param key
- * @param value
- */
- public static void incr_hashmap(HashMap<String, Integer> hashmap, String key, int value) {
- int total_value = hashmap.get(key);
- total_value += value;
- hashmap.put(key, total_value);
+ " C: " + nuc_counts_sequence[2] + " G: " + nuc_counts_sequence[3] + " N: " + nuc_counts_sequence[4] +
+ " other: " + nuc_counts_sequence[5] + "\n");
+ }
+ out.close();
+ } catch (IOException e) {
+ System.out.println("Unable to read: " + WORKING_DIRECTORY + "metrics/GC/" + genome_nr + "/nucleotide_count.txt");
+ System.exit(1);
+ }
+ return nucleotide_count;
}
-
- //String and Long
/**
- *
- * @param hashmap
- * @param key
- * @param value
+ * Read the file with nucleotide counts that was created in a previous run
+ * @param genome_nr
+ * @param nuc_count_per_seq
*/
- public static void incr_hashmap(HashMap<String, Long> hashmap, String key, long value) {
- long new_value = hashmap.get(key);
- new_value += value;
- hashmap.put(key, new_value);
+ public static void read_nucleotide_count(int genome_nr, HashMap<String, long[]> nuc_count_per_seq) {
+ long[] total_count = {0,0,0,0,0,0}; // nucleotide counts for the entire genome, [A, T, C, G, N, other]
+ try (BufferedReader in = new BufferedReader(new FileReader(WORKING_DIRECTORY + "metrics/GC/" + genome_nr + "/nucleotide_count.txt"))) { // read the GFF file
+ String identifier = "";
+ for (int c = 0; in.ready();) {
+ String line = in.readLine().trim();
+ String[] line_array = line.split(" ");
+ if (line.startsWith("#")) {
+ identifier = line_array[1];
+ continue;
+ }
+ int position = 0;
+ long[] sequence_counts = {0,0,0,0,0,0}; // nucleotide counts for a sequence, [A, T, C, G, N, other]
+ for (int i=1; i<= line_array.length-1; i += 2) {
+ sequence_counts[position] = Long.parseLong(line_array[i]);
+ total_count[position] += Long.parseLong(line_array[i]);
+ position ++;
+ }
+ nuc_count_per_seq.put(identifier, sequence_counts);
+ }
+ } catch (IOException ioe) {
+ System.out.println("Failed to read info file");
+ System.exit(1);
+ }
+ nuc_count_per_seq.put(genome_nr + "", total_count);
}
-
+
+ // universal function
/**
- *
+ * String and Integer
* @param hashmap
* @param key
* @param value
*/
- public static void incr_hashmap(HashMap<Integer, Integer> hashmap, int key, int value) {
+ public static void incr_hashmap(HashMap<String, Integer> hashmap, String key, int value) {
int total_value = hashmap.get(key);
total_value += value;
hashmap.put(key, total_value);
}
-
- // Float
- /**
- *
- * @param hashmap
- * @param key
- * @param value
- */
- public static void try_incr_hashmap(HashMap<Float, String> hashmap, float key, String value) {
- String total_value = hashmap.get(key);
- if (total_value != null) {
- total_value += value;
- } else {
- total_value = value;
- }
- hashmap.put(key, total_value);
- }
-
+
/**
*
* @param hashmap
@@ -16443,23 +13720,7 @@ public class Classification {
}
hashmap.put(key, total_value);
}
-
- /**
- *
- * @param hashmap
- * @param key
- * @param value
- */
- public static void try_incr_hashmap(HashMap<Node, Integer> hashmap, Node key, int value) {
- int total_value;
- if (hashmap.containsKey(key)) {
- total_value = hashmap.get(key);
- total_value += value;
- } else {
- total_value = value;
- }
- hashmap.put(key, total_value);
- }
+
/**
*
* @param hashmap
@@ -16476,41 +13737,7 @@ public class Classification {
}
hashmap.put(key, total_value);
}
-
- /**
- *
- * @param hashmap
- * @param key
- * @param value
- */
- public static void try_incr_hashmap(HashMap<Integer, Integer> hashmap, int key, int value) {
- int total_value;
- if (hashmap.containsKey(key)) {
- total_value = hashmap.get(key);
- total_value += value;
- } else {
- total_value = value;
- }
- hashmap.put(key, total_value);
- }
-
- /**
- *
- * @param hashmap
- * @param key
- * @param value
- */
- public static void try_incr_hashmap(HashMap<Integer, Long> hashmap, int key, long value) {
- long total_value;
- if (hashmap.containsKey(key)) {
- total_value = hashmap.get(key);
- total_value += value;
- } else {
- total_value = value;
- }
- hashmap.put(key, total_value);
- }
-
+
/**
*
* @param hashmap
@@ -16526,23 +13753,7 @@ public class Classification {
}
hashmap.put(key, total_value);
}
-
- /**
- *
- * @param hashmap
- * @param key
- * @param value
- */
- public static void try_incr_hashmap(HashMap<String, String> hashmap, String key, String value) {
- String total_value = hashmap.get(key);
- if (total_value != null) {
- total_value += value;
- } else {
- total_value = value;
- }
- hashmap.put(key, total_value);
- }
-
+
/**
*
* @param hashmap
@@ -16559,21 +13770,8 @@ public class Classification {
}
hashmap.put(key, total_value);
}
-
- //Stringbuilders
- //SB String
- /**
- *
- * @param hashmap
- * @param key
- * @param value
- */
- public static void incr_SB_hashmap(HashMap<String, StringBuilder> hashmap, String key, String value) {
- StringBuilder output_builder = hashmap.get(key);
- output_builder.append(value);
- hashmap.put(key, output_builder);
- }
-
+
+ //Stringbuilders
/**
*
* @param hashmap
@@ -16592,18 +13790,6 @@ public class Classification {
}
//SB Integer
- /**
- *
- * @param hashmap
- * @param key
- * @param value
- */
- public static void incr_SB_hashmap(HashMap<Integer, StringBuilder> hashmap, int key, String value) {
- StringBuilder builder= hashmap.get(key);
- builder.append(value);
- hashmap.put(key, builder);
- }
-
/**
*
* @param hashmap
@@ -16638,117 +13824,65 @@ public class Classification {
}
hashmap.put(key, builder);
}
-
+
//ArrayList
- //AL Double
- /**
- *
- * @param hashmap
- * @param key
- * @param value
- */
- public static void try_incr_AL_hashmap(HashMap<Double, ArrayList<String>> hashmap, Double key, String value) {
- ArrayList<String> value_array = hashmap.get(key);
- if (value_array == null) {
- value_array = new ArrayList<>();
- }
- value_array.add(value);
- hashmap.put(key, value_array);
- }
-
+ //AL Double
/**
- *
+ *
* @param hashmap
* @param key
- * @param value
+ * @param value
*/
- public static void try_incr_AL_hashmap(HashMap<Double, ArrayList<Integer>> hashmap, double key, int value) {
- ArrayList<Integer> value_array = hashmap.get(key);
+ public static void try_incr_AL_hashmap(HashMap<String, ArrayList<Object>> hashmap, String key, Object value) {
+ ArrayList<Object> value_array = hashmap.get(key);
if (value_array == null) {
value_array = new ArrayList<>();
}
value_array.add(value);
hashmap.put(key, value_array);
}
-
+
+ //ArrayList
+ //AL Double
/**
- *
+ *
* @param hashmap
* @param key
- * @param value
+ * @param value
*/
- public static void try_incr_AL_hashmap(HashMap<Double, ArrayList<Node>> hashmap, double key, Node value) {
- ArrayList<Node> value_array = hashmap.get(key);
+ public static void try_incr_AL_hashmap(HashMap<Integer, ArrayList<Object>> hashmap, int key, Object value) {
+ ArrayList<Object> value_array = hashmap.get(key);
if (value_array == null) {
value_array = new ArrayList<>();
}
value_array.add(value);
hashmap.put(key, value_array);
}
-
- //AL String
+
+ //ArrayList
+ //AL Double
/**
*
* @param hashmap
* @param key
* @param value
*/
- public static void incr_AL_hashmap(HashMap<String, ArrayList<String>> hashmap, String key, String value) {
+ public static void try_incr_AL_hashmap(HashMap<Double, ArrayList<String>> hashmap, Double key, String value) {
ArrayList<String> value_array = hashmap.get(key);
- value_array.add(value);
- hashmap.put(key, value_array);
- }
-
-
- /**
- *
- * @param hashmap
- * @param key
- * @param value
- */
- public static void incr_AL_hashmap(HashMap<Integer, ArrayList<Node>> hashmap, int key, Node value) {
- ArrayList<Node> value_array = hashmap.get(key);
- value_array.add(value);
- hashmap.put(key, value_array);
- }
-
- /**
- *
- * @param hashmap
- * @param key
- * @param value
- */
- public static void try_incr_AL_hashmap(HashMap<String, ArrayList<Double>> hashmap, String key, Double value) {
- ArrayList<Double> value_array = hashmap.get(key);
- if (value_array == null) {
- value_array = new ArrayList<>();
- }
- value_array.add(value);
- hashmap.put(key, value_array);
- }
-
- /**
- *
- * @param hashmap
- * @param key
- * @param value
- */
- public static void try_incr_AL_hashmap(HashMap<String, ArrayList<Integer>> hashmap, String key, int value) {
- ArrayList<Integer> value_array = hashmap.get(key);
if (value_array == null) {
value_array = new ArrayList<>();
}
value_array.add(value);
hashmap.put(key, value_array);
- }
-
+ }
+
/**
*
* @param hashmap
* @param key
* @param value
*/
- public static void try_incr_AL_hashmap(HashMap<Integer, ArrayList<Integer>> hashmap, int key, int value) {
+ public static void try_incr_AL_hashmap(HashMap<Double, ArrayList<Integer>> hashmap, double key, int value) {
ArrayList<Integer> value_array = hashmap.get(key);
if (value_array == null) {
value_array = new ArrayList<>();
@@ -16757,32 +13891,18 @@ public class Classification {
hashmap.put(key, value_array);
}
- /**
- *
- * @param hashmap
- * @param key
- * @param value
- */
- public static void try_incr_AL_hashmap(HashMap<String, ArrayList<String>> hashmap, String key, String value) {
- ArrayList<String> value_array = hashmap.get(key);
- if (value_array == null) {
- value_array = new ArrayList<>();
- }
- value_array.add(value);
- hashmap.put(key, value_array);
- }
-
+ //AL String
/**
*
* @param hashmap
* @param key
* @param value
*/
- public static void try_incr_AL_hashmap(HashMap<String, ArrayList<Node>> hashmap, String key, Node value) {
- ArrayList<Node> value_array = hashmap.get(key);
+ public static void try_incr_AL_hashmap(HashMap<String, ArrayList<Double>> hashmap, String key, Double value) {
+ ArrayList<Double> value_array = hashmap.get(key);
if (value_array == null) {
value_array = new ArrayList<>();
- }
+ }
value_array.add(value);
hashmap.put(key, value_array);
}
@@ -16793,8 +13913,8 @@ public class Classification {
* @param key
* @param value
*/
- public static void try_incr_AL_hashmap(HashMap<String, ArrayList<Long>> hashmap, String key, long value) {
- ArrayList<Long> value_array = hashmap.get(key);
+ public static void try_incr_AL_hashmap(HashMap<String, ArrayList<Integer>> hashmap, String key, int value) {
+ ArrayList<Integer> value_array = hashmap.get(key);
if (value_array == null) {
value_array = new ArrayList<>();
}
@@ -16802,42 +13922,45 @@ public class Classification {
hashmap.put(key, value_array);
}
- //AL with Integer as key
- /**
- *
- * @param hashmap
- * @param key
- * @param value
- */
- public static void incr_AL_hashmap(HashMap<Integer, ArrayList<Double>> hashmap, int key, Double value) {
- ArrayList<Double> value_array = hashmap.get(key);
+ /**
+ *
+ * @param hashmap
+ * @param key
+ * @param value
+ */
+ public static void try_incr_AL_hashmap(HashMap<String, ArrayList<String>> hashmap, String key, String value) {
+ ArrayList<String> value_array = hashmap.get(key);
+ if (value_array == null) {
+ value_array = new ArrayList<>();
+ }
value_array.add(value);
hashmap.put(key, value_array);
}
-
+
/**
*
* @param hashmap
* @param key
* @param value
*/
- public static void try_incr_AL_hashmap(HashMap<Integer, ArrayList<String>> hashmap, int key, String value) {
- ArrayList<String> value_array = hashmap.get(key);
+ public static void try_incr_AL_hashmap(HashMap<String, ArrayList<Node>> hashmap, String key, Node value) {
+ ArrayList<Node> value_array = hashmap.get(key);
if (value_array == null) {
value_array = new ArrayList<>();
}
value_array.add(value);
hashmap.put(key, value_array);
}
-
+
+ //AL with Integer as key
/**
*
* @param hashmap
* @param key
* @param value
*/
- public static void try_incr_AL_hashmap(HashMap<Integer, ArrayList<Node>> hashmap, int key, Node value) {
- ArrayList<Node> value_array = hashmap.get(key);
+ public static void try_incr_AL_hashmap(HashMap<Integer, ArrayList<String>> hashmap, int key, String value) {
+ ArrayList<String> value_array = hashmap.get(key);
if (value_array == null) {
value_array = new ArrayList<>();
}
@@ -16845,22 +13968,22 @@ public class Classification {
hashmap.put(key, value_array);
}
- //AL long
/**
*
* @param hashmap
* @param key
* @param value
*/
- public static void try_incr_AL_hashmap(HashMap<Long, ArrayList<Node>> hashmap, long key, Node value) {
+ public static void try_incr_AL_hashmap(HashMap<Integer, ArrayList<Node>> hashmap, int key, Node value) {
ArrayList<Node> value_array = hashmap.get(key);
if (value_array == null) {
value_array = new ArrayList<>();
}
value_array.add(value);
hashmap.put(key, value_array);
- }
+ }
+ //AL long
/**
*
* @param hashmap
@@ -16904,24 +14027,7 @@ public class Classification {
}
value_list.add(value);
hashmap.put(key, value_list);
- }
-
- /**
- *
- * @param hashmap
- * @param key
- * @param value
- */
- public synchronized static void try_incr_chashmap(ConcurrentHashMap<String, Long> hashmap, String key, Long value) {
- long total_value;
- if (hashmap.containsKey(key)) {
- total_value = hashmap.get(key);
- total_value += value;
- } else {
- total_value = value;
- }
- hashmap.put(key, total_value);
- }
+ }
/**
*
@@ -16936,37 +14042,7 @@ public class Classification {
}
value_array.add(value);
hashmap.put(key, value_array);
- }
-
- /**
- *
- * @param hashmap
- * @param key
- * @param value
- */
- public synchronized static void try_incr_AL_chashmap(ConcurrentHashMap<Integer, ArrayList<Node>> hashmap, int key, Node value) {
- ArrayList<Node> value_array = hashmap.get(key);
- if (value_array == null) {
- value_array = new ArrayList<>();
- }
- value_array.add(value);
- hashmap.put(key, value_array);
- }
-
- /**
- *
- * @param hashmap
- * @param key
- * @param value
- */
- public synchronized static void try_incr_AL_chashmap(ConcurrentHashMap<Integer, ArrayList<String>> hashmap, int key, String value) {
- ArrayList<String> value_array = hashmap.get(key);
- if (value_array == null) {
- value_array = new ArrayList<>();
- }
- value_array.add(value);
- hashmap.put(key, value_array);
- }
+ }
/**
*
@@ -17026,34 +14102,26 @@ public class Classification {
value_array[position] += value;
hashmap.put(key, value_array);
}
-
+
/**
- *
+ *
* @param hashmap
* @param key
* @param value
- * @param position
+ * @param position
+ * @param array_size
*/
- public static void incr_array_hashmap(HashMap<Node, int[] > hashmap, Node key, int value, int position) {
+ public static void try_incr_array_hashmap(HashMap<String, int[] > hashmap, String key, int value, int position,
+ int array_size) {
int[] value_array = hashmap.get(key);
+ if (value_array == null) {
+ value_array = new int[array_size];
+ }
value_array[position] += value;
hashmap.put(key, value_array);
}
-
//Hashset
//hashset String
- /**
- *
- * @param hashmap
- * @param key
- * @param value
- */
- public static void incr_hashset_hashmap(HashMap<String, HashSet<String>> hashmap, String key, String value) {
- HashSet<String> value_hashset = hashmap.get(key);
- value_hashset.add(value);
- hashmap.put(key, value_hashset);
- }
-
/**
*
* @param hashmap
@@ -17085,36 +14153,6 @@ public class Classification {
}
//Integer
- /**
- *
- * @param hashmap
- * @param key
- * @param value
- */
- public static void try_incr_hashset_hashmap(HashMap<Integer, HashSet<Integer>> hashmap, int key, int value) {
- HashSet<Integer> value_set = hashmap.get(key);
- if (value_set == null) {
- value_set = new HashSet<>();
- }
- value_set.add(value);
- hashmap.put(key, value_set);
- }
-
- /**
- *
- * @param hashmap
- * @param key
- * @param value
- */
- public static void try_incr_hashset_hashmap(HashMap<Integer, HashSet<Node>> hashmap, int key, Node value) {
- HashSet<Node> value_set = hashmap.get(key);
- if (value_set == null) {
- value_set = new HashSet<>();
- }
- value_set.add(value);
- hashmap.put(key, value_set);
- }
-
/**
*
* @param hashmap
@@ -17129,22 +14167,7 @@ public class Classification {
value_set.add(value);
hashmap.put(key, value_set);
}
-
- /**
- *
- * @param hashmap
- * @param key
- * @param value
- */
- public static void try_incr_hashset_hashmap(HashMap<Integer, HashSet<Double>> hashmap, int key, Double value) {
- HashSet<Double> value_set = hashmap.get(key);
- if (value_set == null) {
- value_set = new HashSet<>();
- }
- value_set.add(value);
- hashmap.put(key, value_set);
- }
-
+
/**
*
* @param hashmap
@@ -17160,33 +14183,7 @@ public class Classification {
hashmap.put(key, value_set);
}
- //Average median standard deviation functions
- /**
- * Return the AVERAGE value of an array
- * @param array
- * @return
- */
- public static double get_average_from_array(long[] array) {
- double total_value = 0;
- for (long value : array) {
- total_value += value;
- }
- return total_value/array.length;
- }
-
- /**
- * Return the AVERAGE value of an array
- * @param array
- * @return
- */
- public static double get_average_from_array(double[] array) {
- double total_value = 0;
- for (double value : array) {
- total_value += value;
- }
- return total_value/array.length;
- }
-
+ //Average median standard deviation functions
/**
* Return the AVERAGE value of an array
* @param array
@@ -17250,69 +14247,6 @@ public class Classification {
}
return total_value / list.size();
}
-
- /**
- * Return the MEDIAN value of an array
- * @param array values in array must be sorted
- * @return
- */
- public static long get_median_from_array(long[] array) {
- double median;
- if (array.length == 1) {
- median = array[0];
- } else if (array.length == 2) {
- median = (array[0] + array[1])/2;
- } else if (array.length % 2 == 0) { // array has even length
- int length = array.length/2;
- median = (array[length-1] + array[length])/2;
- } else { // uneven length
- int length = (array.length+1)/2;
- median = array[length-1];
- }
- return (long) median;
- }
-
- /**
- * Return the MEDIAN value of an array
- * @param array values in array must be sorted
- * @return
- */
- public static double get_median_from_array(double[] array) {
- double median;
- if (array.length == 1) {
- median = array[0];
- } else if (array.length == 2) {
- median = (array[0] + array[1])/2;
- } else if (array.length % 2 == 0) { // array has even length
- int length = array.length/2;
- median = (array[length-1] + array[length])/2;
- } else { // uneven length
- int length = (array.length+1)/2;
- median = array[length-1];
- }
- return median;
- }
-
- /**
- * Return the MEDIAN value of an array
- * @param array values in array must be sorted
- * @return
- */
- public static int get_median_from_array(int[] array) {
- int median;
- if (array.length == 1) {
- median = array[0];
- } else if (array.length == 2) {
- median = (array[0] + array[1])/2;
- } else if (array.length % 2 == 0) { // array has even length
- int length = array.length/2;
- median = (array[length-1] + array[length])/2;
- } else { // uneven length
- int length = (array.length+1)/2;
- median = array[length-1];
- }
- return median;
- }
/**
* Return the MEDIAN value of a list
@@ -17420,21 +14354,7 @@ public class Classification {
percentage = 0;
}
return percentage;
- }
-
- /**
- *
- * @param value1
- * @param value2
- * @return
- */
- public static double divide(double value1, double value2) {
- double percentage = value1 / value2;
- if (Double.isNaN(percentage)) {
- percentage = 0;
- }
- return percentage;
- }
+ }
/**
* Return array with [median, average, standard deviation, shortest, longest, total, count]
@@ -17513,40 +14433,6 @@ public class Classification {
return median_average_deviation;
}
- /**
- * Return array with [median, average, standard deviation, shortest, longest, total, count]
- * @param array
- * @return
- */
- public static double[] median_average_stdev_from_array(double[] array) {
- if (array.length == 0 || (array.length == 1 && array[0] == 0)) {
- return new double []{0, 0, 0, 0, 0, 0, 0};
- }
- ArrayList<Double> list = new ArrayList<>();
- for (double value : array) {
- list.add(value);
- }
- double[] median_average_deviation = median_average_stdev_from_AL_double(list);
- return median_average_deviation;
- }
-
- /**
- * Return array with [median, average, standard deviation, shortest, longest, total, count]
- * @param array
- * @return
- */
- public static double[] median_average_stdev_from_array(long[] array) {
- if (array.length == 0 || (array.length == 1 && array[0] == 0)) {
- return new double []{0, 0, 0, 0, 0, 0, 0};
- }
- ArrayList<Long> list = new ArrayList<>();
- for (long value : array) {
- list.add(value);
- }
- double[] median_average_deviation = median_average_stdev_from_AL_long(list);
- return median_average_deviation;
- }
-
/**
*
* @param list
@@ -17555,9 +14441,9 @@ public class Classification {
*/
public static double get_stdev_from_AL_long(ArrayList<Long> list, double average) {
double sum = 0;
- for (int i=0; i < list.size(); i++) {
+ for (int i=0; i < list.size(); i++) {
sum += Math.pow(list.get(i)-average,2);
- }
+ }
double deviation = Math.sqrt(sum/(list.size()));
return deviation;
}
@@ -17592,19 +14478,6 @@ public class Classification {
return deviation;
}
- /**
- *
- * @param array
- * @return
- */
- public static long sum_of_array(long[] array) {
- long total = 0;
- for (long number : array) {
- total += number;
- }
- return total;
- }
-
/**
*
* @param array
@@ -17631,18 +14504,4 @@ public class Classification {
ArrayList tester = new ArrayList<>(newList);
return tester;
}
-
- /**
- *
- * @param list
- * @return
- */
- public static ArrayList<String> remove_duplicates_from_AL_str(ArrayList<String> list) {
- List<String> newList = list.stream()
- .distinct()
- .collect(Collectors.toList());
- Collections.sort(newList);
- ArrayList tester = new ArrayList<>(newList);
- return tester;
- }
}
diff --git a/src/pangenome/ExecCommand.java b/src/main/java/nl/wur/bif/pantools/pangenome/ExecCommand.java
similarity index 96%
rename from src/pangenome/ExecCommand.java
rename to src/main/java/nl/wur/bif/pantools/pangenome/ExecCommand.java
index 9fc3ad30749bfae5cca6ac93971fe1461671b95a..0d6d109cb52a0af4a47c6c09eb160a177dca01e3 100644
--- a/src/pangenome/ExecCommand.java
+++ b/src/main/java/nl/wur/bif/pantools/pangenome/ExecCommand.java
@@ -1,4 +1,4 @@
-package pangenome;
+package nl.wur.bif.pantools.pangenome;
import java.io.BufferedReader;
import java.io.IOException;
@@ -6,11 +6,11 @@ import java.io.InputStreamReader;
import java.io.PrintWriter;
import java.util.ArrayList;
import java.util.concurrent.Semaphore;
-import static pantools.Pantools.LOG;
-import static pantools.Pantools.write_log;
+import static nl.wur.bif.pantools.pantools.Pantools.LOG;
+import static nl.wur.bif.pantools.pantools.Pantools.write_log;
import java.io.BufferedWriter;
import java.io.FileWriter;
-import static pantools.Pantools.WORKING_DIRECTORY;
+import static nl.wur.bif.pantools.pantools.Pantools.WORKING_DIRECTORY;
/**
* Original code from https://bjurr.com/runtime-exec-hangs-a-complete-solution/
@@ -145,7 +145,6 @@ public class ExecCommand {
Thread.currentThread().interrupt();
}
}
- //System.out.println("UITKOMST " + WORKING_DIRECTORY + "LOG\n" + output);
if (write_log && output != null) {
try (BufferedWriter out = new BufferedWriter(new FileWriter(WORKING_DIRECTORY + "LOG"))) {
out.write(output);
diff --git a/src/pangenome/FunctionalAnnotations.java b/src/main/java/nl/wur/bif/pantools/pangenome/FunctionalAnnotations.java
similarity index 82%
rename from src/pangenome/FunctionalAnnotations.java
rename to src/main/java/nl/wur/bif/pantools/pangenome/FunctionalAnnotations.java
index dc560c2e4051f264b811cd5de816eeb4834cee77..7c8f43f2bd368068f6f9a3e52159f6c9e7c94a15 100644
--- a/src/pangenome/FunctionalAnnotations.java
+++ b/src/main/java/nl/wur/bif/pantools/pangenome/FunctionalAnnotations.java
@@ -3,7 +3,7 @@
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
-package pangenome;
+package nl.wur.bif.pantools.pangenome;
import cern.jet.stat.Gamma;
import java.io.BufferedReader;
@@ -29,81 +29,76 @@ import org.neo4j.graphdb.Relationship;
import org.neo4j.graphdb.RelationshipType;
import org.neo4j.graphdb.ResourceIterator;
import org.neo4j.graphdb.Transaction;
-import static pangenome.Classification.try_incr_SB_hashmap;
-import static pangenome.Classification.try_incr_hashset_hashmap;
-import static pangenome.Classification.incr_array_hashmap;
-import static pangenome.Classification.try_incr_AL_hashmap;
-import static pangenome.Classification.try_incr_hashmap;
-import static pangenome.Classification.get_percentage_str;
-import static pantools.Pantools.geno_pheno_map;
-import static pantools.Pantools.phenotype_map;
-import pantools.Pantools;
-import static pantools.Pantools.K_SIZE;
-import static pantools.Pantools.Mode;
-import static pantools.Pantools.NODE_ID;
-import static pantools.Pantools.PATH_TO_THE_ANNOTATIONS_FILE;
-import static pantools.Pantools.PHENOTYPE;
-import pantools.Pantools.RelTypes;
-import static pantools.Pantools.SELECTED_NAME;
-import static pantools.Pantools.WD_full_path;
-import static pantools.Pantools.WORKING_DIRECTORY;
-import static pantools.Pantools.adj_total_genomes;
-import static pantools.Pantools.bgc_label;
-import static pantools.Pantools.COG_label;
-import static pantools.Pantools.check_if_graphDb_is_available;
-import static pantools.Pantools.gene_label;
-import static pantools.Pantools.go_label;
-import static pantools.Pantools.graphDb;
-import static pantools.Pantools.homology_group_label;
-import static pantools.Pantools.interpro_label;
-import static pantools.Pantools.mRNA_label;
-import static pantools.Pantools.pangenome_label;
-import static pantools.Pantools.pantools_path;
-import static pantools.Pantools.pfam_label;
-import static pantools.Pantools.phobius_label;
-import static pantools.Pantools.tigrfam_label;
-import static pantools.Pantools.total_genomes;
-import static pantools.Pantools.phenotype_threshold;
-import static pantools.Pantools.phenotype_threshold_map;
-import static pantools.Pantools.count_nodes;
-import static pantools.Pantools.check_if_panproteome;
-import static pantools.Pantools.create_directory_in_DB;
-import static pantools.Pantools.write_SB_to_file_in_DB;
-import static pantools.Pantools.write_string_to_file_in_DB;
-import static pantools.Pantools.SELECTED_LABEL;
-import static pantools.Pantools.check_if_file_exists;
-import static pantools.Pantools.delete_file_full_path;
-import static pantools.Pantools.copy_file;
-import static pangenome.create_skip_arrays.create_skip_arrays;
-import static pantools.Pantools.test_if_correct_label;
-import static pantools.Pantools.retrieve_phenotypes;
-import static pantools.Pantools.append_SB_to_file_full_path;
-import static pantools.Pantools.remove_first_position_array;
-import static pantools.Pantools.is_node_present;
-import static pantools.Pantools.hmgroup_class_map;
-import static pantools.Pantools.stop_if_no_active_grouping_present;
-import static pantools.Pantools.annotation_identifiers; // inferred by get_annotation_identifiers()
-import static pantools.Pantools.PROTEOME;
-import static pantools.Pantools.stop_if_panproteome;
-import static pantools.Pantools.core_threshold;
-import static pantools.Pantools.unique_threshold;
-import static pangenome.Classification.find_last_correct_rank;
-import static pangenome.Classification.get_annotation_identifiers;
-import static pangenome.Classification.percentage;
-import static pangenome.Classification.create_mrna_node_map_for_genome;
-import static pangenome.Classification.try_incr_treeset_hashmap;
-import static pantools.Pantools.INPUT_FILE;
-import static pantools.Pantools.NODE_VALUE;
-import static pantools.Pantools.SELECTED_HMGROUPS;
-import static pantools.Pantools.classification;
-import static pantools.Pantools.NODE_ID_long;
-import static pantools.Pantools.genome_label;
-import static pantools.Pantools.skip_array;
-import static pantools.Pantools.append_string_to_file_full_path;
-import static pantools.Pantools.write_string_to_file_full_path;
+
+import static nl.wur.bif.pantools.pangenome.Classification.*;
+import static nl.wur.bif.pantools.pantools.Pantools.geno_pheno_map;
+import static nl.wur.bif.pantools.pantools.Pantools.phenotype_map;
+import nl.wur.bif.pantools.pantools.Pantools;
+import static nl.wur.bif.pantools.pantools.Pantools.K_SIZE;
+import static nl.wur.bif.pantools.pantools.Pantools.Mode;
+import static nl.wur.bif.pantools.pantools.Pantools.NODE_ID;
+import static nl.wur.bif.pantools.pantools.Pantools.PATH_TO_THE_ANNOTATIONS_FILE;
+import static nl.wur.bif.pantools.pantools.Pantools.PHENOTYPE;
+import nl.wur.bif.pantools.pantools.Pantools.RelTypes;
+import static nl.wur.bif.pantools.pantools.Pantools.SELECTED_NAME;
+import static nl.wur.bif.pantools.pantools.Pantools.WD_full_path;
+import static nl.wur.bif.pantools.pantools.Pantools.WORKING_DIRECTORY;
+import static nl.wur.bif.pantools.pantools.Pantools.adj_total_genomes;
+import static nl.wur.bif.pantools.pantools.Pantools.bgc_label;
+import static nl.wur.bif.pantools.pantools.Pantools.COG_label;
+import static nl.wur.bif.pantools.pantools.Pantools.check_if_graphDb_is_available;
+import static nl.wur.bif.pantools.pantools.Pantools.gene_label;
+import static nl.wur.bif.pantools.pantools.Pantools.go_label;
+import static nl.wur.bif.pantools.pantools.Pantools.graphDb;
+import static nl.wur.bif.pantools.pantools.Pantools.homology_group_label;
+import static nl.wur.bif.pantools.pantools.Pantools.interpro_label;
+import static nl.wur.bif.pantools.pantools.Pantools.mRNA_label;
+import static nl.wur.bif.pantools.pantools.Pantools.pangenome_label;
+import static nl.wur.bif.pantools.pantools.Pantools.pantools_path;
+import static nl.wur.bif.pantools.pantools.Pantools.pfam_label;
+import static nl.wur.bif.pantools.pantools.Pantools.phobius_label;
+import static nl.wur.bif.pantools.pantools.Pantools.tigrfam_label;
+import static nl.wur.bif.pantools.pantools.Pantools.total_genomes;
+import static nl.wur.bif.pantools.pantools.Pantools.phenotype_threshold;
+import static nl.wur.bif.pantools.pantools.Pantools.phenotype_threshold_map;
+import static nl.wur.bif.pantools.pantools.Pantools.count_nodes;
+import static nl.wur.bif.pantools.pantools.Pantools.check_if_panproteome;
+import static nl.wur.bif.pantools.pantools.Pantools.create_directory_in_DB;
+import static nl.wur.bif.pantools.pantools.Pantools.write_SB_to_file_in_DB;
+import static nl.wur.bif.pantools.pantools.Pantools.write_string_to_file_in_DB;
+import static nl.wur.bif.pantools.pantools.Pantools.SELECTED_LABEL;
+import static nl.wur.bif.pantools.pantools.Pantools.check_if_file_exists;
+import static nl.wur.bif.pantools.pantools.Pantools.delete_file_full_path;
+import static nl.wur.bif.pantools.pantools.Pantools.copy_file;
+import static nl.wur.bif.pantools.pangenome.create_skip_arrays.create_skip_arrays;
+import static nl.wur.bif.pantools.pantools.Pantools.test_if_correct_label;
+import static nl.wur.bif.pantools.pantools.Pantools.retrieve_phenotypes;
+import static nl.wur.bif.pantools.pantools.Pantools.append_SB_to_file_full_path;
+import static nl.wur.bif.pantools.pantools.Pantools.remove_first_position_array;
+import static nl.wur.bif.pantools.pantools.Pantools.is_node_present;
+import static nl.wur.bif.pantools.pantools.Pantools.hmgroup_class_map;
+import static nl.wur.bif.pantools.pantools.Pantools.stop_if_no_active_grouping_present;
+import static nl.wur.bif.pantools.pantools.Pantools.annotation_identifiers; // inferred by get_annotation_identifiers()
+import static nl.wur.bif.pantools.pantools.Pantools.PROTEOME;
+import static nl.wur.bif.pantools.pantools.Pantools.stop_if_panproteome;
+import static nl.wur.bif.pantools.pantools.Pantools.core_threshold;
+import static nl.wur.bif.pantools.pantools.Pantools.unique_threshold;
+import static nl.wur.bif.pantools.pantools.Pantools.INPUT_FILE;
+import static nl.wur.bif.pantools.pantools.Pantools.NODE_VALUE;
+import static nl.wur.bif.pantools.pantools.Pantools.SELECTED_HMGROUPS;
+import static nl.wur.bif.pantools.pantools.Pantools.classification;
+import static nl.wur.bif.pantools.pantools.Pantools.NODE_ID_long;
+import static nl.wur.bif.pantools.pantools.Pantools.genome_label;
+import static nl.wur.bif.pantools.pantools.Pantools.skip_array;
+import static nl.wur.bif.pantools.pantools.Pantools.append_string_to_file_full_path;
+import static nl.wur.bif.pantools.pantools.Pantools.write_string_to_file_full_path;
import java.text.SimpleDateFormat;
import java.util.Date;
-import static pantools.Pantools.signalp_label;
+import java.util.concurrent.atomic.AtomicInteger;
+
+import static nl.wur.bif.pantools.pantools.Pantools.signalp_label;
+import org.json.*;
+
/**
*
@@ -288,7 +283,7 @@ public class FunctionalAnnotations {
}
overview_builder.append(mrna_with_anno).append("/").append(value.length).append(" ").append(mrna_or_prot).append(" have a functional annotation\n")
- .append(info_per_mrna.toString());
+ .append(info_per_mrna);
genome_builder.append(mrna_with_anno).append("/").append(value.length).append(" ").append(mrna_or_prot).append(" have a functional annotation\n\n");
create_function_per_genome_overview(function_count_map, genome_builder, mrnas_with_function);
if (mrna_with_anno == 0) {
@@ -301,12 +296,12 @@ public class FunctionalAnnotations {
write_SB_to_file_in_DB(overview_builder, path + "function_overview_per_" + mrna_or_prot_file + ".txt");
write_SB_to_file_in_DB(genome_builder, path + "function_overview_per_genome.txt");
- System.out.println("");
+ System.out.println();
}
/**
*
- * @param gene_node
+ * @param gene_node a 'gene' node
* @param overview_builder
* @param function_count_map
* @return
@@ -333,13 +328,14 @@ public class FunctionalAnnotations {
* @param genome_builder
* @param mrnas_with_function
*/
- public static void create_function_per_genome_overview(HashMap<String, Integer> function_count_map, StringBuilder genome_builder, int[] mrnas_with_function) {
+ public static void create_function_per_genome_overview(HashMap<String, Integer> function_count_map,
+ StringBuilder genome_builder, int[] mrnas_with_function) {
String mrna_or_prot = "mRNA's";
if (PROTEOME) {
mrna_or_prot = "proteins";
}
int[] function_count_array = new int[8]; //go, pfam, interpro, tigrfam, cog, bgc, effector, receptor, transmembrane
- StringBuilder pfam = new StringBuilder("");
+ StringBuilder pfam = new StringBuilder();
StringBuilder signalp = new StringBuilder("with SignalP signal peptides: ");
StringBuilder phobius_signalpep = new StringBuilder("with Phobius signal peptides: ");
StringBuilder p_transmembrane = new StringBuilder("with Phobius transmembrane: ");
@@ -432,15 +428,15 @@ public class FunctionalAnnotations {
}
genome_builder.append("\nFound functions\n")
.append("GO: ").append("\n")
- .append(go.toString()).append("\n")
- .append(go_bp.toString()).append("\n")
- .append(go_mf.toString()).append("\n")
- .append(go_cl.toString()).append("\n")
- .append("PFAM domains: ").append("\n").append(pfam.toString()).append("\n")
- .append("InterPro domains: ").append("\n").append(interpro.toString()).append("\n")
- .append("TIGRFAMs: ").append("\n").append(tigrfam.toString()).append("\n")
- .append("Biosynthetic gene clusters: ").append("\n").append(bgc.toString()).append("\n")
- .append("COG proteins: ").append("\n").append(cog.toString()).append("\n");
+ .append(go).append("\n")
+ .append(go_bp).append("\n")
+ .append(go_mf).append("\n")
+ .append(go_cl).append("\n")
+ .append("PFAM domains: ").append("\n").append(pfam).append("\n")
+ .append("InterPro domains: ").append("\n").append(interpro).append("\n")
+ .append("TIGRFAMs: ").append("\n").append(tigrfam).append("\n")
+ .append("Biosynthetic gene clusters: ").append("\n").append(bgc).append("\n")
+ .append("COG proteins: ").append("\n").append(cog).append("\n");
String signalp_str = signalp.toString();
if (signalp_str.endsWith(": ")) {
@@ -481,7 +477,7 @@ public class FunctionalAnnotations {
}
if (SELECTED_HMGROUPS != null) {
- ArrayList<Node> hm_node_list = Classification.read_hmgroup_input_file();
+ ArrayList<Node> hm_node_list = read_hmgroup_input_file();
if (hm_node_list.isEmpty()) {
HashMap<Integer, String[]> hms_per_genome = Classification.read_unique_hmgroups();
for (Map.Entry<Integer, String[]> entry : hms_per_genome.entrySet()) {
@@ -520,7 +516,7 @@ public class FunctionalAnnotations {
try_incr_AL_hashmap(temp_genes_per_genome, genome_nr, mrna_node);
}
}
- System.out.println("");
+ System.out.println();
}
} else if (NODE_ID != null) {
if (NODE_ID_long != null) {
@@ -640,6 +636,8 @@ public class FunctionalAnnotations {
while (all_nodes.hasNext()) {
StringBuilder line_builder = new StringBuilder();
StringBuilder mrna_info_builder = new StringBuilder();
+ StringBuilder all_mrnas = new StringBuilder();
+ HashSet<Long> hmgroups_set = new HashSet<>();
Node function_node = all_nodes.next();
long funtion_node_id = function_node.getId();
String function_name = (String) function_node.getProperty("name");
@@ -671,7 +669,7 @@ public class FunctionalAnnotations {
continue;
}
}
-
+ all_mrnas.append(mrna_node_id).append(",");
Relationship hm_rel = mrna_node.getSingleRelationship(RelTypes.has_homolog, Direction.INCOMING);
String hm_id_str = "not grouped";
if (hm_rel == null) {
@@ -679,6 +677,7 @@ public class FunctionalAnnotations {
} else {
Node hm_node = hm_rel.getStartNode();
long hm_id = hm_node.getId();
+ hmgroups_set.add(hm_id);
hm_id_str = hm_id +"";
String hmgroup_class = hmgroup_class_map.get(hm_node);
if (hmgroup_class == null) {
@@ -710,12 +709,14 @@ public class FunctionalAnnotations {
rel_per_genome_array[genome_nr] += 1;
}
- if (first_rel) { //function node is not connected to any node
+ if (first_rel) { // true means the function node is not connected to any node
missing.append(function_id).append(",").append(function_name).append(",").append(funtion_node_id).append("\n");
total_array[2] += 1;
} else {
line_builder.append(Arrays.toString(frequency_array).replace("[","").replace("]","").replace(",",";").replace(" ",""));
- output_builder.append(line_builder.toString()).append(";").append(mrna_info_builder.toString()).append("\n");
+ String hmgroups_str = hmgroups_set.toString().replace("[","").replace("]","").replace(" ","").replaceFirst(".$","");
+ output_builder.append(line_builder).append(";").append(all_mrnas).append(";").append(hmgroups_str).append(";")
+ .append(mrna_info_builder).append("\n");
}
}
total_array[0] = counted_nodes;
@@ -742,17 +743,15 @@ public class FunctionalAnnotations {
for (int i=1; i <= total_genomes; i++) {
results.append("occurance in genome ").append(i).append(";");
}
- if (!PROTEOME) {
- results.append("Remaining columns contain information of connected mRNA's (seperated by commas): genome number, "
- + "mRNA name, mRNA id, mRNA node id, homology group node id\n");
- } else {
- results.append("Remaining columns contain information of connected proteins (seperated by commas): genome number, "
- + "protein name, protein node id, homology group node id\n");
- }
- results.append(output_builder.toString())
+
+ results.append("mRNA identifiers (seperated by commas);homology group identifiers (seperated by commas);"
+ + "Remaining columns contain information of connected mRNA's (seperated by commas): genome number, "
+ + "mRNA name, mRNA id, mRNA node id, homology group node id\n");
+
+ results.append(output_builder)
.append("\n#Not connected functions\n")
.append("function id, function name, node id\n")
- .append(missing.toString()).append("\n");
+ .append(missing).append("\n");
add_missing_groups_to_stringbuilder(hmgroups_per_class, results, label_str);
System.out.print("\r "); // spaces are intentional
return results;
@@ -929,9 +928,9 @@ public class FunctionalAnnotations {
value = info_per_genome_map.get(i + "#phobius_transmembrane");
transmembrane_builder.append("Genome ").append(i).append("\n").append(value.toString()).append("\n\n");
}
- output_builder.append(signalp_signalpep_builder.toString())
- .append("\n").append(phobius_signalpep_builder.toString())
- .append("\n").append(transmembrane_builder.toString());
+ output_builder.append(signalp_signalpep_builder)
+ .append("\n").append(phobius_signalpep_builder)
+ .append("\n").append(transmembrane_builder);
add_missing_groups_to_stringbuilder(hmgroups_per_class, output_builder, "phobius");
if (output_builder.length() > 0) {
@@ -1240,16 +1239,18 @@ public class FunctionalAnnotations {
}
/**
- *
+ * Create csv overview file for biosynthetic gene clusters
*/
- public void bgc_overview() {
- StringBuilder overview_bulder = new StringBuilder();
- HashMap<String, ArrayList<Node>> type_cluster_map = new HashMap<>();
+ public void bgc_overview() {
+ if (PROTEOME) { // genecluster cannot be added to panproteomes
+ return;
+ }
+ HashMap<String, int[]> counts_per_type = new HashMap<>(); // key is type, value are the counts per genome
+ int longest_cluster = 0;
+ int[] counter_array = new int[total_genomes+1]; // first position is total count for all genomes
ResourceIterator<Node> bgc_nodes = graphDb.findNodes(bgc_label);
- int[] counter_array = new int[total_genomes+1];
while (bgc_nodes.hasNext()) {
Node bgc_node = bgc_nodes.next();
- String type = (String) bgc_node.getProperty("type");
int genome_nr = (int) bgc_node.getProperty("genome");
if (PROTEOME && skip_array[genome_nr-1]) {
continue;
@@ -1259,115 +1260,92 @@ public class FunctionalAnnotations {
continue;
}
}
- counter_array[0] += 1;
+ String type = (String) bgc_node.getProperty("type");
+ int length = (int) bgc_node.getProperty("length");
+ if (length > longest_cluster) {
+ longest_cluster = length;
+ }
+ counter_array[0] += 1; // total for all genomes
counter_array[genome_nr] += 1;
- ArrayList<Node> cluster_nodes = type_cluster_map.get(type);
- if (cluster_nodes == null) {
- cluster_nodes = new ArrayList<>();
+ String[] type_array = type.split(","); // type can consists of multiple types. example: NRPS,NRPS-like
+ for (String cluster_type : type_array) {
+ try_incr_array_hashmap(counts_per_type, cluster_type,1, (genome_nr-1), total_genomes);
}
- cluster_nodes.add(bgc_node);
- type_cluster_map.put(type, cluster_nodes);
- }
-
- for (int i=0; i < counter_array.length; i++) {
- if (i ==0) {
- overview_bulder.append("Total BGCs: ").append(counter_array[0]).append("\n");
- } else {
- overview_bulder.append("Genome ").append(i).append(": ").append(counter_array[i]).append("\n");
+ if (type_array.length > 1) { // also add the cluster combination
+ try_incr_array_hashmap(counts_per_type, type.replace(",", " "), 1, (genome_nr-1), total_genomes);
}
}
-
- overview_bulder.append("\n#Information is ordered by cluster type\n")
- .append("#The initial five lines of a gene cluster are: genome number, address, number (counted per_genome), bgc node id\n")
- .append("#The rest of the lines is information of the individual genes: Position in cluster, gene name, gene id, gene node id\n\n");
- for (Map.Entry<String, ArrayList<Node>> entry : type_cluster_map.entrySet()) {
- HashSet<Integer> found_genome_set = new HashSet<>();
- String key = entry.getKey();
- ArrayList<Node> value = entry.getValue();
- overview_bulder.append("#").append(key);
- counter_array = new int[total_genomes];
- StringBuilder hits_builder = new StringBuilder();
- for (Node bgc_node: value) {
- long bgc_node_id = bgc_node.getId();
- int genome = (int) bgc_node.getProperty("genome");
- int length = (int) bgc_node.getProperty("length");
- int number = (int) bgc_node.getProperty("number");
- int[] address = (int[]) bgc_node.getProperty("address");
- counter_array[genome-1] += 1;
- found_genome_set.add(genome);
- hits_builder.append("Genome ").append(genome)
- .append("\nAddress ").append(address[0]).append(" ").append(address[1]).append(" ").append(address[2]).append(" ").append(address[3])
- .append("\nNumber ").append(number)
- .append("\nNumber of genes ") .append(length)
- .append("\nNode id ").append(bgc_node_id).append("\n");
- Iterable<Relationship> rels = bgc_node.getRelationships();
- Node[] gene_node_array = new Node[length];
- int counter = 0;
- for (Relationship rel: rels) {
- Node gene_node = rel.getStartNode();
- gene_node_array[counter] = gene_node;
- counter++;
- }
-
- Node[] ordered_node_array = order_node_array_based_on_position(gene_node_array);
- int position = 1;
- for (Node gene_node: ordered_node_array) {
- String gene_name = (String) gene_node.getProperty("name");
- if (gene_name.equals("")) {
- gene_name = "-";
- }
- String gene_id = (String) gene_node.getProperty("id");
- long node_id = gene_node.getId();
- hits_builder.append(position).append(",").append(gene_name).append(",").append(gene_id).append(",").append(node_id).append("\n");
- position ++;
- }
- hits_builder.append("\n");
- }
- String hit_str = hits_builder.toString();
- overview_bulder.append("\nTotal occurances in genomes: ").append(found_genome_set.size()).append("\n")
- .append(Arrays.toString(counter_array)).append("\n\n").append(hit_str).append("\n");
- }
- if (overview_bulder.length() > 0) {
- write_SB_to_file_in_DB(overview_bulder, "function/bgc_overview.txt");
+
+ //create the header for 2nd part of overview
+ StringBuilder info_per_cluster= new StringBuilder("type,number of genes,address,bgc node (identifier),");
+ StringBuilder header_id = new StringBuilder();
+ StringBuilder header_node = new StringBuilder();
+ for (int i=1; i <= longest_cluster; i++) {
+ header_id.append("position ").append(i).append(". gene id,");
+ header_node.append("position ").append(i).append(" gene node,");
+ }
+ info_per_cluster.append(header_id).append(header_node).append("\n");
+
+ bgc_nodes = graphDb.findNodes(bgc_label); // go over nodes again, now we know the length of the longest cluster
+ while (bgc_nodes.hasNext()) {
+ Node bgc_node = bgc_nodes.next();
+ int[] address = (int[]) bgc_node.getProperty("address");
+ String type = (String) bgc_node.getProperty("type");
+ int length = (int) bgc_node.getProperty("length");
+ Iterable<Relationship> rels = bgc_node.getRelationships();
+ info_per_cluster.append(type.replace(","," ")).append(",").append(length).append(",")
+ .append(address[0]).append(" ").append(address[1]).append(" ").append(address[2]).append(" ")
+ .append(address[3]).append(",").append(bgc_node.getId()).append(",");
+ StringBuilder gene_node_per_cluster = new StringBuilder();
+ StringBuilder gene_id_per_cluster = new StringBuilder();
+ for (Relationship rel : rels) {
+ Node gene_node = rel.getStartNode();
+ String id = (String) gene_node.getProperty("id");
+ gene_node_per_cluster.append(gene_node.getId()).append(",");
+ gene_id_per_cluster.append(id).append(",");
+ }
+ int extra_commas = longest_cluster-length;
+ StringBuilder commas = new StringBuilder();
+ for (int i=0; i < extra_commas; i++) {
+ commas.append(",");
+ }
+ info_per_cluster.append(gene_id_per_cluster).append(commas).append(gene_node_per_cluster).append("\n");
}
- }
-
- /**
- * Works for both 'Gene' and 'mRNA' nodes
- *
- * @param node_array
- * @return
- */
- public static Node[] order_node_array_based_on_position(Node[] node_array) {
- HashMap<Integer, Node> position_node_map = new HashMap<>();
- Node[] new_node_array = new Node[node_array.length];
- int[] positions = new int[node_array.length];
- int counter = 0;
- for (Node gene_node: node_array) {
- int[] gene_address = (int[]) gene_node.getProperty("address");
- positions[counter] = gene_address[2];
- counter ++;
- position_node_map.put(gene_address[2], gene_node);
+
+ StringBuilder occ_per_genome = new StringBuilder("Cluster type (product),");
+ for (int i=1; i <= total_genomes; i++) {
+ occ_per_genome.append("occurrence in genome ").append(i).append(",");
}
- Arrays.sort(positions);
- counter = 0;
- for (int position : positions) {
- Node gene_node = position_node_map.get(position);
- new_node_array[counter] = gene_node;
- counter ++;
+ occ_per_genome.append("\ntotal clusters").append(",");
+ for (int i=1; i < counter_array.length; i++) { // skip first position
+ occ_per_genome.append(counter_array[i]).append(",");
+ }
+ occ_per_genome.append("\n");
+ for (String type : counts_per_type.keySet()){
+ int[] counts_per_genome = counts_per_type.get(type);
+ String occ_per_genome_str = Arrays.toString(counts_per_genome).replace("[","")
+ .replace("]","").replace(", ","");occ_per_genome.append(type)
+ .append(",").append(occ_per_genome_str).append("\n");
+ }
+
+ if (counter_array[0] > 0) {
+ write_string_to_file_in_DB("Total BGCs: " + counter_array[0] + "\n\n" + occ_per_genome + "\n" +
+ info_per_cluster, "function/bgc_overview.csv");
}
- return new_node_array;
}
-
+
/**
- *
- * @param mrna_node
- * @param function_counter_map
- * @param genome_nr
- * @param output_builder
+ * Check for Phobius properties on 'mrna' node
+ * @param mrna_node a 'mrna' node
+ * @param function_counter_map key is functional annotation (id or description). value is array with counts per genome
+ * @param genome_nr a genome number
+ * @param output_builder write directly to builder for 'functions_per_group_and_mrna'
*/
- public static void incr_function_counter_map_phobius(Node mrna_node, HashMap<String, int[]> function_counter_map, int genome_nr, StringBuilder output_builder) {
- if (!mrna_node.hasLabel(phobius_label) || !mrna_node.hasProperty("phobius_signal_peptide") || !mrna_node.hasProperty("phobius_signal_peptide")) {
+ public static void incr_function_counter_map_phobius(Node mrna_node, HashMap<String, int[]> function_counter_map,
+ int genome_nr, StringBuilder output_builder) {
+
+ if (!mrna_node.hasLabel(phobius_label) || !mrna_node.hasProperty("phobius_signal_peptide")
+ || !mrna_node.hasProperty("phobius_signal_peptide")) {
output_builder.append("-;");
return;
}
@@ -1376,22 +1354,12 @@ public class FunctionalAnnotations {
int transmembrane_domains = (int) mrna_node.getProperty("phobius_transmembrane");
if (signal_peptide.equals("yes")) {
output += "Phobius signal peptide,";
- int[] counter_array = function_counter_map.get("Phobius signal peptide");
- if (counter_array == null) {
- counter_array = new int[total_genomes];
- }
- counter_array[genome_nr-1] += 1;
- function_counter_map.put("Phobius signal peptide", counter_array);
+ try_incr_array_hashmap(function_counter_map, "Phobius signal peptide,",1, (genome_nr-1), total_genomes);
}
if (transmembrane_domains > 0) {
output += transmembrane_domains + " Phobius transmembrane domains";
- int[] counter_array = function_counter_map.get("Phobius transmembrane domains");
- if (counter_array == null) {
- counter_array = new int[total_genomes];
- }
- counter_array[genome_nr-1] += 1;
- function_counter_map.put("Phobius transmembrane domains", counter_array);
+ try_incr_array_hashmap(function_counter_map, "Phobius transmembrane domains,",1, (genome_nr-1), total_genomes);
}
if (output.endsWith(",")) {
output = output.replaceFirst(".$",""); // removes last character
@@ -1400,47 +1368,42 @@ public class FunctionalAnnotations {
}
/**
- *
- * @param mrna_node
- * @param function_counter_map
- * @param genome_nr
- * @param output_builder
+ * Check for signalP properties on 'mrna' node
+ * @param mrna_node a 'mrna' node
+ * @param function_counter_map key is functional annotation (id or description). value is array with counts per genome
+ * @param genome_nr a genome number
+ * @param output_builder write directly to builder for 'functions_per_group_and_mrna'
*/
- public static void incr_function_counter_map_signalp(Node mrna_node, HashMap<String, int[]> function_counter_map, int genome_nr, StringBuilder output_builder) {
+ public static void incr_function_counter_map_signalp(Node mrna_node, HashMap<String, int[]> function_counter_map,
+ int genome_nr, StringBuilder output_builder) {
+
if (!mrna_node.hasLabel(signalp_label) || !mrna_node.hasProperty("signalp_signal_peptide")) {
output_builder.append("-;");
return;
- }
-
+ }
+
String signal_peptide = (String) mrna_node.getProperty("signalp_signal_peptide"); // can be "yes", "SP(Sec/SPI)", "LIPO(Sec/SPII)" or "TAT(Tat/SPI)"
if (signal_peptide.equals("yes")) {
output_builder.append("SignalP signal peptide,");
- int[] counter_array = function_counter_map.get("SignalP signal peptide");
- if (counter_array == null) {
- counter_array = new int[total_genomes];
- }
- counter_array[genome_nr-1] += 1;
- function_counter_map.put("SignalP signal peptide", counter_array);
+ try_incr_array_hashmap(function_counter_map, "SignalP signal peptide,",1, (genome_nr-1), total_genomes);
} else {
output_builder.append("SignalP ").append(signal_peptide).append(" signal peptide,");
- int[] counter_array = function_counter_map.get("SignalP " + signal_peptide + " signal peptide");
- if (counter_array == null) {
- counter_array = new int[total_genomes];
- }
- counter_array[genome_nr-1] += 1;
- function_counter_map.put("SignalP " + signal_peptide + " signal peptide", counter_array);
+ try_incr_array_hashmap(function_counter_map, "SignalP " + signal_peptide + " signal peptide,",1,
+ (genome_nr-1), total_genomes);
}
output_builder.append(";");
}
/**
- *
- * @param mrna_node
- * @param function_counter_map
- * @param genome_nr
- * @param output_builder
+ * Check for COG properties on 'mrna' node
+ * @param mrna_node a 'mrna' node
+ * @param function_counter_map key is functional annotation (id or description). value is array with counts per genome
+ * @param genome_nr a genome number
+ * @param output_builder write directly to builder for 'functions_per_group_and_mrna'
*/
- public static void incr_function_counter_map_cog(Node mrna_node, HashMap<String, int[]> function_counter_map, int genome_nr, StringBuilder output_builder) {
+ public static void incr_function_counter_map_cog(Node mrna_node, HashMap<String, int[]> function_counter_map,
+ int genome_nr, StringBuilder output_builder) {
+
if (!mrna_node.hasLabel(COG_label)) {
output_builder.append("-;");
return;
@@ -1448,52 +1411,51 @@ public class FunctionalAnnotations {
String cog_category = (String) mrna_node.getProperty("COG_category");
String[] cog_cat_array = cog_category.split(""); // the category can be multiple letters, e.g. AB, DE
for (String cog_category1 : cog_cat_array) {
- int[] counter_array = function_counter_map.get("COG category " + cog_category);
- if (counter_array == null) {
- counter_array = new int[total_genomes];
- }
- counter_array[genome_nr-1] += 1;
+ try_incr_array_hashmap(function_counter_map, "COG category " + cog_category + ",",1,
+ (genome_nr-1), total_genomes);
output_builder.append("COG category ").append(cog_category1).append(",");
- function_counter_map.put("COG category " + cog_category1, counter_array);
+
}
output_builder.append(";");
}
/**
* function is currently disabled, do not remove
- * @param gene_node
- * @param function_counter_map
- * @param genome_nr
- * @param output_builder
+ * @param gene_node a 'gene' node
+ * @param function_counter_map key is functional annotation (id or description). value is array with counts per genome
+ * @param genome_nr a genome number
+ * @param output_builder write directly to builder for 'functions_per_group_and_mrna'
*/
- public static void incr_function_counter_map_bgc(Node gene_node, HashMap<String, int[] > function_counter_map, int genome_nr, StringBuilder output_builder) {
- /*
- Iterable<Relationship> bgc_rels = gene_node.getRelationships(RelTypes.part_of); // releation to bgc node
- for (Relationship rel : bgc_rels) {
+ public static void incr_function_counter_map_bgc(Node gene_node, HashMap<String, int[] > function_counter_map,
+ int genome_nr, StringBuilder output_builder) {
+ if (PROTEOME) { // no geneclusters present in panproteome
+ return;
+ }
+ Iterable<Relationship> bgc_rels = gene_node.getRelationships(RelTypes.part_of); // relation to bgc node
+ boolean bgc_present = false;
+ for (Relationship rel : bgc_rels) {
+ bgc_present = true;
int position = (int) rel.getProperty("position");
Node bgc_node = rel.getEndNode();
String type = (String) bgc_node.getProperty("type");
+ type = type.replace(",", " ");
int length = (int) bgc_node.getProperty("length");
- int number = (int) bgc_node.getProperty("number");
- String info = "gene " + position + "/" + length + " of '" + type + "'(" + number + ") bgc";
- output_builder.append(info).append(",");
- String simple_inf = type + " bgc";
- int[] counter_array = function_counter_map.get(simple_inf);
- if (counter_array == null) {
- counter_array = new int[total_genomes];
- }
- counter_array[genome_nr-1] += 1;
- function_counter_map.put(simple_inf, counter_array);
- }*/
+ output_builder.append("gene ").append(position).append("/").append(length).append(" of ").append(type)
+ .append(" bgc ").append(bgc_node.getId()).append(",");
+ try_incr_array_hashmap(function_counter_map, type + " bgc,",1, (genome_nr-1), total_genomes);
+ }
+ if (!bgc_present) {
+ output_builder.append("-");
+ }
}
/**
* Function node can be GO, InterPro, Pfam, Tigrfam
- * @param mrna_node
- * @param function_counter_map
- * @param genome_nr
- * @param function_reltype
- * @param output_builder
+ * @param mrna_node a 'mrna' node
+ * @param function_counter_map key is functional annotation (id or description). value is array with counts per genome
+ * @param genome_nr a genome number
+ * @param function_reltype a relationship type
+ * @param output_builder write directly to builder for 'functions_per_group_and_mrna'
*/
public static void incr_function_counter_map(Node mrna_node, HashMap<String, int[]> function_counter_map, int genome_nr,
RelTypes function_reltype, StringBuilder output_builder) {
@@ -1502,17 +1464,11 @@ public class FunctionalAnnotations {
StringBuilder function_builder = new StringBuilder();
for (Relationship function_rel : function_rels) {
Node function_node = function_rel.getEndNode();
-
String function_id = (String) function_node.getProperty("id"); // GO:0001, PFAM12, etc
String function_name = (String) function_node.getProperty("name");
+ function_name = function_name.replace(",",";");
function_builder.append(function_id).append(",");
- String key = function_id + "," + function_name;
- int[] counter_array = function_counter_map.get(key);
- if (counter_array == null) {
- counter_array = new int[total_genomes];
- }
- counter_array[genome_nr-1] += 1;
- function_counter_map.put(key, counter_array);
+ try_incr_array_hashmap(function_counter_map, function_id + "," + function_name,1, (genome_nr-1), total_genomes);
}
if (function_builder.length() == 0) {
@@ -1522,12 +1478,11 @@ public class FunctionalAnnotations {
}
/**
- *
- * @param frequency_array
- * @return
+ * @param frequency_array frequency array from 'homology_group' node
+ * @return 'core', 'accessory' or 'unique'
*/
public static String determine_if_core_accessory_unique(int[] frequency_array) {
- String class1 = "core";
+ String hm_class = "core";
int present_counter = 0;
for (int i = 0; i < frequency_array.length; i++) {
if (skip_array[i]) {
@@ -1541,46 +1496,86 @@ public class FunctionalAnnotations {
if (present_counter >= adj_total_genomes) {
// core is default
} else if (present_counter == 1) {
- class1 = "unique";
+ hm_class = "unique";
} else { // if (present_counter < adj_total_genomes) {
- class1 = "accessory";
+ hm_class = "accessory";
}
- return class1;
+ return hm_class;
}
-
+
/**
*
- * @param hm_nodes_list
- * @param output_path
*/
- public static void function_overview_per_group(ArrayList<Node> hm_nodes_list, String output_path) {
+ public static void read_core_accessory_unique_groups() {
hmgroup_class_map = new HashMap<>();
+ // with gene_classification2 the files are placed in group_identifiers directory
+ //boolean exists1 = check_if_file_exists(WORKING_DIRECTORY + "gene_classification/group_identifiers/core_groups.csv");
+ //boolean exists2 = check_if_file_exists(WORKING_DIRECTORY + "gene_classification/group_identifiers/accessory_groups.csv");
+ //boolean exists3 = check_if_file_exists(WORKING_DIRECTORY + "gene_classification/group_identifiers/unique_groups.csv");
+ boolean exists1 = check_if_file_exists(WORKING_DIRECTORY + "gene_classification/core_groups.csv");
+ boolean exists2 = check_if_file_exists(WORKING_DIRECTORY + "gene_classification/accessory_groups.csv");
+ boolean exists3 = check_if_file_exists(WORKING_DIRECTORY + "gene_classification/unique_groups.csv");
+ if (!exists1 || !exists2 || !exists3) {
+ System.out.println("This analysis requires the gene content to be classified with gene_classification2");
+ System.exit(1);
+ }
+
+ SELECTED_HMGROUPS = WORKING_DIRECTORY + "gene_classification/core_groups.csv";
+ ArrayList<Node> hm_node_list = read_hmgroup_input_file();
+ for (Node hm_node : hm_node_list) {
+ hmgroup_class_map.put(hm_node, "core");
+ }
+ SELECTED_HMGROUPS = WORKING_DIRECTORY + "gene_classification/accessory_groups.csv";
+ hm_node_list = read_hmgroup_input_file();
+ for (Node hm_node : hm_node_list) {
+ hmgroup_class_map.put(hm_node, "accessory");
+ }
+ SELECTED_HMGROUPS = WORKING_DIRECTORY + "gene_classification/unique_groups.csv";
+ hm_node_list = read_hmgroup_input_file();
+ for (Node hm_node : hm_node_list) {
+ hmgroup_class_map.put(hm_node, "unique");
+ }
+ }
+
+ /**
+ *
+ * @param hm_nodes_list list with 'homology_group' node identifiers
+ * @param output_path Output directory
+ */
+ public static void function_overview_per_group(ArrayList<Node> hm_nodes_list, String output_path) {
+ if (Mode.contains("CLASSIFICATION")) {
+ read_core_accessory_unique_groups();
+ } else {
+ hmgroup_class_map = new HashMap<>();
+ }
StringBuilder output_builder = new StringBuilder("#split this file on a semicolon\n");
if (!PROTEOME) {
output_builder.append("#homology group node id;genome;mRNA identifier;mRNA node id;gene name;gene identifier;gene node id;");
} else {
output_builder.append("#homology group node id;genome;protein identifier;protein node id;");
}
- output_builder.append("GO terms;Pfam domains,Interpro domains;TIGRFAM annotations;COG annotation;Phobius annotation;SignalP annotation\n");
-
- StringBuilder counts_per_genome = new StringBuilder("#split this file on a comma\nhomology group or function,");
+ output_builder.append("GO terms;Pfam domains;Interpro domains;TIGRFAM annotations;COG annotation;" +
+ "Phobius annotation;SignalP annotation");
+ if (!PROTEOME) {
+ output_builder.append(";Biosynthetic gene clusters\n");
+ } else {
+ output_builder.append("\n");
+ }
+ StringBuilder counts_per_genome = new StringBuilder("#split this file on a comma\nhomology group or function," +
+ "description,");
for (int i=1; i <= total_genomes; i++) {
counts_per_genome.append("genome ").append(i).append(",");
}
counts_per_genome.append("\n");
- int total_hmgroups;
if (hm_nodes_list == null) {
hm_nodes_list = new ArrayList<>();
- total_hmgroups = (int) count_nodes(homology_group_label); // count nodes with a specific label
ResourceIterator<Node> hm_nodes = graphDb.findNodes(homology_group_label);
while (hm_nodes.hasNext()) {
Node hm_node = hm_nodes.next();
hm_nodes_list.add(hm_node);
}
- } else {
- total_hmgroups = hm_nodes_list.size();
}
-
+ int total_hmgroups = hm_nodes_list.size();
int hm_counter = 0, no_annotation = 0;
HashMap<String, HashSet<Node>> annotated_hmgroup_count_map = new HashMap<>();
for (Node hm_node : hm_nodes_list) {
@@ -1589,6 +1584,7 @@ public class FunctionalAnnotations {
System.out.print("\rGathering functions from homology groups: " + hm_counter + "/" + total_hmgroups );
}
HashMap<String, int[]> function_counter_map = new HashMap<>();
+ // key is functional annotation (id or description). value is array with counts per genome
int[] temp_copy_number = (int[]) hm_node.getProperty("copy_number");
int[] copy_number = remove_first_position_array(temp_copy_number);
@@ -1614,11 +1610,13 @@ public class FunctionalAnnotations {
if (gene_name.equals("")) {
gene_name = "-";
}
- output_builder.append(hm_node_id).append(";").append(genome_nr).append(";").append(mrna_id).append(";").append(mrna_node_id).append(";")
- .append(gene_name).append(";").append(gene_id).append(";").append(gene_node_id).append(";");
- } else { // proteome only has mrna node
+ output_builder.append(hm_node_id).append(";").append(genome_nr).append(";").append(mrna_id)
+ .append(";").append(mrna_node_id).append(";").append(gene_name).append(";").append(gene_id)
+ .append(";").append(gene_node_id).append(";");
+ } else { // proteome only has an mrna node
String mrna_id = (String) mrna_node.getProperty("protein_ID");
- output_builder.append(hm_node_id).append(";").append(genome_nr).append(";").append(mrna_id).append(";").append(mrna_node_id).append(";");
+ output_builder.append(hm_node_id).append(";").append(genome_nr).append(";").append(mrna_id)
+ .append(";").append(mrna_node_id).append(";");
}
incr_function_counter_map(mrna_node, function_counter_map, genome_nr, RelTypes.has_go, output_builder);
incr_function_counter_map(mrna_node, function_counter_map, genome_nr, RelTypes.has_pfam, output_builder);
@@ -1627,69 +1625,95 @@ public class FunctionalAnnotations {
incr_function_counter_map_cog(mrna_node, function_counter_map, genome_nr, output_builder);
incr_function_counter_map_phobius(mrna_node, function_counter_map, genome_nr, output_builder);
incr_function_counter_map_signalp(mrna_node, function_counter_map, genome_nr, output_builder);
+ incr_function_counter_map_bgc(gene_node, function_counter_map, genome_nr, output_builder);
present = true;
- if (!PROTEOME) {
- incr_function_counter_map_bgc(gene_node, function_counter_map, genome_nr, output_builder);
- }
output_builder.append("\n");
}
+
if (!present) {
continue;
}
- String hmgroup_class = determine_if_core_accessory_unique(copy_number); // loop over freq array, can be 'core', 'accessory' or 'unique'
- hmgroup_class_map.put(hm_node, hmgroup_class);
- output_builder.append("\n");
- boolean no_anno = true;
- counts_per_genome.append("Homology group ").append(hm_node_id).append(", ").append(num_members).append(" genes. ")
- .append(Arrays.toString(copy_number).replace("[","").replace("]","").replace(" ","")).append("\n");
-
- for (String function : function_counter_map.keySet()) {
- no_anno = false;
- int[] value_array = function_counter_map.get(function);
- counts_per_genome.append(function).append(" ").append(Arrays.toString(value_array).replace("[","").replace("]","").replace(" ","")).append("\n");
+
+ String hmgroup_class;
+ if (Mode.contains("CLASSIFICATION")) {
+ hmgroup_class = hmgroup_class_map.get(hm_node);
+ if (hmgroup_class == null) {
+ System.out.println("The 'homology_group' node " + hm_node + " was not part of the previous 'gene_classification' run\n" +
+ "Make sure you have the same genome/sequence selection");
+ System.exit(1);
+ }
+ } else {
+ // loop over copy_number array, can be 'core', 'accessory' or 'unique'
+ hmgroup_class = determine_if_core_accessory_unique(copy_number);
+ hmgroup_class_map.put(hm_node, hmgroup_class);
}
- counts_per_genome.append("\n");
-
- if (no_anno) {
+
+ if (function_counter_map.isEmpty()) { // no function found for this homology group
no_annotation ++;
try_incr_hashset_hashmap(annotated_hmgroup_count_map, hmgroup_class + "_missing", hm_node);
} else {
+ String copy_nr_str = Arrays.toString(copy_number).replace("[","")
+ .replace("]","").replace(" ","");
try_incr_hashset_hashmap(annotated_hmgroup_count_map, hmgroup_class + "_anno", hm_node);
+ counts_per_genome.append("Homology group ").append(hm_node_id).append(",").append(num_members)
+ .append(" genes,").append(copy_nr_str).append("\n");
+
+ for (String function : function_counter_map.keySet()) {
+ int[] value_array = function_counter_map.get(function);
+ copy_nr_str = Arrays.toString(value_array).replace("[","")
+ .replace("]","")
+ .replace(" ","");
+ counts_per_genome.append(function).append(",").append(copy_nr_str).append("\n");
+ }
+ counts_per_genome.append("\n");
}
}
- System.out.println("");
- int annotated_groups = (int) total_hmgroups - no_annotation;
- if (annotated_groups == 0) {
- System.out.println("\nNo functional annotations are present in the pangenome\n");
- System.exit(1);
+ int annotated_groups = total_hmgroups - no_annotation;
+ if (annotated_groups == 0) { // no functional annotations in the pangenome
+ return;
}
- HashSet<Node> core_anno = retrieve_hashet_return_empty_when_null(annotated_hmgroup_count_map, "core_anno");
- HashSet<Node> core_noanno = retrieve_hashet_return_empty_when_null(annotated_hmgroup_count_map, "core_missing");
- HashSet<Node> accessory_anno = retrieve_hashet_return_empty_when_null(annotated_hmgroup_count_map, "accessory_anno");
- HashSet<Node> accessory_noanno = retrieve_hashet_return_empty_when_null(annotated_hmgroup_count_map, "accessory_missing");
- HashSet<Node> unique_anno = retrieve_hashet_return_empty_when_null(annotated_hmgroup_count_map, "unique_anno");
- HashSet<Node> unique_noanno = retrieve_hashet_return_empty_when_null(annotated_hmgroup_count_map, "unique_missing");
-
- String core_percentage = get_percentage_str(core_anno.size(), core_anno.size() + core_noanno.size(), 2);
- String accessory_percentage = get_percentage_str(accessory_anno.size(), accessory_anno.size() + accessory_noanno.size(), 2);
- String unique_percentage = get_percentage_str(unique_anno.size(), unique_anno.size() + unique_noanno.size(), 2);
- String total_percentage = get_percentage_str((total_hmgroups-no_annotation), total_hmgroups, 2);
- String start_str = "Homology groups with any assigned function: " + (total_hmgroups-no_annotation) + " out of " + total_hmgroups + " (" + total_percentage + "%)"
- + "\n Core (" + adj_total_genomes + "): " + core_anno.size() + "/" + (core_anno.size() + core_noanno.size()) + " (" + core_percentage + "%)"
- + "\n Accessory : " + accessory_anno.size() + "/" + (accessory_anno.size() + accessory_noanno.size()) + " (" + accessory_percentage + "%)"
- + "\n Unique (1): " + unique_anno.size() + "/" + (unique_anno.size() + unique_noanno.size()) + " (" + unique_percentage + "%)\n\n";
-
+ int core_anno = return_size_of_hashset_in_hashmap(annotated_hmgroup_count_map, "core_anno");
+ int core_noanno = return_size_of_hashset_in_hashmap(annotated_hmgroup_count_map, "core_missing");
+ int accessory_anno = return_size_of_hashset_in_hashmap(annotated_hmgroup_count_map, "accessory_anno");
+ int accessory_noanno = return_size_of_hashset_in_hashmap(annotated_hmgroup_count_map, "accessory_missing");
+ int unique_anno = return_size_of_hashset_in_hashmap(annotated_hmgroup_count_map, "unique_anno");
+ int unique_noanno = return_size_of_hashset_in_hashmap(annotated_hmgroup_count_map, "unique_missing");
+
+ String core_percentage = get_percentage_str(core_anno, core_anno + core_noanno,2);
+ String accessory_percentage = get_percentage_str(accessory_anno, accessory_anno + accessory_noanno, 2);
+ String unique_percentage = get_percentage_str(unique_anno, unique_anno + unique_noanno, 2);
+ String total_percentage = get_percentage_str((total_hmgroups-no_annotation), total_hmgroups, 2);
+ String start_str = "Homology groups with any assigned function: " + (total_hmgroups-no_annotation) + " out of "
+ + total_hmgroups + " (" + total_percentage + "%)"
+ + "\n Core (" + adj_total_genomes + "): " + core_anno + "/" + (core_anno + core_noanno) + " (" + core_percentage + "%)"
+ + "\n Accessory : " + accessory_anno + "/" + (accessory_anno + accessory_noanno) + " (" + accessory_percentage + "%)"
+ + "\n Unique (1): " + unique_anno + "/" + (unique_anno + unique_noanno) + " (" + unique_percentage + "%)\n\n";
+
add_missing_groups_to_stringbuilder(annotated_hmgroup_count_map, output_builder, "annotation");
- write_string_to_file_full_path(start_str + output_builder.toString() + "\n", output_path + "functions_per_group_and_mrna.csv");
- write_string_to_file_full_path(counts_per_genome.toString(), output_path + "function_counts_per_group.csv");
+ write_string_to_file_full_path(start_str + output_builder + "\n", output_path + "functions_per_group_and_mrna.csv");
+ write_string_to_file_full_path(counts_per_genome.toString(), output_path + "function_counts_per_group.csv");
}
-
+
/**
- *
- * @param map
- * @param key
- * @return
+ * returns the size of hashset in a hashmap. 0 when empty
+ * @param map hashmap
+ * @param key hashmap key
+ * @return size of hashmap
+ */
+ public static int return_size_of_hashset_in_hashmap(HashMap<String, HashSet<Node>> map, String key) {
+ if (map.containsKey(key)) {
+ HashSet<Node> hashset = map.get(key);
+ return hashset.size();
+ }
+ return 0;
+ }
+
+ /**
+ * return a new hashset when the key doesn't exist yet
+ * @param map hashmap
+ * @param key hashmap key
+ * @return hashmap value or new hashset
*/
public static HashSet<Node> retrieve_hashet_return_empty_when_null(HashMap<String, HashSet<Node>> map, String key) {
HashSet<Node> hashset = new HashSet<>();
@@ -1788,25 +1812,25 @@ public class FunctionalAnnotations {
- /**
- *
- * @return
- */
- public static String check_blast_strictness() {
- String strictness = "strong";
- if (SELECTED_LABEL == null) {
- System.out.println("\nNo strictness provided via --label, using strong. Identity > 65% and alignment length must be 65% of input sequence length");
- return strictness;
- } else {
- SELECTED_LABEL = SELECTED_LABEL.toUpperCase();
- if (SELECTED_LABEL.equals("NORMAL")) {
- strictness = "normal";
- } else if (SELECTED_LABEL.equals("SOFT")) {
- strictness = "soft";
- }
- }
- return strictness;
- }
+// /**
+// *
+// * @return
+// */
+// public static String check_blast_strictness() {
+// String strictness = "strong";
+// if (SELECTED_LABEL == null) {
+// System.out.println("\nNo strictness provided via --label, using strong. Identity > 65% and alignment length must be 65% of input sequence length");
+// return strictness;
+// } else {
+// SELECTED_LABEL = SELECTED_LABEL.toUpperCase();
+// if (SELECTED_LABEL.equals("NORMAL")) {
+// strictness = "normal";
+// } else if (SELECTED_LABEL.equals("SOFT")) {
+// strictness = "soft";
+// }
+// }
+// return strictness;
+// }
/**
*
@@ -1938,7 +1962,7 @@ public class FunctionalAnnotations {
}
//write_SB_to_file_in_DB(background_logbuilder, "function/go_enrichment/background_go_ids.log");
//write_SB_to_file_in_DB(background_logbuilder2, "function/go_enrichment/background_node_ids.log");
- System.out.println("");
+ System.out.println();
return mrna_with_go_per_genome;
}
@@ -1994,7 +2018,7 @@ public class FunctionalAnnotations {
tx.success();
} catch (NotFoundException nfe) {
System.out.println("Unable to start the database");
- return;
+ System.exit(1);
}
if (NODE_VALUE == null) {
System.out.println("No --value was given. False discovery rate is set to 5%");
@@ -2271,7 +2295,7 @@ public class FunctionalAnnotations {
+ "Rank, GO identifier, p value, Critical p value Benjamini-Hochberg, Critical p value Bonferroni, pass Benjamini-Hochberg, "
+ "pass Bonferroni, Total genes (N), Subset genes (n), GOterm occurace (K), "
+ "GOterm in subset (k), Expected occurance, Over- or underrepresented\n";
- write_string_to_file_in_DB(header + output_builder.toString(), "/function/go_enrichment/results_per_genome/" + genome_nr + "/go_enrichment.csv");
+ write_string_to_file_in_DB(header + output_builder, "/function/go_enrichment/results_per_genome/" + genome_nr + "/go_enrichment.csv");
}
}
@@ -2279,7 +2303,7 @@ public class FunctionalAnnotations {
*
* @param go_category
* @param go_name
- * @param genome_nr
+ * @param genome_nr a genome number
* @param go_tree_per_genome
* @param color
*/
@@ -2348,7 +2372,7 @@ public class FunctionalAnnotations {
}
}
}
- System.out.println("");
+ System.out.println();
}
/**
@@ -2425,7 +2449,7 @@ public class FunctionalAnnotations {
delete_file_full_path(dir + "cell_comp.txt.pdf");
delete_file_full_path(dir + "cell_comp.txt.ps");
}
- System.out.println("");
+ System.out.println();
}
/**
@@ -2456,23 +2480,18 @@ public class FunctionalAnnotations {
public static boolean check_if_functional_annotations_present(boolean extensive) {
int go_nodes = (int) count_nodes(go_label);
if (!extensive) {
- if (go_nodes == 0) {
- return false;
- } else {
- return true;
- }
+ return go_nodes != 0;
}
int bgc_nodes = (int) count_nodes(bgc_label); // count nodes with a specific label
int phobius_nodes = (int) count_nodes(phobius_label);
int cog_nodes = (int) count_nodes(COG_label);
- if (bgc_nodes == 0 && go_nodes == 0 && phobius_nodes == 0 && cog_nodes == 0) {
- return false; // no functions are present
- }
- return true;
+ return bgc_nodes != 0 || go_nodes != 0 || phobius_nodes != 0 || cog_nodes != 0; // no functions are present
}
/**
- * #functional_annotation_overview(), FA_overview()
+ * functional_annotation_overview() fa_overview()
+ *
+ * Proteins must be clustered
*/
public void functional_annotation_overview() {
System.out.println("\nFunctional annotation overview\n");
@@ -2486,7 +2505,7 @@ public class FunctionalAnnotations {
tx.success();
} catch (NotFoundException nfe) {
System.out.println("Unable to start the database\n");
- return;
+ System.exit(1);
}
create_directory_in_DB("function");
@@ -2623,16 +2642,14 @@ public class FunctionalAnnotations {
if (mrna_per_category == null) {
all_mrnas_with_cog.append("\n");
} else {
- all_mrnas_with_cog.append(mrna_per_category.toString());
+ all_mrnas_with_cog.append(mrna_per_category);
}
}
HashMap<String, String> cog_log2_map = create_COG_rscript_input(cog_counter_map, cog_cat_counter_map);
String freq_abundance_output = create_COG_abundance_frequency_tables(cog_log2_map, cog_cat_counter_map);
-
-
- write_string_to_file_in_DB(header_builder.toString() + output_builder2.toString() +
- freq_abundance_output + all_mrnas_with_cog.toString() + missing_builder.toString(),
+ write_string_to_file_in_DB(header_builder.toString() + output_builder2 +
+ freq_abundance_output + all_mrnas_with_cog + missing_builder,
"function/cog_overview.csv");
create_COG_rscript();
System.out.print("\r ");
@@ -2671,7 +2688,7 @@ public class FunctionalAnnotations {
}
abundance_builder.append("\n");
}
- return abundance_builder.toString() + frequency_builder.toString();
+ return abundance_builder.toString() + frequency_builder;
}
/**
@@ -2714,7 +2731,7 @@ public class FunctionalAnnotations {
System.out.print(dir + "cog_overview.csv\n "
+ dir + "cog_per_class.R\n\n");
} else {
- System.out.println("");
+ System.out.println();
}
}
@@ -2799,7 +2816,7 @@ public class FunctionalAnnotations {
}
}
overview_builder.append("\n");
- System.out.println("");
+ System.out.println();
}
/**
@@ -2932,7 +2949,7 @@ public class FunctionalAnnotations {
String percentage_core = get_percentage_str(class_count_array[1], class_count_array[0], 2);
String percentage_accessory = get_percentage_str(class_count_array[2], class_count_array[0], 2);
String percentage_unique = get_percentage_str(class_count_array[3], class_count_array[0], 2);
- System.out.println("");
+ System.out.println();
overview_builder.append("#").append(type_str).append("\n")
.append("Total ").append(type_str).append(" nodes: ").append(total_nodes)
.append("\nNodes with connection: ").append(class_count_array[0])
@@ -2961,8 +2978,8 @@ public class FunctionalAnnotations {
annotation_identifiers = get_annotation_identifiers(false, false); // do not print, USE the input via -af
tx.success();
} catch (NotFoundException nfe) {
- System.out.println("Unable to start the pangenome database");
- return;
+ System.out.println("Unable to start the database");
+ System.exit(1);
}
try (Transaction tx = graphDb.beginTx()) {
@@ -3075,9 +3092,9 @@ public class FunctionalAnnotations {
write_SB_to_file_in_DB(shared_builder, "function/functional_classification/phenotype_shared_functions.txt");
write_SB_to_file_in_DB(exclusive_builder, "function/functional_classification/phenotype_exclusive_functions.txt");
overview_builder.append("#Number of phenotype SHARED, SPECIFIC and EXCLUSIVE functions\n")
- .append(shared_nr_builder.toString()).append("\n")
- .append(specific_nr_builder.toString()).append("\n")
- .append(exclusive_nr_builder.toString());
+ .append(shared_nr_builder).append("\n")
+ .append(specific_nr_builder).append("\n")
+ .append(exclusive_nr_builder);
}
/**
* Accessory functions are the number of genomes between the core and unique thresholds
@@ -3134,6 +3151,15 @@ public class FunctionalAnnotations {
HashMap<String, HashSet<String>> tigrfam_node_map, HashMap<String, HashSet<String>> pfam_node_map, HashMap<String, int[]> phobius_node_map,
HashMap<String, String> signalp_map, String path_to_gff, HashMap<String, HashSet<String>> all_added_ids) {
+ boolean add_interpro = false;
+ try (Transaction tx = graphDb.beginTx()) {
+ int total_ipro = (int) count_nodes(interpro_label);
+ if (total_ipro > 0) {
+ add_interpro = true;
+ }
+ tx.success();
+ }
+
try (BufferedReader in = new BufferedReader(new FileReader(path_to_gff))) { // read the GFF file
String prev_p_name = ""; // used for Phobius since these are on multiple lines
int transmembrane_counter = 0, signal_peptide_counter = 0;
@@ -3175,8 +3201,7 @@ public class FunctionalAnnotations {
signalp_map.put(prot_name, "yes");
}
-
- if (attribute_field.contains("IPR")) { // Interpro domain can be found on multiple lines: PFAM, TIGRFAM, etc.
+ if (add_interpro && attribute_field.contains("IPR")) { // Interpro domain can be found on multiple lines: PFAM, TIGRFAM, etc.
String[] attribute_array = attribute_field.split("IPR");
for (int i=1; i<= attribute_array.length-1; i += 2) {
String line_str = attribute_array[i];
@@ -3250,12 +3275,12 @@ public class FunctionalAnnotations {
/**
*
- * @param string1
+ * @param string
* @return
*/
- public static boolean check_if_string_can_be_converted_to_int(String string1) {
- try{
- int result1 = Integer.parseInt(string1);
+ public static boolean check_if_string_can_be_converted_to_int(String string) {
+ try {
+ int result1 = Integer.parseInt(string);
} catch (NumberFormatException nee) {
//do nothing
return false;
@@ -3483,8 +3508,7 @@ public class FunctionalAnnotations {
}
/**
- * Alternative names: add_functions()
-
+ * Alternative names: add_functions()
* Requires:
* -dp database path
* -if text file with full path to gff/eggnog files
@@ -3505,23 +3529,23 @@ public class FunctionalAnnotations {
annotation_identifiers = get_annotation_identifiers(false, false); // do not print, USE the input via -af
tx.success();
} catch (NotFoundException nfe) {
- System.out.println("Unable to start the pangenome database\n");
- return;
+ System.out.println("Unable to start the database\n");
+ System.exit(1);
}
+ String date = new SimpleDateFormat("dd-MM-yyyy HH:mm:ss").format(new Date() );
+ StringBuilder log_builder = new StringBuilder("## LOG of run on " + date + "\n");
try (Transaction tx = graphDb.beginTx()) {
int total_go = (int) count_nodes(go_label); // count nodes with a specific label
if (total_go == 0) {
- include_functional_annotation_databases();
+ checkIfDatabasesInputExists(log_builder);
+ includeFunctionalDatabases();
}
annotation_node_map = find_all_F_annotation_nodes();
tx.success();
}
- create_directory_in_DB("function");
- String date = new SimpleDateFormat("dd-MM-yyyy HH:mm:ss").format(new Date() );
- StringBuilder log_builder = new StringBuilder("## LOG of run on " + date + "\n");
-
+ create_directory_in_DB("function");
TreeSet<Integer> genomes_with_missing_mrna = new TreeSet<>();
TreeSet<Integer> genomes_with_added_functions = new TreeSet<>(); // genome were at least 1 annotation got added
try (BufferedReader in = new BufferedReader(new FileReader(INPUT_FILE))) { // read the GFF file
@@ -3578,13 +3602,13 @@ public class FunctionalAnnotations {
// COG information is directly added in read_eggnogmapper_input() function
connect_mrnas_to_function(tigrfam_node_map, tigrfam_label, RelTypes.has_tigrfam, mrna_node_map, annotation_node_map,
- log_builder, "TIGRFAM", genome_nr_str, not_found_ids_mrnas);
+ log_builder, "TIGRFAM", genome_nr_str, not_found_ids_mrnas);
connect_mrnas_to_function(interpro_node_map, interpro_label, RelTypes.has_interpro, mrna_node_map, annotation_node_map,
- log_builder, "InterPro", genome_nr_str, not_found_ids_mrnas);
+ log_builder, "InterPro", genome_nr_str, not_found_ids_mrnas);
connect_mrnas_to_function(pfam_node_map, pfam_label, RelTypes.has_pfam, mrna_node_map, annotation_node_map,
- log_builder, "PFAM", genome_nr_str, not_found_ids_mrnas);
+ log_builder, "PFAM", genome_nr_str, not_found_ids_mrnas);
connect_mrnas_to_function(goterm_node_map, go_label, RelTypes.has_go, mrna_node_map, annotation_node_map,
- log_builder, "GO", genome_nr_str, not_found_ids_mrnas);
+ log_builder, "GO", genome_nr_str, not_found_ids_mrnas);
add_phobius_information(phobius_node_map, mrna_node_map, not_found_ids_mrnas, log_builder);
add_signalp_information(signalp_map, mrna_node_map, not_found_ids_mrnas, log_builder);
@@ -3611,14 +3635,14 @@ public class FunctionalAnnotations {
System.out.println("\n\nWARNING! Not all genes in the annotation file can be found in genome(s): " + genomes_str +
"\nPlease check the log file.");
} else {
- System.out.println("");
+ System.out.println();
}
graphDb.shutdown();
String header = "";
if (!check_if_file_exists(WORKING_DIRECTORY + "log/add_functional_annotations.log")) {
header = "#This file is updated after each run!\n";
}
- append_string_to_file_full_path(log_builder.toString() + "\n", WORKING_DIRECTORY + "log/add_functional_annotations.log");
+ append_string_to_file_full_path(log_builder + "\n", WORKING_DIRECTORY + "log/add_functional_annotations.log");
System.out.println("\nLog file written to:\n "
+ WORKING_DIRECTORY + "log/add_functional_annotations.log\n");
}
@@ -3807,7 +3831,7 @@ public class FunctionalAnnotations {
*
* @param not_found_ids_mrnas, has only two keys 'function_id' and 'protein_id'
* @param log_builder
- * @param genome_nr_str
+ * @param genome_nr_str a genome number (formatted as string)
*/
public static void increase_add_fa_log_with_missing_info(HashMap<String, HashSet<String>> not_found_ids_mrnas, StringBuilder log_builder,
String genome_nr_str) {
@@ -3920,7 +3944,7 @@ public class FunctionalAnnotations {
The frequency is influenced by --skip/--reference and --annotations-file.
*/
public static void update_all_FA_nodes_frequency() {
- System.out.println("");
+ System.out.println();
update_fa_nodes_frequency(go_label, RelTypes.has_go);
update_fa_nodes_frequency(interpro_label, RelTypes.has_interpro);
update_fa_nodes_frequency(pfam_label, RelTypes.has_pfam);
@@ -4022,6 +4046,12 @@ public class FunctionalAnnotations {
* @param go_id_node_id
*/
public static void include_pfam(HashMap<String, Node> go_id_node_id) {
+ boolean pfamExistsA = check_if_file_exists(pantools_path + "addons/Pfam-A.clans.tsv");
+ boolean pfamExistsB = check_if_file_exists(pantools_path + "addons/gene_ontology.txt");
+ if (!pfamExistsA || !pfamExistsB) {
+ return; // one of the input files does not exist
+ }
+
HashMap<String, ArrayList<String>> pfam_go_map = new HashMap<>();
try (BufferedReader in = new BufferedReader(new FileReader(pantools_path + "/addons/gene_ontology.txt"))) {
for (int c = 0; in.ready();) {
@@ -4070,6 +4100,19 @@ public class FunctionalAnnotations {
* @param go_id_node_id
*/
public void include_tigrfam(HashMap<String, Node> go_id_node_id) {
+ boolean tigrfamExistsA = check_if_file_exists(pantools_path + "addons/tigrfam/TIGRFAMS_GO_LINK");
+ boolean tigrfamExistsB = check_if_file_exists(pantools_path + "addons/tigrfam/TIGRFAMS_ROLE_LINK");
+ boolean tigrfamExistsC = check_if_file_exists(pantools_path + "addons/tigrfam/TIGR_ROLE_NAMES");
+ boolean tigrfamExistsD = check_if_file_exists(pantools_path + "addons/tigrfam/TIGR00001.INFO");
+ boolean tigrfamExistsE = check_if_file_exists(pantools_path + "addons/tigrfam/COMBINED_INFO_FILES");
+ if (!tigrfamExistsA || !tigrfamExistsB || !tigrfamExistsC ) {
+ return;
+ }
+ if (!tigrfamExistsD && !tigrfamExistsE) {
+ return; // only 1 of these two files is requires. return if both are missing
+ }
+
+
HashMap<String, String> tigrfam_roleId = new HashMap<>();
HashMap<String, Node> tigrfam_nodeId = new HashMap<>();
HashMap<String, String> tigrfam_role_name = new HashMap<>();
@@ -4250,6 +4293,9 @@ public class FunctionalAnnotations {
* @param go_id_node_id
*/
public static void include_interpro(HashMap<String, Node> go_id_node_id) {
+ if (!check_if_file_exists(pantools_path + "addons/interpro.xml")) {
+ return;
+ }
HashMap<Node, ArrayList<String>> interpro_GO = new HashMap<>();
HashMap<String, String> interpro_id_function_map = new HashMap<>();
int interpro_counter = 0, go_counter = 0;
@@ -4348,9 +4394,12 @@ public class FunctionalAnnotations {
* @param go_id_node_id
*/
public static void build_go_hierarchy(HashMap<String, Node> go_id_node_id) {
+ if (!check_if_file_exists(pantools_path + "addons/go-basic.obo")){
+ return;
+ }
HashMap<String, ArrayList<String>> go_relations = new HashMap<>();
int go_count = 0;
- try (BufferedReader in2 = new BufferedReader(new FileReader(pantools_path + "/addons/go-basic.obo"))) {
+ try (BufferedReader in2 = new BufferedReader(new FileReader(pantools_path + "addons/go-basic.obo"))) {
Node go_node = graphDb.getNodeById(0);
String go_str = "a";
for (int c = 0; in2.ready();) {
@@ -4407,17 +4456,17 @@ public class FunctionalAnnotations {
}
}
} catch (IOException ioe) {
- System.out.println("Unable to read: " + pantools_path + "/addons/go-basic.obo\n");
+ System.out.println("Unable to read: " + pantools_path + "addons/go-basic.obo\n");
System.exit(1);
}
+
+ // loop is used to count the number of relations between GO nodes
int rel_count = 0;
- for (Map.Entry<String, ArrayList<String>> entry : go_relations.entrySet()) {
- String key = entry.getKey();
+ for (String key : go_relations.keySet()) {
String[] key_array = key.split("#");
- ArrayList<String> go_rels_list = entry.getValue();
- String node_id = key_array[0];
- long node_id_long = Long.parseLong(node_id);
- Node current_go = graphDb.getNodeById(node_id_long);
+ ArrayList<String> go_rels_list = go_relations.get(key);
+ long node_id = Long.parseLong(key_array[0]);
+ Node current_go = graphDb.getNodeById(node_id);
String relation_type = key_array[1];
for (String go_id : go_rels_list) {
Node current_go_node = go_id_node_id.get(go_id);
@@ -4461,7 +4510,7 @@ public class FunctionalAnnotations {
* @param annotation_node_id_map
* @param log_builder
* @param type
- * @param genome_nr_str
+ * @param genome_nr_str a genome number (formatted as string)
* @param not_found_ids_mrnas
*/
public static void connect_mrnas_to_function(HashMap<String, HashSet<String>> annotation_node_map, Label node_label, RelationshipType reltype,
@@ -4471,6 +4520,7 @@ public class FunctionalAnnotations {
if (annotation_node_map.isEmpty()) {
return;
}
+
Transaction tx = graphDb.beginTx();
try {
int counter = 0, skipped_counter = 0;
@@ -4578,16 +4628,96 @@ public class FunctionalAnnotations {
/**
* Interpro file (~200 Mb) must be downloaded by user to avoid a large git repository
+ * four databases, stop if none of them exist
+ * @param log_builder
*/
- public void check_if_ipro_xml_exists() {
+ public void checkIfDatabasesInputExists(StringBuilder log_builder) {
+ int correctCount = 0;
+ StringBuilder correct = new StringBuilder("Correct : ");
+ StringBuilder incorrect = new StringBuilder("Incorrect: ");
+ StringBuilder downloadBuilder = new StringBuilder(" cd " + pantools_path + "addons/\n");
+ boolean goExists = check_if_file_exists(pantools_path + "addons/go-basic.obo");
+ if (goExists) {
+ correctCount++;
+ correct.append("GO, ");
+ } else {
+ downloadBuilder.append(" wget http://purl.obolibrary.org/obo/go/go-basic.obo\n");
+ incorrect.append("GO, ");
+ }
+ boolean pfamExistsA = check_if_file_exists(pantools_path + "addons/Pfam-A.clans.tsv");
+ boolean pfamExistsB = check_if_file_exists(pantools_path + "addons/gene_ontology.txt");
+ if (pfamExistsA && pfamExistsB) {
+ correctCount++;
+ correct.append("Pfam, ");
+ } else {
+ if (!pfamExistsA) {
+ downloadBuilder.append(" wget ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases//Pfam35.0/Pfam-A.clans.tsv.gz\n");
+ }
+ if (!pfamExistsB) {
+ downloadBuilder.append(" wget ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases//Pfam35.0/database_files/gene_ontology.txt.gz\n");
+ }
+ incorrect.append("Pfam, ");
+ }
+ boolean interproExists = check_if_file_exists(pantools_path + "addons/interpro.xml");
+ if (interproExists) {
+ correctCount++;
+ correct.append("InterPro, ");
+ } else {
+ downloadBuilder.append(" wget https://ftp.ebi.ac.uk/pub/databases/interpro/interpro.xml.gz\n");
+ incorrect.append("InterPro, ");
+ }
+
+ boolean tigrfamExistsA = check_if_file_exists(pantools_path + "addons/tigrfam/TIGRFAMS_GO_LINK");
+ boolean tigrfamExistsB = check_if_file_exists(pantools_path + "addons/tigrfam/TIGRFAMS_ROLE_LINK");
+ boolean tigrfamExistsC = check_if_file_exists(pantools_path + "addons/tigrfam/TIGR_ROLE_NAMES");
+ boolean tigrfamExistsD = check_if_file_exists(pantools_path + "addons/tigrfam/TIGR00001.INFO");
+ boolean tigrfamExistsE = check_if_file_exists(pantools_path + "addons/tigrfam/COMBINED_INFO_FILES");
+ if (tigrfamExistsA && tigrfamExistsB && tigrfamExistsC && ( tigrfamExistsD || tigrfamExistsE)) {
+ correctCount++;
+ correct.append("TIGRGAM");
+ } else {
+ incorrect.append("TIGRGAM");
+ downloadBuilder.append(" cd ").append(pantools_path).append("addons/tigrfam/\n");
+ if (!tigrfamExistsA) {
+ downloadBuilder.append(" wget https://ftp.ncbi.nlm.nih.gov/hmm/TIGRFAMs/release_15.0/TIGRFAMS_GO_LINK\n");
+ }
+
+ if (!tigrfamExistsB) {
+ downloadBuilder.append(" wget https://ftp.ncbi.nlm.nih.gov/hmm/TIGRFAMs/release_15.0/TIGRFAMS_ROLE_LINK\n");
+ }
+
+ if (!tigrfamExistsC) {
+ downloadBuilder.append(" wget https://ftp.ncbi.nlm.nih.gov/hmm/TIGRFAMs/release_15.0/TIGR_ROLE_NAMES\n");
+ }
+
+ if (!tigrfamExistsD) {
+ downloadBuilder.append(" wget https://ftp.ncbi.nlm.nih.gov/hmm/TIGRFAMs/release_15.0/TIGRFAMs_15.0_INFO.tar.gz\n")
+ .append(" tar -xvf *.tar.gz");
+ }
+ }
+
+ System.out.println("\r" + correct);
+ System.out.println(incorrect);
+
if (!check_if_file_exists(pantools_path + "addons/interpro.xml")) {
- System.out.println("\rThe .xml formatted InterPro database must first be downloaded before functions can be added to the database.\n\n"
- + "How to proceed:\n"
- + " cd " + pantools_path + "addons/\n"
- + " wget https://ftp.ebi.ac.uk/pub/databases/interpro/interpro.xml.gz\n"
- + " gzip -d interpro.xml.gz\n");
+ String info = "If you want these databases to be included. This is how to proceed.\n"
+ + "\n"
+ + "1. Make sure there are no functions in the pangenome.\n"
+ + " pantools remove_nodes -dp " + WORKING_DIRECTORY + "addons/\n"
+ + "\n"
+ + "2. Download the database(s).\n" +
+ downloadBuilder +
+ " gzip -d *.gz\n"
+ + "\n"
+ + "3. Rerun this function.\n";
+ System.out.println("\r" + info);
+ log_builder.append(info).append("\n");
+ }
+
+ if (correctCount == 0) {
+ System.out.println("At least one functional database must be downloaded\n");
System.exit(1);
- }
+ }
}
/* Only needs to be run once per database
@@ -4595,8 +4725,7 @@ public class FunctionalAnnotations {
Requires files in addons directory release 15 of tigrfam
TIGRFAMS_GO_LINK, TIGRFAMS_ROLE_LINK, TIGR_ROLE_NAMES and the .info file
*/
- public void include_functional_annotation_databases() {
- check_if_ipro_xml_exists();
+ public void includeFunctionalDatabases() {
System.out.println("\rFirst time running this function. Including PFAM, InterPro annotations and TIGRFAM and building the GO hierarchy\n");
HashMap<String, Node> go_id_node_id = new HashMap<>();
int total_pfam_nodes = (int) count_nodes(pfam_label); // count nodes with a specific label
@@ -4664,7 +4793,7 @@ public class FunctionalAnnotations {
tx.success();
} catch (NotFoundException nfe) {
System.out.println("Unable to start the database\n");
- return;
+ System.exit(1);
}
ArrayList<Node> go_nodes = retrieve_go_nodes_via_name_or_node();
@@ -4806,7 +4935,6 @@ public class FunctionalAnnotations {
while (go_nodes.hasNext()) {
output_builder = new StringBuilder();
Node go_node = go_nodes.next();
- String go_id = (String) go_node.getProperty("id");
String go_name = (String) go_node.getProperty("name");
int counter = 1;
String all_go = go_node.toString();
@@ -5008,7 +5136,7 @@ public class FunctionalAnnotations {
tx.success();
} catch (NotFoundException nfe) {
System.out.println("Unable to start the database\n");
- return;
+ System.exit(1);
}
ArrayList<Node> go_nodes = retrieve_go_nodes_via_name_or_node();
@@ -5159,10 +5287,11 @@ public class FunctionalAnnotations {
Requirements:
-dp
- -if
+ -if: A text file with on each line a genome number and the full path to the corresponding antiSMASH output file,
+ separated by a space.
Optional
- -af
+ -af:
overwrite is currently hardcoded
@@ -5170,9 +5299,19 @@ public class FunctionalAnnotations {
With .gbk file
antismash --cb-general --cb-knownclusters --cb-subclusters --asf --pfam2go --smcog-trees streptomyces_coelicolor.gbk
With genome fasta and .gff
-
+
+ Example antismash geneclusters input file.
+ Five columns.
+ 1 Sequence identifier,
+ 2 Complete fasta header,
+ 3 Cluster type
+ 4 The gene original identifiers,
+ 5 Renamed gene identifiers
+
+ CP004601.1 Saccharomyces cerevisiae YJM993 chromosome II other H779_YJM993B00213;H779_YJM993B00214;H779_YJM993B00215
+ CP006151.1 CP006151.1 Saccharomyces cerevisiae YJM993 chromosome VIII terpene H779_YJM993H00245;H779_YJM993H00247;H779_YJM993H00248
*/
- public void add_antismash_results() {
+ public void add_antismash() {
System.out.println("\nAdding biosynthetic gene cluster nodes to the pangenome\n");
check_if_graphDb_is_available(); // starts up the graph database if needed
try (Transaction tx = graphDb.beginTx()) {
@@ -5183,224 +5322,493 @@ public class FunctionalAnnotations {
tx.success();
} catch (NotFoundException nfe) {
System.out.println("Unable to start the database\n");
- return;
+ System.exit(1);
}
- StringBuilder log_builder = new StringBuilder();
+
+ String date = new SimpleDateFormat("dd-MM-yyyy HH:mm:ss").format(new Date() );
+ StringBuilder log_builder = new StringBuilder("## LOG of run on " + date + "\n");
create_directory_in_DB("function");
create_directory_in_DB("log");
- int new_count = 0, exist_count = 0;
- HashMap<Integer, String> input_files = read_antismash_geneclusters_txt();
- for (int i = 1; i <= total_genomes; i++) {
- if (!input_files.containsKey(i)) {
+
+ HashMap<Integer, ArrayList<String>> input_files = read_input_files_for_antismash();
+ System.out.println("\rGenome\tClusters added");
+ for (int genome_nr : input_files.keySet()) {
+ String annotation_id = annotation_identifiers.get(genome_nr - 1);
+ if (annotation_id.endsWith("_0")) {
+ System.out.println(genome_nr + "\t0\tGene clusters cannot be added because no annotation is available");
continue;
- }
- String annotation_id = annotation_identifiers.get(i-1);
- try (Transaction tx = graphDb.beginTx()) { // start database transaction
- String input_file = input_files.get(i);
- HashMap<String, String> gene_locus_ids = retrieve_gene_ids_for_clusters(input_file);
- log_builder.append("#Genome ").append(i).append("\n");
- HashMap<String, Node> gene_map = prepare_gene_map_antismash(i); // retrieve all genes for a genome
- //System.out.print("\rAdding BGC's to pangenome. Genome " + i + " ");
- HashMap<String, Integer> cluster_count_map = new HashMap<>();
- try (BufferedReader in = new BufferedReader(new FileReader(input_file))) {
- while (in.ready()) {
- String line = in.readLine().trim();
- String[] line_array = line.split("\t");
- String[] gene_array = line_array[3].split(";");
- int cluster_count = 0;
- if (cluster_count_map.containsKey(line_array[2])) {
- cluster_count = cluster_count_map.get(line_array[2]);
- }
-
- cluster_count ++;
- cluster_count_map.put(line_array[2], cluster_count);
- Node[] gene_node_array = new Node[gene_array.length];
- boolean exists = check_if_bgc_exists_simple(line_array[2], i, gene_node_array, log_builder);
- if (exists) {
- exist_count ++;
- continue;
- }
- int[] bgc_address = retrieve_gene_cluster_address(gene_array, gene_map, gene_node_array, i, gene_locus_ids);
- boolean exists2 = check_if_bgc_exists(line_array[2], bgc_address, i, gene_node_array, log_builder);
- if (exists2) {
- exist_count ++;
+ }
+ HashMap<String, Node> gene_map = prepare_gene_map_antismash(genome_nr); // retrieve all genes for a genome
+ ArrayList<String> input_file_list = input_files.get(genome_nr);
+ for (String input_file : input_file_list) {
+ AtomicInteger new_counter = new AtomicInteger(0);
+ AtomicInteger exists_counter = new AtomicInteger(0);
+ String log;
+ if (input_file.endsWith(".json")) {
+ log = add_antismash_from_json(input_file, gene_map, genome_nr, exists_counter, new_counter);
+ } else {
+ System.out.println(input_file + " is not a json file");
+ //log = add_antismash_from_geneclusters_txt(input_file, gene_map, genome_nr, exists_counter,
+ // new_counter);
+ continue;
+ }
+ System.out.print("\r ");
+ System.out.println("\r" + genome_nr + "\t" + new_counter.get());
+ log_builder.append("##Genome ").append(genome_nr).append(". file ").append(input_file).append("\n")
+ .append(new_counter.get()).append(" gene clusters added, ").append(exists_counter).append(" were already known\n")
+ .append(log).append("\n");
+ }
+ }
+
+ System.out.println("\nLog written to\n "
+ + WORKING_DIRECTORY + "log/add_antismash.log\n");
+ append_SB_to_file_full_path(log_builder, WORKING_DIRECTORY + "log/add_antismash.log");
+ graphDb.shutdown();
+ }
+
+ /**
+ * Parse antismash v6.? json output
+ * @param path_to_json file location of json file
+ * @return key is cluster number, value is string with cluster type + "#" gene identifiers separated by commas
+ */
+ public static String add_antismash_from_json(String path_to_json, HashMap<String, Node> gene_map,
+ int genome_nr, AtomicInteger exists_counter,
+ AtomicInteger new_counter) {
+
+ StringBuilder log_builder = new StringBuilder();
+ log_builder.append("\nCluster info\ntype,number of genes,address,cluster added?,bgc node identifier, gene node identifiers\n");
+ String json = "";
+ try (BufferedReader in = new BufferedReader(new FileReader(path_to_json))) {
+ String line;
+ while ((line = in.readLine()) != null) {
+ json = line.trim();
+ }
+ } catch (IOException ioe) {
+ System.out.println("\nFailed to read: " + path_to_json + "\n");
+ }
+ JSONObject obj2 = new JSONObject(json);
+ JSONArray records = obj2.getJSONArray("records");
+ int cluster_end_pos = 0, cluster_start_pos = 0;
+ StringBuilder cluster_type = new StringBuilder();
+ ArrayList<String> gene_identiers = new ArrayList();
+ String earlier_CDS = "";
+ int[] earlier_address = new int[0];
+ for (int i = 0; i < records.length(); i++) { // j is feature number
+ JSONArray features = records.getJSONObject(i).getJSONArray("features");
+ boolean in_cluster = false;
+ for (int j = 0; j < features.length(); j++) {
+ String location = features.getJSONObject(j).getString("location"); // example [1:1000]
+ String type = features.getJSONObject(j).getString("type");
+ JSONObject qualifiers = features.getJSONObject(j).getJSONObject("qualifiers");
+ if (type.equals("protocluster")) {
+ JSONArray product = qualifiers.getJSONArray("product");
+ in_cluster = true;
+ int[] cluster_start_stop_pos = start_stop_from_json_location(location);
+ cluster_start_pos = cluster_start_stop_pos[0];
+ cluster_end_pos = cluster_start_stop_pos[1];
+
+ Object cluster_product = product.get(0);
+ if (cluster_type.length() == 0) {
+ cluster_type = new StringBuilder(cluster_product.toString());
+ } else { // multiple products for a cluster
+ cluster_type.append(",").append(cluster_product.toString());
+ }
+ if (!earlier_CDS.equals("")){ // for some clusters the CDS property comes before protocluster
+ if (earlier_address[0] >= cluster_start_pos) {
+ gene_identiers.add(earlier_CDS);
}
- log_builder.append("New BGC '").append(line_array[2]).append("', ").append(gene_array.length).append(" genes\n");
- new_count ++;
- Node bgc_node = graphDb.createNode(bgc_label);
- bgc_node.setProperty("type", line_array[2]);
- bgc_node.setProperty("length", gene_array.length);
- bgc_node.setProperty("genome", i);
- bgc_node.setProperty("address", bgc_address);
- bgc_node.setProperty("number", cluster_count);
- bgc_node.setProperty("annotation_id", annotation_id);
- int position = 1;
- for (Node gene_node : gene_node_array) {
- Relationship rel = gene_node.createRelationshipTo(bgc_node, Pantools.RelTypes.part_of);
- rel.setProperty("position", position);
- position ++;
- }
- }
- } catch (IOException ioe) {
- System.out.println("\nFailed to read: " + input_file + "\n");
- return;
+ }
+ continue;
+ } else if (type.equals("CDS")) {
+ try {
+ earlier_CDS = (String) qualifiers.getJSONArray("gene").get(0);
+ } catch (JSONException jse) {
+ System.out.println("\n\nUnable to retrieve gene identifiers from the antiSMASH output.\n"
+ + "This is most likely because antiSMASH was run without GFF file.\n");
+ System.exit(1);
+ }
+ earlier_address = start_stop_from_json_location(location);
+ }
+ int gene_end_pos;
+ if (in_cluster && type.equals("gene")) {
+ String gene_id = (String) qualifiers.getJSONArray("ID").get(0);
+ int[] gene_start_stop_pos = start_stop_from_json_location(location);
+ int gene_start_pos = gene_start_stop_pos[0];
+ gene_end_pos = gene_start_stop_pos[1];
+ if (gene_start_pos < cluster_end_pos && !gene_identiers.contains(gene_id)) {
+ gene_identiers.add(gene_id);
+ }
+ } else if (in_cluster && type.equals("CDS")) {
+ String gene_id = (String) qualifiers.getJSONArray("gene").get(0);
+ int[] gene_start_stop_pos = start_stop_from_json_location(location);
+ int gene_start_pos = gene_start_stop_pos[0];
+ gene_end_pos = gene_start_stop_pos[1];
+ if (gene_start_pos < cluster_end_pos && !gene_identiers.contains(gene_id)) {
+ gene_identiers.add(gene_id);
+ }
+ } else {
+ continue;
}
- tx.success(); // commit changes after every cgenome
- log_builder.append("\n");
- }
+
+ if (gene_end_pos >= cluster_end_pos) { // the current gene has a coordinate higher as the cluster
+ in_cluster = false;
+ if (gene_identiers.isEmpty()) {
+ continue;
+ }
+ ArrayList<Node> gene_node_list = retrieve_gene_nodes_from_ids(gene_identiers, gene_map, null, log_builder);
+ int[] bgc_address = create_gene_cluster_address(genome_nr, gene_node_list);
+ String cluster_type_str = cluster_type.toString();
+ boolean cluster_exists = check_if_bgc_exists(cluster_type_str, bgc_address, gene_node_list, log_builder);
+ cluster_type = new StringBuilder(); // reset for the next cluster
+ gene_identiers = new ArrayList<>(); // reset for the next cluster
+ if (cluster_exists) {
+ exists_counter.incrementAndGet();
+ continue;
+ }
+ new_counter.incrementAndGet();
+ create_BGC_node(cluster_type_str, gene_node_list, genome_nr, bgc_address, log_builder,
+ cluster_start_pos, cluster_end_pos);
+ }
+ }
}
- if (new_count != 0) {
- System.out.println("\nCreated " + new_count + " new BGC's");
+ return log_builder.toString();
+ }
+
+ public static int[] start_stop_from_json_location(String location) {
+ int gene_start_pos, gene_end_pos;
+ if (location.startsWith("join")) {
+ // location example "join{[19678:22672](-), […](-), [18596:19037](-)}"
+ String[] loc_array = location.split(":");
+ String first_value_str = loc_array[0].replaceAll("[^0-9]",""); // remove all except numbers
+ String last_value_str = loc_array[loc_array.length-1].replaceAll("[^0-9]",""); // remove all except numbers
+ int first_value = Integer.parseInt(first_value_str);
+ int last_value = Integer.parseInt(last_value_str);
+ gene_start_pos = first_value;
+ if (location.contains("+")) {
+ //System.out.println("+ " + first_value + " " + last_value);
+ gene_end_pos = last_value;
+ } else {
+ //System.out.println("- " + last_value + " " + first_value);
+ gene_end_pos = first_value;
+ gene_start_pos = last_value;
+ }
} else {
- System.out.println("");
+ String[] loc_array = location.split(":");
+ String[] loc_array2 = loc_array[1].split("]");
+ gene_start_pos = Integer.parseInt(loc_array[0].replace("[",""));
+ gene_end_pos = Integer.parseInt(loc_array2[0].replace("]",""));
}
-
- if (exist_count != 0) {
- System.out.println("Found " + exist_count + " already existing BGC's\n");
- } else {
- System.out.println("");
+ return new int []{gene_start_pos, gene_end_pos};
+ }
+
+ /**
+ *
+ * @param input_file
+ * @param gene_map
+ * @param genome_nr a genome number
+ * @param exist_counter
+ * @param new_counter
+
+ public static String add_antismash_from_geneclusters_txt(String input_file, HashMap<String, Node> gene_map, int genome_nr,
+ AtomicInteger exist_counter,
+ AtomicInteger new_counter) {
+ StringBuilder log_builder = new StringBuilder();
+ log_builder.append("\nCluster info\ntype,number of genes,address,cluster added?,bgc node identifier, gene node identifiers\n");
+ HashMap<String, String> gene_locus_ids = retrieve_gene_ids_for_clusters(input_file);
+ try (Transaction tx = graphDb.beginTx()) { // start database transaction
+ try (BufferedReader in = new BufferedReader(new FileReader(input_file))) {
+ while (in.ready()) {
+ String[] line_array = in.readLine().trim().split("\t"); //split line on tab
+ if (line_array.length < 4) {
+ System.out.println("Unable to correctly parse " + input_file + "\n" +
+ "Requires 4 columns that are tab-seperated. " + line_array.length + " detected.");
+ System.exit(1);
+ }
+
+ String[] gene_array = line_array[3].split(";"); // array with gene identifiers
+ String cluster_type = line_array[2];
+
+ ArrayList<Node> gene_node_list = retrieve_gene_nodes_from_ids(gene_array, gene_map, gene_locus_ids, log_builder);
+ int[] bgc_address = create_gene_cluster_address(genome_nr, gene_node_list);
+ boolean cluster_exists = check_if_bgc_exists(cluster_type, bgc_address, gene_node_list, log_builder);
+
+ if (cluster_exists) {
+ exist_counter.incrementAndGet();
+ continue;
+ }
+ new_counter.incrementAndGet();
+ create_BGC_node(cluster_type, gene_node_list, genome_nr, bgc_address, log_builder, 0, 0);
+ }
+ } catch (IOException ioe) {
+ System.out.println("\nFailed to read: " + input_file + "\n");
+ return log_builder.toString();
+ }
+ tx.success();
+ }
+ return log_builder.toString();
+ }*/
+
+ /**
+ *
+ * @param cluster_type cluster product
+ * @param gene_node_list list of 'gene' nodes
+ * @param genome_nr a genome number
+ * @param bgc_address genomic coordinates of cluster
+ * @param log_builder the log to store in file
+ */
+ public static void create_BGC_node(String cluster_type, ArrayList<Node> gene_node_list, int genome_nr, int[] bgc_address,
+ StringBuilder log_builder, int cluster_start_pos, int cluster_end_pos) {
+
+ try (Transaction tx = graphDb.beginTx()) { // start database transaction
+ StringBuilder gene_id_builder = new StringBuilder();
+ String annotation_id = annotation_identifiers.get(genome_nr - 1);
+ Node bgc_node = graphDb.createNode(bgc_label);
+ bgc_node.setProperty("type", cluster_type);
+ String[] cluster_types = cluster_type.split(","); // type can consists of multiple types. example: NRPS,NRPS-like
+ for (int j = 0; j < cluster_types.length; j++) {
+ bgc_node.setProperty("type_" + (j + 1), cluster_types[j]);
+ }
+ bgc_node.setProperty("length", gene_node_list.size());
+ bgc_node.setProperty("genome", genome_nr);
+ bgc_node.setProperty("sequence", bgc_address[1]);
+ bgc_node.setProperty("address_genes", bgc_address);
+ if (cluster_start_pos == 0) {
+ cluster_start_pos ++;
+ }
+ bgc_address[2] = cluster_start_pos;
+ bgc_address[3] = cluster_end_pos;
+ bgc_node.setProperty("address", bgc_address);
+ bgc_node.setProperty("annotation_id", annotation_id);
+ int position = 1;
+ for (Node gene_node : gene_node_list) {
+ gene_id_builder.append(gene_node.getId()).append(" ");
+ if (gene_node.getId() == 0) {
+ continue;
+ }
+ Relationship rel = gene_node.createRelationshipTo(bgc_node, Pantools.RelTypes.part_of);
+ rel.setProperty("position", position);
+ position++;
+ }
+
+ log_builder.append(cluster_type.replace(",", " ")) // cluster product
+ .append(",").append(gene_node_list.size()).append(",") // cluster length
+ .append(bgc_address[0]).append(" ").append(bgc_address[1]).append(" ")
+ .append(bgc_address[2]).append(" ").append(bgc_address[3]) // cluster address
+ .append(",yes,") // cluster was added
+ .append(bgc_node.getId()).append(",") // bgc node identifier
+ .append(gene_id_builder).append("\n"); // gene node identififers of cluster
+ tx.success();
}
- System.out.println("\nLogfile written to\n "
- + WORKING_DIRECTORY + "log/add_antismash_results.log\n");
- write_SB_to_file_in_DB(log_builder, "log/add_antismash_results.log");
- graphDb.shutdown();
}
-
+
/**
- * This function is required in case a different id was give to a gene by antismash
- * @param original_input_file
+ * This function is required in case a different id was give to a gene by antiSMASH
+ * Important, This only works on antismash 4 output directory
+ * @param original_input_file path to a antismash geneclusters input file
* @return
*/
public static HashMap<String, String> retrieve_gene_ids_for_clusters(String original_input_file) {
HashMap<String, String> gene_ids = new HashMap<>();
- String[] input_array = original_input_file.split("/");
- String input_directory = "", input_file = "";
- for (int i=0; i <= input_array.length-2; i++) {
- input_directory += input_array[i] + "/";
- }
-
- File folder = new File(input_directory);
- String[] files = folder.list();
- for (String file : files) {
- if (file.endsWith(".final.gbk")) {
- input_file = file;
+ try (Transaction tx = graphDb.beginTx()) { // start database transaction
+ String[] input_array = original_input_file.split("/");
+ StringBuilder input_directory = new StringBuilder();
+ String gbk_final_file = "";
+ for (int i = 0; i <= input_array.length - 2; i++) {
+ input_directory.append(input_array[i]).append("/");
}
- }
- try (BufferedReader in = new BufferedReader(new FileReader(input_directory + input_file))) {
- String locus = "";
- while (in.ready()) {
- String line = in.readLine().trim();
- if (line.contains("locus_tag")) {
- String[] line_array = line.split("locus_tag=");
- locus = line_array[1].replace("\"","");
+ File folder = new File(input_directory.toString());
+ String[] files = folder.list();
+ assert files != null;
+ for (String file : files) {
+ if (file.endsWith(".final.gbk")) {
+ gbk_final_file = file;
}
- if (line.contains("/ID=")) {
- String[] line_array = line.split("/ID=");
- String id = line_array[1].replace("\"","");
- //System.out.println(locus + " " + id );
- gene_ids.put(locus, id);
+ }
+ if (gbk_final_file.equals("")) { // no file present
+ return null;
+ }
+
+ try (BufferedReader in = new BufferedReader(new FileReader(input_directory + gbk_final_file))) {
+ String locus = "";
+ while (in.ready()) {
+ String line = in.readLine().trim();
+ if (line.contains("locus_tag")) {
+ String[] line_array = line.split("locus_tag=");
+ locus = line_array[1].replace("\"", "");
+ }
+ if (line.contains("/ID=")) {
+ String[] line_array = line.split("/ID=");
+ String id = line_array[1].replace("\"", "");
+ gene_ids.put(locus, id);
+ }
}
+ } catch (IOException ioe) {
+ System.out.println("\nFailed to read: " + gbk_final_file + "\n");
}
- } catch (IOException ioe) {
- System.out.println("\nFailed to read: " + input_file + "\n");
+ tx.success();
}
return gene_ids;
}
/**
* Create the address of the gene cluster based on the first and last position found of the genes.
- * @param gene_array
+ * @param gene_identifiers
* @param gene_map
- * @param gene_node_array
- * @param genome_nr
* @param gene_locus_ids
+ * @param log_builder
* @return
*/
- public static int[] retrieve_gene_cluster_address(String[] gene_array, HashMap<String, Node> gene_map, Node[] gene_node_array,
- int genome_nr, HashMap<String, String> gene_locus_ids) {
-
+ public static ArrayList<Node> retrieve_gene_nodes_from_ids(ArrayList<String> gene_identifiers, HashMap<String, Node> gene_map,
+ HashMap<String, String> gene_locus_ids,
+ StringBuilder log_builder) {
+
+ ArrayList<Node> gene_nodes = new ArrayList<>();
+ try (Transaction tx = graphDb.beginTx()) { // start database transaction
+ Node gene_node = graphDb.getNodeById(0);
+ for (String gene_id : gene_identifiers) {
+ if (gene_map.containsKey(gene_id)) {
+ gene_node = gene_map.get(gene_id);
+ } else {
+ String extra_id = "";
+ if (gene_locus_ids != null && !gene_locus_ids.isEmpty()) { // when a final_gbk file was present
+ extra_id = gene_locus_ids.get(gene_id);
+ if (gene_map.containsKey(extra_id)) {
+ gene_node = gene_map.get(extra_id);
+ }
+ extra_id = " or " + extra_id;
+ }
+
+ if (gene_node.getId() == 0) { // gene still not found
+ String new_gene_id = split_gene_id_try_every_option(gene_id, gene_map);
+ if (new_gene_id.equals(gene_id)) {
+ log_builder.append("Unable to find ").append(gene_id).append(extra_id).append("\n");
+ } else {
+ gene_node = gene_map.get(new_gene_id);
+ }
+ }
+ }
+
+ if (!gene_nodes.contains(gene_node) || gene_node.getId() == 0) {
+ gene_nodes.add(gene_node);
+ }
+ }
+ tx.success();
+ }
+ return gene_nodes;
+ }
+
+ /**
+ *
+ * @param genome_nr a genome number
+ * @param gene_nodes a list of 'gene' nodes
+ * @return address of bgc genome number, sequence number, start position, end position
+ */
+ public static int[] create_gene_cluster_address(int genome_nr, ArrayList<Node> gene_nodes) {
int sequence_nr = -1, highest = 0, lowest = 999999999;
- int counter = 0;
int[] bgc_address = new int[4];
- Node gene_node = graphDb.getNodeById(0);
- for (String gene : gene_array) {
- if (gene_map.containsKey(gene)) {
- gene_node = gene_map.get(gene);
- } else {
- String protein_id = gene_locus_ids.get(gene);
- if (gene_map.containsKey(protein_id)) {
- gene_node = gene_map.get(gene);
- } else {
- System.out.println("\nUnable to find gene '" + gene + " or " + protein_id + " (" + genome_nr + ")");
- System.exit(1);
+ try (Transaction tx = graphDb.beginTx()) { // start database transaction
+ for (Node gene_node : gene_nodes) { // go over all nodes, else incorrect addres if genes are not in correct order
+ int[] address = (int[]) gene_node.getProperty("address");
+ sequence_nr = address[1];
+ if (address[2] < lowest) {
+ lowest = address[2];
+ }
+ if (address[3] > highest) {
+ highest = address[3];
}
}
-
- int[] address = (int[]) gene_node.getProperty("address");
- sequence_nr = address[1];
- if (address[2] < lowest) {
- lowest = address[2];
- }
- if (address[3] > highest) {
- highest = address[3];
- }
- gene_node_array[counter] = gene_node;
- counter += 1;
- }
- bgc_address[0] = genome_nr;
- bgc_address[1] = sequence_nr;
- bgc_address[2] = lowest;
- bgc_address[3] = highest;
+ bgc_address[0] = genome_nr;
+ bgc_address[1] = sequence_nr;
+ bgc_address[2] = lowest;
+ bgc_address[3] = highest;
+ tx.success();
+ }
return bgc_address;
}
-
- /*
- Gather all gene nodes of a genome and put this in a hashmap. key is the id, value is the node.
- ANTISMASH output must have the 'id' or the information cannot be added.
- Only works on pangenome
- */
+
+ /**
+ *
+ * @param gene_id a gene identifier (from GFF)
+ * @param gene_map
+ * @return string. is the same as the input gene_id when no correct id was found
+ */
+ public static String split_gene_id_try_every_option(String gene_id, HashMap<String, Node> gene_map) {
+ String[] gene_id_array = gene_id.split("_");
+ String new_gene_id = "";
+ for (int i=0; i < gene_id_array.length; i++) {
+ if (!new_gene_id.equals("")){
+ new_gene_id += "_";
+ }
+ new_gene_id += gene_id_array[i];
+ if (gene_map.containsKey(new_gene_id)){
+ return new_gene_id;
+ }
+ }
+ return new_gene_id;
+ }
+
+
+ /**
+ * Gather all gene nodes of a genome and put this in a hashmap.
+ * ANTISMASH output must have the 'id' or the information cannot be added.
+ * @param genome_nr number of a genome in the pangenome database
+ * @return hashmap. key is a gene id, value is the gene node.
+ */
public static HashMap<String, Node> prepare_gene_map_antismash(int genome_nr) {
- String annotation_id = annotation_identifiers.get(genome_nr-1);
- ResourceIterator<Node> gene_nodes = graphDb.findNodes(gene_label, "annotation_id", annotation_id);
HashMap<String, Node> gene_map = new HashMap<>();
- int counter = 0;
- while (gene_nodes.hasNext()) {
- counter ++;
- if (counter % 101 == 0 ) {
- System.out.print("\rGathering genes: Genome " + genome_nr + ". " + counter + " ");
- }
- Node gene_node = gene_nodes.next();
- String id = (String) gene_node.getProperty("id");
- String name = (String) gene_node.getProperty("name");
- String locus_tag = (String) gene_node.getProperty("locus_tag");
- gene_map.put(id, gene_node);
- gene_map.put(id + "_gene", gene_node);
- gene_map.put(name, gene_node);
- gene_map.put(locus_tag, gene_node);
- }
- // extends this function with mRNA and CDS nodes when a gene still cannot be found.
+ try (Transaction tx = graphDb.beginTx()) { // start database transaction
+ String annotation_id = annotation_identifiers.get(genome_nr - 1);
+ ResourceIterator<Node> gene_nodes = graphDb.findNodes(gene_label, "annotation_id", annotation_id);
+ int gene_counter = 0;
+ while (gene_nodes.hasNext()) {
+ gene_counter++;
+ if (gene_counter % 10000 == 0 || gene_counter == 1) {
+ System.out.print("\rGathering genes: " + gene_counter + " "); // spaces are intentional
+ }
+ Node gene_node = gene_nodes.next();
+ String id = (String) gene_node.getProperty("id");
+ String name = (String) gene_node.getProperty("name");
+ gene_map.put(id, gene_node);
+ gene_map.put(id + "_gene", gene_node);
+ gene_map.put(name, gene_node);
+ if (gene_node.hasProperty("locus_tag")) {
+ String locus_tag = (String) gene_node.getProperty("locus_tag");
+ gene_map.put(locus_tag, gene_node);
+ }
+ }
+ tx.success();
+ }
+ // This function can be extended with mRNA and CDS nodes when a gene still cannot be found?
return gene_map;
}
/**
* Must have two columns: first genome number, second is a full path to geneclusters.txt
- * @return
+ * @return hashmap. key is genome number. value is (multiple) paths to antismash cluster file
*/
- public static HashMap<Integer, String> read_antismash_geneclusters_txt() {
+ public static HashMap<Integer, ArrayList<String>> read_input_files_for_antismash() {
if (INPUT_FILE == null) {
- System.out.println("No geneclusters provided via --input-file/-if\n");
+ System.out.println("No gene clusters provided via --input-file/-if\n");
System.exit(1);
}
- HashMap<Integer, String> input_files = new HashMap<>();
+ HashMap<Integer, ArrayList<String>> input_files = new HashMap<>();
try (BufferedReader in = new BufferedReader(new FileReader(INPUT_FILE))) {
while (in.ready()) {
String line = in.readLine().trim();
String[] line_array = line.split(" ");
if (line_array.length != 2) {
- System.out.println("Input file is not formatted correctly. Should be 2 columns seperated by a space. Line is " + line_array.length + " columns\n");
+ System.out.println("\rInput file is not formatted correctly!" +
+ " Should be 2 columns separated by a space. Line has " + line_array.length + " columns\n");
System.exit(1);
}
- input_files.put(Integer.parseInt(line_array[0]), line_array[1]);
+ int genome_nr = 0;
+ try {
+ genome_nr = Integer.parseInt(line_array[0]);
+ } catch (NumberFormatException nee) {
+ System.out.println(line_array[0] + " is not a number");
+ continue;
+ }
+ try_incr_AL_hashmap(input_files, genome_nr, line_array[1]);
}
} catch (IOException ioe) {
System.out.println("\nFailed to read: " + INPUT_FILE + "\n");
@@ -5410,49 +5818,36 @@ public class FunctionalAnnotations {
}
/**
- * Check if there already is a bgc node with the address
- * @param new_type
- * @param bgc_address
- * @param genome
- * @param gene_node_array
+ * Check if there already is a bgc node with same type and address
+ * @param cluster_type cluster product
+ * @param bgc_address genomic coordinates of cluster
* @param log_builder
- * @return
+ * @return boolean. whether the cluster is already present or not
*/
- public static boolean check_if_bgc_exists(String new_type, int[] bgc_address, int genome, Node[] gene_node_array, StringBuilder log_builder) {
- boolean skip = false;
- try {
- Node bgc_node1 = graphDb.findNode(bgc_label, "address", bgc_address);
- String type = (String) bgc_node1.getProperty("type");
- int current_genome = (int) bgc_node1.getProperty("genome");
- if (type.equals(new_type) && current_genome == genome) {
- log_builder.append("BGC '").append(type).append("' (").append(gene_node_array.length).append(") already exists\n");
- skip = true;
- }
- } catch (NullPointerException nul) {
-
- }
- return skip;
- }
-
- /*
- This function only checks the number of genes, not the address. This can be done before the address is calculated and is faster.
- */
- public static boolean check_if_bgc_exists_simple(String new_type, int genome, Node[] gene_node_array, StringBuilder log_builder) {
- boolean skip = false;
- ResourceIterator<Node> bgc_nodes = graphDb.findNodes(bgc_label, "type", new_type);
- while (bgc_nodes.hasNext()) {
- Node bgc_node1 = bgc_nodes.next();
- int current_genome = (int) bgc_node1.getProperty("genome");
- int length = (int) bgc_node1.getProperty("length");
- if (gene_node_array.length == length && current_genome == genome) {
- log_builder.append("BGC '").append(new_type).append("' (").append(gene_node_array.length).append(") already exists\n");
- //System.out.println("BGC '" + new_type + "' (" + gene_node_array.length + ") already exists\n");
- skip = true;
+ public static boolean check_if_bgc_exists(String cluster_type, int[] bgc_address, ArrayList<Node> gene_node_list, StringBuilder log_builder) {
+ boolean cluster_present = false;
+ try (Transaction tx = graphDb.beginTx()) { // start database transaction
+ try {
+ Node bgc_node = graphDb.findNode(bgc_label, "address_genes", bgc_address);
+ String type = (String) bgc_node.getProperty("type");
+ if (type.equals(cluster_type)) {
+ log_builder.append(type.replace(","," ")).append(",") // cluster product
+ .append(gene_node_list.size()).append(",") // number of genes in cluster
+ .append(bgc_address[0]).append(" ").append(bgc_address[1]).append(" ")
+ .append(bgc_address[2]).append(" ").append(bgc_address[3]) // cluster address
+ .append(",not added, same type (product) and address as bgc node ")
+ .append(bgc_node.getId()).append("\n"); // bgc node identifier
+ cluster_present = true;
+ }
+ } catch (NullPointerException npe) {
+ // if node with the specific address is not found, the exception is caught
+ return cluster_present;
}
+ tx.success();
}
- return skip;
+ return cluster_present;
}
-
+
/**
* @param function_label
* @param function_reltype
diff --git a/src/pangenome/GenomeLayer.java b/src/main/java/nl/wur/bif/pantools/pangenome/GenomeLayer.java
similarity index 88%
rename from src/pangenome/GenomeLayer.java
rename to src/main/java/nl/wur/bif/pantools/pangenome/GenomeLayer.java
index 8f18f751f1c083023f11a4d61ae4f2470ec1259e..8f8cc79f2c9d3886df5658808daf6e0bcf5f1474 100755
--- a/src/pangenome/GenomeLayer.java
+++ b/src/main/java/nl/wur/bif/pantools/pangenome/GenomeLayer.java
@@ -3,10 +3,10 @@
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
-package pangenome;
+package nl.wur.bif.pantools.pangenome;
-import alignment.BoundedLocalSequenceAlignment;
-import alignment.LocalSequenceAlignment;
+import nl.wur.bif.pantools.alignment.BoundedLocalSequenceAlignment;
+import nl.wur.bif.pantools.alignment.LocalSequenceAlignment;
import htsjdk.samtools.SAMException;
import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.SAMFileWriter;
@@ -16,18 +16,16 @@ import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SAMSequenceRecord;
import htsjdk.samtools.fastq.FastqReader;
import htsjdk.samtools.fastq.FastqRecord;
-import index.IndexDatabase;
-import sequence.SequenceScanner;
-import index.IndexPointer;
-import index.IndexScanner;
-import index.kmer;
-import java.io.BufferedReader;
-import java.io.BufferedWriter;
-import java.io.FileReader;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.io.File;
-import java.io.InputStreamReader;
+import nl.wur.bif.pantools.index.IndexDatabase;
+import nl.wur.bif.pantools.sequence.SequenceScanner;
+import nl.wur.bif.pantools.index.IndexPointer;
+import nl.wur.bif.pantools.index.IndexScanner;
+import nl.wur.bif.pantools.index.kmer;
+
+import java.io.*;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
import java.util.Arrays;
import org.neo4j.graphdb.GraphDatabaseService;
import org.neo4j.graphdb.Node;
@@ -36,22 +34,23 @@ import org.neo4j.graphdb.RelationshipType;
import org.neo4j.graphdb.ResourceIterator;
import org.neo4j.graphdb.Transaction;
import org.neo4j.graphdb.Direction;
-import static pantools.Pantools.GENOME_DATABASE_PATH;
-import static pantools.Pantools.GRAPH_DATABASE_PATH;
-import pantools.Pantools.RelTypes;
-import static pantools.Pantools.PATH_TO_THE_GENOMES_FILE;
-import static pantools.Pantools.PATH_TO_THE_REGIONS_FILE;
-import static pantools.Pantools.PATH_TO_THE_GENOME_NUMBERS_FILE;
-import static pantools.Pantools.RAW_ABUNDANCE_FILE;
-import static pantools.Pantools.num_bases;
-import static pantools.Pantools.num_degenerates;
-import static pantools.Pantools.num_edges;
-import static pantools.Pantools.num_nodes;
-import static pantools.Pantools.phaseTime;
-import static pantools.Pantools.MAX_TRANSACTION_SIZE;
-import static pantools.Pantools.ANCHORS_DISTANCE;
-import static pantools.Pantools.complement;
-import static pantools.Pantools.write_fasta;
+import static nl.wur.bif.pantools.pantools.Pantools.GENOME_DATABASE_PATH;
+import static nl.wur.bif.pantools.pantools.Pantools.GRAPH_DATABASE_PATH;
+import nl.wur.bif.pantools.pantools.Pantools.RelTypes;
+import static nl.wur.bif.pantools.pantools.Pantools.PATH_TO_THE_GENOMES_FILE;
+import static nl.wur.bif.pantools.pantools.Pantools.PATH_TO_THE_REGIONS_FILE;
+import static nl.wur.bif.pantools.pantools.Pantools.PATH_TO_THE_GENOME_NUMBERS_FILE;
+import static nl.wur.bif.pantools.pantools.Pantools.RAW_ABUNDANCE_FILE;
+import static nl.wur.bif.pantools.pantools.Pantools.num_bases;
+import static nl.wur.bif.pantools.pantools.Pantools.num_degenerates;
+import static nl.wur.bif.pantools.pantools.Pantools.num_edges;
+import static nl.wur.bif.pantools.pantools.Pantools.num_nodes;
+import static nl.wur.bif.pantools.pantools.Pantools.phaseTime;
+import static nl.wur.bif.pantools.pantools.Pantools.MAX_TRANSACTION_SIZE;
+import static nl.wur.bif.pantools.pantools.Pantools.ANCHORS_DISTANCE;
+import static nl.wur.bif.pantools.pantools.Pantools.complement;
+import static nl.wur.bif.pantools.pantools.Pantools.write_fasta;
+import static nl.wur.bif.pantools.pantools.Pantools.write_SB_to_file_in_DB;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Comparator;
@@ -68,57 +67,60 @@ import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.concurrent.TimeUnit;
import java.util.concurrent.atomic.AtomicLong;
+import java.util.zip.GZIPInputStream;
+
import org.neo4j.graphdb.NotFoundException;
-import static pantools.Pantools.DEBUG;
-import static pantools.Pantools.GAP_EXT;
-import static pantools.Pantools.GAP_OPEN;
-import static pantools.Pantools.K_SIZE;
-import static pantools.Pantools.PATH_TO_THE_FIRST_SRA;
-import static pantools.Pantools.PATH_TO_THE_SECOND_SRA;
-import static pantools.Pantools.SHOW_KMERS;
-import static pantools.Pantools.CLIPPING_STRINGENCY;
-import static pantools.Pantools.OUTFORMAT;
-import static pantools.Pantools.OUTPUT_PATH;
-import static pantools.Pantools.THREADS;
-import static pantools.Pantools.degenerate_label;
-import static pantools.Pantools.genome_label;
-import static pantools.Pantools.nucleotide_label;
-import static pantools.Pantools.pangenome_label;
-import static pantools.Pantools.sequence_label;
-import static pangenome.Classification.genome_overview;
-import static pantools.Pantools.stop_if_panproteome;
-import static pantools.Pantools.ALIGNMENT_BOUND;
-import static pantools.Pantools.ALIGNMENT_MODE;
-import static pantools.Pantools.INDEX_DATABASE_PATH;
-import static pantools.Pantools.INTERLEAVED;
-import static pantools.Pantools.NUM_KMER_SAMPLES;
-import static pantools.Pantools.MAX_ALIGNMENT_LENGTH;
-import static pantools.Pantools.MAX_FRAGMENT_LENGTH;
-import static pantools.Pantools.MIN_HIT_LENGTH;
-import static pantools.Pantools.MIN_IDENTITY;
-import static pantools.Pantools.MAX_NUM_LOCATIONS;
-import static pantools.Pantools.SHOULDER;
-import static pantools.Pantools.VERYSENSITIVE;
-import static pantools.Pantools.WORKING_DIRECTORY;
-import static pantools.Pantools.binary;
-import static pantools.Pantools.check_if_file_exists;
-import static pantools.Pantools.check_if_program_exists_stdout;
-import static pantools.Pantools.connect_pangenome;
-import static pantools.Pantools.create_pangenome_database;
-import static pantools.Pantools.disconnect_pangenome;
-import static pantools.Pantools.genomeDb;
-import static pantools.Pantools.graphDb;
+import static nl.wur.bif.pantools.pantools.Pantools.DEBUG;
+import static nl.wur.bif.pantools.pantools.Pantools.GAP_EXT;
+import static nl.wur.bif.pantools.pantools.Pantools.GAP_OPEN;
+import static nl.wur.bif.pantools.pantools.Pantools.K_SIZE;
+import static nl.wur.bif.pantools.pantools.Pantools.PATH_TO_THE_FIRST_SRA;
+import static nl.wur.bif.pantools.pantools.Pantools.PATH_TO_THE_SECOND_SRA;
+import static nl.wur.bif.pantools.pantools.Pantools.SHOW_KMERS;
+import static nl.wur.bif.pantools.pantools.Pantools.CLIPPING_STRINGENCY;
+import static nl.wur.bif.pantools.pantools.Pantools.OUTFORMAT;
+import static nl.wur.bif.pantools.pantools.Pantools.OUTPUT_PATH;
+import static nl.wur.bif.pantools.pantools.Pantools.THREADS;
+import static nl.wur.bif.pantools.pantools.Pantools.degenerate_label;
+import static nl.wur.bif.pantools.pantools.Pantools.genome_label;
+import static nl.wur.bif.pantools.pantools.Pantools.nucleotide_label;
+import static nl.wur.bif.pantools.pantools.Pantools.pangenome_label;
+import static nl.wur.bif.pantools.pantools.Pantools.sequence_label;
+import static nl.wur.bif.pantools.pangenome.Classification.genome_overview;
+import static nl.wur.bif.pantools.pantools.Pantools.stop_if_panproteome;
+import static nl.wur.bif.pantools.pantools.Pantools.ALIGNMENT_BOUND;
+import static nl.wur.bif.pantools.pantools.Pantools.ALIGNMENT_MODE;
+import static nl.wur.bif.pantools.pantools.Pantools.INDEX_DATABASE_PATH;
+import static nl.wur.bif.pantools.pantools.Pantools.INTERLEAVED;
+import static nl.wur.bif.pantools.pantools.Pantools.NUM_KMER_SAMPLES;
+import static nl.wur.bif.pantools.pantools.Pantools.MAX_ALIGNMENT_LENGTH;
+import static nl.wur.bif.pantools.pantools.Pantools.MAX_FRAGMENT_LENGTH;
+import static nl.wur.bif.pantools.pantools.Pantools.MIN_HIT_LENGTH;
+import static nl.wur.bif.pantools.pantools.Pantools.MIN_IDENTITY;
+import static nl.wur.bif.pantools.pantools.Pantools.MAX_NUM_LOCATIONS;
+import static nl.wur.bif.pantools.pantools.Pantools.SHOULDER;
+import static nl.wur.bif.pantools.pantools.Pantools.VERYSENSITIVE;
+import static nl.wur.bif.pantools.pantools.Pantools.WORKING_DIRECTORY;
+import static nl.wur.bif.pantools.pantools.Pantools.binary;
+import static nl.wur.bif.pantools.pantools.Pantools.check_if_file_exists;
+import static nl.wur.bif.pantools.pantools.Pantools.check_if_program_exists_stdout;
+import static nl.wur.bif.pantools.pantools.Pantools.connect_pangenome;
+import static nl.wur.bif.pantools.pantools.Pantools.create_pangenome_database;
+import static nl.wur.bif.pantools.pantools.Pantools.disconnect_pangenome;
+import static nl.wur.bif.pantools.pantools.Pantools.genomeDb;
+import static nl.wur.bif.pantools.pantools.Pantools.graphDb;
-import static pantools.Pantools.indexDb;
-import static pantools.Pantools.indexSc;
-import static pantools.Pantools.reverse_complement;
-import static pantools.Pantools.write_SB_to_file_full_path;
-import static pantools.Pantools.write_string_to_file_full_path;
+import static nl.wur.bif.pantools.pantools.Pantools.indexDb;
+import static nl.wur.bif.pantools.pantools.Pantools.indexSc;
+import static nl.wur.bif.pantools.pantools.Pantools.reverse_complement;
+import static nl.wur.bif.pantools.pantools.Pantools.write_SB_to_file_full_path;
+import static nl.wur.bif.pantools.pantools.Pantools.write_string_to_file_full_path;
-import static pantools.Pantools.report_number_of_threads;
-import static pantools.Pantools.target_genome;
-import static pantools.Pantools.adj_total_genomes;
-import static pangenome.Classification.get_rv_complement;
+import static nl.wur.bif.pantools.pantools.Pantools.report_number_of_threads;
+import static nl.wur.bif.pantools.pantools.Pantools.target_genome;
+import static nl.wur.bif.pantools.pantools.Pantools.adj_total_genomes;
+import static nl.wur.bif.pantools.pantools.Pantools.create_directory_in_DB;
+import static nl.wur.bif.pantools.pantools.Pantools.total_genomes;
/**
* Implements all the functionalities related to the sequence layer of the pangenome
@@ -2063,14 +2065,15 @@ public class GenomeLayer {
try (BufferedReader in = new BufferedReader(new FileReader(PATH_TO_THE_GENOMES_FILE))) { // first check if all files exist
for (int c = 0; in.ready();) {
line_counter ++;
- if (line_counter % 100 == 0 || line_counter < 10){
+ if (line_counter % 100 == 0 || line_counter < 10) {
System.out.print("\rVerifying if all input files exist: " + line_counter);
}
String line = in.readLine().trim();
new_genomes_file.append(line).append("\n");
String[] line_array = line.split(" ");
if (line_array.length != 1) {
- System.out.println(line_counter + " " + line + " is not allowed to have a space character!");
+ System.out.println("\nLine" + line_counter + ": " + line + " is not allowed to have a space character!\n"
+ + "Please include the full path to the genome fasta file\n");
System.exit(1);
}
boolean file_exists = check_if_file_exists(line);
@@ -2107,7 +2110,7 @@ public class GenomeLayer {
*/
public boolean check_if_nucleotide_sequence(String fasta_file) {
boolean correct = true;
- try (BufferedReader in = new BufferedReader(new FileReader(fasta_file))) {
+ try (BufferedReader in = new BufferedReader(new InputStreamReader(openTextFile(fasta_file)))) {
for (int c = 0; in.ready();) {
String line = in.readLine().trim();
if (line.startsWith(">")) {
@@ -2135,6 +2138,23 @@ public class GenomeLayer {
}
return correct;
}
+
+ /**
+ * Open a text file as an input stream. If the path ends with a .gz extension, it is assumed to be gzipped. If not,
+ * the file is assumed to be uncompressed.
+ * @param path path to (gzip-compressed) text file to open.
+ * @return input stream.
+ */
+ public InputStream openTextFile(String path) throws IOException {
+ // TODO: use Path for clarity instead of String
+ // TODO: make more robust, e.g. with library (commons compress?)
+
+ final InputStream stream = new FileInputStream(path);
+ if (path.toLowerCase().endsWith(".gz"))
+ return new GZIPInputStream(stream);
+
+ return stream;
+ }
/**
* Only KMC 2.3 and 3.0 (seem to) work. Stop when using another version
@@ -2289,24 +2309,21 @@ public class GenomeLayer {
}
/**
- * Retrieves some genomic regions from the genome database.
+ * Retrieves a selection of genomic regions from the genome database.
*
*/
public void retrieve_regions() {
- String[] fields;
- String line, out_file_name;
- StringBuilder seq;
- int genome, sequence, begin, end, num_regions = 0, proper_regions = 0;
+ int genome_nr, sequence_nr, begin, end, num_regions = 0, proper_regions = 0;
System.out.println("\nRetrieving genomic regions from the pangenome\n");
if (PATH_TO_THE_REGIONS_FILE == null) {
- System.out.println("PATH_TO_THE_REGIONS_FILE is empty.");
+ System.out.println("No --regions-file or -rf was provided.\n");
System.exit(1);
}
- seq = new StringBuilder();
+
try {
BufferedReader in = new BufferedReader(new FileReader(PATH_TO_THE_REGIONS_FILE));
- while ((line = in.readLine()) != null) {
- line = line.trim();
+ while (in.ready()) {
+ String line = in.readLine().trim();
if (line.equals("")) {
continue;
}
@@ -2314,60 +2331,159 @@ public class GenomeLayer {
}
in.close();
} catch (IOException e) {
- System.out.println(e.getMessage());
+ System.out.println("Failed to read: " + PATH_TO_THE_REGIONS_FILE + "\n");
System.exit(1);
}
+
connect_pangenome();
indexSc = new IndexScanner(indexDb);
K_SIZE = indexSc.get_K();
+ total_genomes = genomeDb.num_genomes;
genomeSc = new SequenceScanner(genomeDb, 1, 1, K_SIZE, indexSc.get_pre_len());
+ create_directory_in_DB("retrieval/genomes");
+ create_directory_in_DB("retrieval/regions");
+ int line_counter = 0;
+ StringBuilder log_builder = new StringBuilder("# split on semicolon\nline number;region;recognized as;successfull?\n");
+ String combi_output_file = WORKING_DIRECTORY + "retrieval/regions/regions_combined.fasta";
try (Transaction tx = graphDb.beginTx()) {
try (BufferedReader in = new BufferedReader(new FileReader(PATH_TO_THE_REGIONS_FILE))) {
- fields = PATH_TO_THE_REGIONS_FILE.split("\\/");
- out_file_name = OUTPUT_PATH + "/" + fields[fields.length - 1] + ".fasta";
- BufferedWriter out = new BufferedWriter(new FileWriter(out_file_name));
- while ((line = in.readLine()) != null) {
+ BufferedWriter out = new BufferedWriter(new FileWriter(combi_output_file)); // file to combine the sequences
+ while (in.ready()) {
+ String line = in.readLine().trim();
+ StringBuilder seq = new StringBuilder();
line = line.trim();
if (line.equals("")) {
continue;
}
- fields = line.trim().split("\\s");
- try {
- genome = Integer.parseInt(fields[0]);
- sequence = Integer.parseInt(fields[1]);
- begin = Integer.parseInt(fields[2]);
- end = Integer.parseInt(fields[3]);
- } catch(NumberFormatException e) {
- System.out.println("Unable to correctly retrieve four numbers in: " + line);
- out.close();
- continue;
- }
- if (genome >= 1 && genome <= genomeDb.num_genomes && sequence <= genomeDb.num_sequences[genome] &&
- begin >= 1 && end <= genomeDb.sequence_length[genome][sequence]) {
-
- proper_regions++;
- out.write(">genome" + genome + "_sequence" + sequence + "_" + begin + ":" + end + "\n");
- begin -= 1;
- end -= 1;
- seq.setLength(0);
- genomeSc.get_sub_sequence(seq, genome, sequence, begin, end - begin + 1, true);
- if (line.endsWith("-") || line.endsWith("rv")) { // manual only mentions '-'
- String rv_sequence = get_rv_complement(seq.toString());
- write_fasta(out, rv_sequence, 70);
- } else {
- write_fasta(out, seq.toString(), 70);
- }
- } else {
- System.out.println(line + "is not a proper coordinate!");
+ line_counter ++;
+ String region_file = WORKING_DIRECTORY + "retrieval/regions/region_" + line_counter + ".fasta";
+ String[] fields = line.trim().split("\\s");
+
+ log_builder.append(line_counter).append(";").append(line).append(";");
+ switch (fields.length) {
+ case 1: // a genome number is provided OR the row is not split correctly
+ log_builder.append("genome;");
+ try {
+ genome_nr = Integer.parseInt(fields[0]);
+ if (!rr_check_if_appropriate_genome(genome_nr, log_builder, line)){
+ continue;
+ }
+ log_builder.append("yes\n");
+ proper_regions ++;
+ write_genome_file(genome_nr);
+ } catch(NumberFormatException e) {
+ log_builder.append("no, cannot be converted a number\n");
+ System.out.println(line + " -> Unable to be converted to a genome number");
+ }
+ break;
+ case 2: // a genome number + sequence number is provided OR the row is not split correctly
+ log_builder.append("genome & sequence;");
+ try {
+ genome_nr = Integer.parseInt(fields[0]);
+ sequence_nr = Integer.parseInt(fields[1]);
+ if (!rr_check_if_appropriate_genome(genome_nr, log_builder, line)) {
+ continue;
+ }
+ if (!rr_check_if_appropriate_sequence(genome_nr, sequence_nr, log_builder, line)) {
+ continue;
+ }
+ log_builder.append("yes\n");
+ begin = 0;
+ end = (int) genomeDb.sequence_length[genome_nr][sequence_nr] - 1;
+ genomeSc.get_sub_sequence(seq, genome_nr, sequence_nr, begin, end - begin + 1, true);
+ out.write(">genome" + genome_nr + "_sequence" + sequence_nr + "\n");
+ write_fasta(out, seq.toString(), 80);
+
+ BufferedWriter region_writer = new BufferedWriter(new FileWriter(region_file));
+ region_writer.write(">genome" + genome_nr + "_sequence" + sequence_nr + "\n");
+ write_fasta(region_writer, seq.toString(), 80);
+ region_writer.close();
+ proper_regions ++;
+ } catch(NumberFormatException e) {
+ System.out.println(line + " -> Unable to be converted to a genome & sequence number");
+ }
+ break;
+ case 4: case 5:
+ // 4: a genome number + sequence number + region start + region end position are provided
+ // 5: all numbers AND the strand orientation is provided
+ log_builder.append("genome,sequence, start coordinate, stop coordinate");
+ if (fields.length == 5) {
+ log_builder.append(",strand");
+ }
+ log_builder.append(";");
+ try {
+ genome_nr = Integer.parseInt(fields[0]);
+ sequence_nr = Integer.parseInt(fields[1]);
+ begin = Integer.parseInt(fields[2]);
+ end = Integer.parseInt(fields[3]);
+ } catch(NumberFormatException e) {
+ System.out.println(line + " -> Unable to correctly retrieve four numbers (Integers)");
+ continue;
+ }
+
+ if (!rr_check_if_appropriate_genome(genome_nr, log_builder, line)) {
+ continue;
+ }
+ if (!rr_check_if_appropriate_sequence(genome_nr, sequence_nr, log_builder, line)) {
+ continue;
+ }
+
+ long last_sequence_position = genomeDb.sequence_length[genome_nr][sequence_nr];
+ if (begin < 1 || begin > last_sequence_position) {
+ System.out.println(line + " -> The start coordinate should be between 1 and " +
+ last_sequence_position + " for genome " + genome_nr);
+ log_builder.append("no, the start coordinate should be between 1 and ").append(last_sequence_position)
+ .append(" for genome ").append(genome_nr).append("\n");
+ continue;
+ }
+
+ if (end <= begin || end > genomeDb.sequence_length[genome_nr][sequence_nr]) {
+ System.out.println(line + " -> The end coordinate should be between " + (begin+1) + " and " + last_sequence_position
+ + " for genome " + genome_nr);
+ log_builder.append("no, the end coordinate should be between ").append((begin+1)).append(" and ")
+ .append(last_sequence_position).append(" for genome ").append(genome_nr).append("\n");
+ continue;
+ }
+
+ log_builder.append("yes\n");
+ proper_regions ++;
+ out.write(">genome" + genome_nr + "_sequence" + sequence_nr + "_" + begin + "_" + end + "\n");
+ begin -= 1;
+ end -= 1;
+
+ if (line.endsWith("-") || line.endsWith("rv")) { // manual only mentions '-'
+ genomeSc.get_sub_sequence(seq, genome_nr, sequence_nr, begin, end - begin + 1, false); // reverse complement
+ } else {
+ genomeSc.get_sub_sequence(seq, genome_nr, sequence_nr, begin, end - begin + 1, true);
+ }
+ write_fasta(out, seq.toString(), 80);
+ BufferedWriter region_writer = new BufferedWriter(new FileWriter(region_file));
+ region_writer.write(">genome" + genome_nr + "_sequence" + sequence_nr + "_" + (begin+1) + "_" + (end+1) + "\n");
+ write_fasta(region_writer, seq.toString(), 80);
+ region_writer.close();
+ break;
+
+ default:
+ log_builder.append("region not recognized\n");
+ break;
}
}
in.close();
out.close();
+ write_SB_to_file_in_DB(log_builder, "retrieval/regions/retrieve_regions.log");
+ if (proper_regions != num_regions) {
+ System.out.println("");
+ }
System.out.println(proper_regions + " out of " + num_regions + " genomic regions found and retrieved successfully!\n\n"
- + "Output written to:\n "
- + out_file_name + "\n" );
+ + "Log written to:\n"
+ + " " + WORKING_DIRECTORY + "retrieval/regions/retrieve_regions.log\n"
+ + "\n"
+ + "Output written to:\n"
+ + " " + WORKING_DIRECTORY + "retrieval/\n"
+ + " " + combi_output_file + "\n");
+
} catch (IOException ioe) {
- System.out.println("Failed to read file names!");
+ System.out.println("Failed to write: " + combi_output_file + "\n");
System.exit(1);
}
tx.success();
@@ -2375,10 +2491,72 @@ public class GenomeLayer {
disconnect_pangenome();
}
+ /**
+ * Part of the retrieve_regions function, check if the genome number is correct
+ * @param genome_nr
+ * @param log_builder
+ * @param line
+ * @return
+ */
+ public boolean rr_check_if_appropriate_genome(int genome_nr, StringBuilder log_builder, String line) {
+ if (genome_nr > total_genomes || genome_nr < 1) {
+ System.out.println(line + " -> Genome number should be between 1 and " + total_genomes);
+ log_builder.append("no, genome number should be between 1 and ").append(total_genomes).append("\n");
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ * Part of the retrieve_regions function, check if the sequence number is correct
+ * @param genome_nr
+ * @param sequence_nr
+ * @param log_builder
+ * @param line
+ * @return
+ */
+ public boolean rr_check_if_appropriate_sequence(int genome_nr, int sequence_nr, StringBuilder log_builder, String line) {
+ int allowed_sequence_nr = genomeDb.num_sequences[genome_nr];
+ if (sequence_nr > allowed_sequence_nr || sequence_nr < 1) {
+ log_builder.append("no, the sequence number should be between 1 and ").append(allowed_sequence_nr).append(" for genome ").append(genome_nr).append("\n");
+ System.out.println(line + " -> Sequence number should be between 1 and " + allowed_sequence_nr + " for genome " + genome_nr);
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ * @param genome
+ */
+ public void write_genome_file(int genome) {
+ StringBuilder seq = new StringBuilder();
+ try {
+ BufferedWriter out = new BufferedWriter(new FileWriter(WORKING_DIRECTORY + "/retrieval/genomes/genome_" + genome + ".fasta"));
+ for (int sequence = 1; sequence <= genomeDb.num_sequences[genome]; ++sequence) {
+ out.write(">" + genomeDb.sequence_titles[genome][sequence] + "\n");
+ int begin = 0;
+ int end = (int) genomeDb.sequence_length[genome][sequence] - 1;
+ genomeSc.get_sub_sequence(seq, genome, sequence, begin, end - begin + 1, true);
+ write_fasta(out, seq.toString(), 80);
+ seq.setLength(0);
+ }
+ out.close();
+ } catch (IOException e) {
+ System.out.println("Unable to write a genome to " + WORKING_DIRECTORY + "/retrieval/genome_" + genome + ".fasta\n");
+ System.exit(1);
+ }
+ }
+
/**
* Retrieves some complete genomes from the genome database.
*/
public void retrieve_genomes() {
+ System.out.println("\nAs of PanTools version 3.3, this functionality is integrated into 'retrieve_regions'.\n" +
+ "\nCheck the manual on how to run:\n\n" +
+ " pantools retrieve_regions --help\n");
+ System.exit(0);
+ /*
BufferedReader in;
BufferedWriter out;
String genome_number;
@@ -2444,6 +2622,7 @@ public class GenomeLayer {
}
System.out.println("\nGenomes were stored in "+ OUTPUT_PATH + "\n");
disconnect_pangenome();
+ */
}
/**
diff --git a/src/main/java/nl/wur/bif/pantools/pangenome/MultipleSequenceAlignment.java b/src/main/java/nl/wur/bif/pantools/pangenome/MultipleSequenceAlignment.java
new file mode 100644
index 0000000000000000000000000000000000000000..698fa82b922f1d739cf0f807204e4666fe143b0a
--- /dev/null
+++ b/src/main/java/nl/wur/bif/pantools/pangenome/MultipleSequenceAlignment.java
@@ -0,0 +1,2143 @@
+package nl.wur.bif.pantools.pangenome;
+
+import static nl.wur.bif.pantools.pantools.Pantools.*;
+import static nl.wur.bif.pantools.pangenome.create_skip_arrays.create_skip_arrays;
+
+import nl.wur.bif.pantools.index.IndexScanner;
+import nl.wur.bif.pantools.sequence.SequenceScanner;
+import org.neo4j.graphdb.*;
+
+import java.io.*;
+import java.util.*;
+import java.util.concurrent.*;
+import java.util.concurrent.atomic.AtomicInteger;
+import java.util.stream.Collectors;
+
+public class MultipleSequenceAlignment {
+ private String outDirMsa;
+ private final String method;
+ private final boolean variation;
+ private final boolean progress;
+ private final boolean hmFile;
+ private boolean alignProtein;
+ private boolean alignNucleotide;
+ private ArrayList<Node> hmNodeList;
+ private ArrayList<String> msaNames;
+
+ final private String[] COLORCODES = new String[]{"#fabebe","#bfef45","#42d4f4","#ffd8b1","#aaffc3","#fffac8","#e6beff","#469990","#e6194B","#f58231", "#ffe119",
+ "#3cb44b","#4363d8","#911eb4","#a9a9a9","#800000","#808000","#9A6324","#000075","#f032e6"};
+ final private String[] COLORNAMES = new String[]{"Pink","Lime","Cyan","Apricot","Mint","Beige","Lavender","Teal","Red","Orange","Yellow","Green","Blue","Purple","Grey","Maroon",
+ "Olive", "Brown", "Navy","Magenta"};
+
+ /**
+ *
+ * @param method can be either: "per_group", "multiple_groups"
+ * @param variation whether to use variation
+ * @param progress show progress
+ * @param hmFile if true, read from SELECTED_HMGROUPS as file; if false read from SELECTED_HMGROUPS as string of hm groups
+ */
+ public MultipleSequenceAlignment(String method, boolean variation, boolean progress, boolean hmFile) {
+ this.method = method;
+ this.variation = variation; //TODO: not yet implemented
+ if (LOG) {
+ this.progress = true;
+ } else {
+ this.progress = progress;
+ }
+ this.hmFile = hmFile;
+
+ prepareSequences();
+ }
+
+ /**
+ * Creates input files for multiple sequence alignment
+ */
+ private void prepareSequences() {
+ if (progress) {
+ System.out.println("\nMultiple sequence alignment for " + method + ".\n");
+ report_number_of_threads(true, true); // prints how many threads were selected by user
+ }
+
+ check_if_graphDb_is_available(); // starts up the graph database if needed
+
+ // get variables from pangenome & check that 1) it is a pangenome, 2) a grouping is set
+ try (Transaction tx = graphDb.beginTx()) { // start database transaction
+ Node pangenomeNode = graphDb.findNodes(pangenome_label).next();
+
+ check_if_panproteome(pangenomeNode); // sets PROTEOME boolean that controls functions, retrieves K_size & total_genomes
+ create_skip_arrays(false, true); // create skip array if --skip/-ref is provided by user
+ checkModeForMsa(); //not sure if needed here or for aligning only
+
+ if (variation) { //stop if no variants were added
+ checkIfAccessions();
+ }
+
+ if (PHENOTYPE != null) {
+ retrieve_phenotypes(); // Creates and fills geno_pheno_map and phenotype_map when a phenotype was provided by the user
+ }
+
+ check_current_grouping_version(); // check which version of homology grouping is active
+ if (grouping_version < 1) {
+ System.out.println("\nNo homology grouping is active\n");
+ System.exit(1);
+ }
+
+ tx.success(); // transaction successful, commit changes
+ } catch (NotFoundException nfe) {
+ System.out.println("Unable to start the pangenome database\n");
+ System.exit(1);
+ }
+
+ if (!PROTEOME) {
+ graphDb.shutdown();
+ connect_pangenome();
+ }
+
+ if (PHENOTYPE == null && progress) {
+ System.out.println("No --phenotype was provided, unable to find phenotype specific SNPs\n");
+ }
+
+ //prepare sequences //TODO create input should not be this amount of copying code, can be simplified
+ try (Transaction tx = graphDb.beginTx()) { // start database transaction
+ switch(method) { //set outDir + create input files + set msaNames
+ case "per_group":
+ this.outDirMsa = WORKING_DIRECTORY + "alignments/msa_" + method + "/grouping_v" + grouping_version + "/";
+ this.msaNames = createInputMsaPerGroup(false);
+ break;
+ case "multiple_groups":
+ this.outDirMsa = WORKING_DIRECTORY + "alignments/msa_" + method + "/grouping_v" + grouping_version + "/";
+ this.msaNames = createInputMsaMultipleGroups();
+ break;
+ case "regions":
+ this.outDirMsa = WORKING_DIRECTORY + "alignments/msa_" + method + "/";
+ this.msaNames = createInputMsaRegions();
+ break;
+ case "functions":
+ this.outDirMsa = WORKING_DIRECTORY + "alignments/msa_" + method + "/";
+ this.msaNames = createInputMsaFunctions();
+ break;
+ default:
+ System.out.println("Did not recognise the following MSA method: " + method);
+ System.exit(1);
+ }
+
+ tx.success(); // transaction successful, commit changes
+ }
+ }
+
+ /**
+ * Mode align nucleotide, protein or both type of sequences
+ * --mode fast, do not create phylogenies
+ * --variants, use variants (still TODO)
+ * Mode can be set to NUCLEOTIDE, PROTEIN or BOTH
+ * The original mode options were 0,1,2. 0 was both, 1 was protein, 2 was nucleotide
+ */
+ private void checkModeForMsa() {
+ if (FAST) { // using --mode fast was the old argument to skip tree constructions. New argument is --fast
+ if (progress) {
+ System.out.println("\r--fast was included: not creating any phylogenies.");
+ }
+ FAST = true;
+ }
+
+ if (PROTEOME) {
+ this.alignProtein = true;
+ this.alignNucleotide = false;
+ if (progress) {
+ System.out.println("\rRunning against a proteome. Only aligning protein sequences.");
+ }
+// } else if (VARIANTS) { //TODO not the same as variants yet
+// if (progress) {
+// System.out.println("\rRunning with variants. Only aligning nucleotide sequences.");
+// }
+// this.alignProtein = false;
+// this.alignNucleotide = true;
+ } else {
+ if (Mode.contains("NUCLEOTIDE")) {
+ if (progress) {
+ System.out.println("\rNucleotide mode selected. Only aligning nucleotide sequences.");
+ }
+ this.alignProtein = false;
+ this.alignNucleotide = true;
+ } else if (Mode.contains("PROTEIN")) {
+ if (progress) {
+ System.out.println("\rProtein mode selected. Only aligning protein sequences.");
+ }
+ this.alignProtein = true;
+ this.alignNucleotide = false;
+ } else if (Mode.equals("0")) { // nothing was included
+ if (progress) {
+ System.out.println("\rNo --mode protein or nucleotide was selected. Aligning both types of sequences, if applicable.");
+ }
+ this.alignProtein = true;
+ this.alignNucleotide = true;
+ } else {
+ this.alignProtein = true;
+ this.alignNucleotide = true;
+ }
+ }
+ }
+
+ /**
+ * Checks if this pangenome contains accessions (variants in VCF format) that were added with add_accessions; if not, exit
+ */
+ private void checkIfAccessions() {
+ try{
+ String type = (String) graphDb.findNodes(accession_label).next().getProperty("type");
+ assert type.equals("VCF");
+ } catch (NotFoundException | NoSuchElementException nee) {
+ System.out.println("\nNo variants were found in this pangenome. Please run add_accessions first.\n");
+ System.exit(1);
+ } catch (AssertionError e) {
+ System.out.println("\nSomehow variants were found, but they appear to not to be in VCF format.\n");
+ System.exit(1);
+ }
+ }
+
+ /**
+ * Reads /skipped_genomes.info and checks if this is correct with current skip array
+ * @param inputPath path to location of skipped_genomes.info
+ * @return boolean if skipping is correct
+ */
+ private boolean checkIfSkippingIsCorrect(String inputPath) {
+ boolean correctSkipping = false;
+
+ String[] stringSkipArray = new String[skip_array.length];
+ for (int i = 0; i < skip_array.length; i++) {
+ if (skip_array[i]) {
+ stringSkipArray[i] = "T";
+ } else {
+ stringSkipArray[i] = "F";
+ }
+ }
+ String skipArrayString = String.join(",", stringSkipArray);
+
+ try (BufferedReader file = new BufferedReader(new FileReader(inputPath + "/skipped_genomes.info"))) {
+ int counter = 1;
+ while (file.ready()) {
+ if (counter > 1) {
+ continue;
+ }
+ String line = file.readLine().trim();
+ if (line.equals(skipArrayString)) {
+ correctSkipping = true;
+ }
+ counter++;
+ }
+ } catch (FileNotFoundException e) { //first time running this function
+ correctSkipping = true;
+ write_string_to_file_full_path(skipArrayString, inputPath + "/skipped_genomes.info");
+ } catch (IOException e) {
+ e.printStackTrace();
+ System.exit(1);
+ }
+ return correctSkipping;
+ }
+
+ /**
+ * Prepare several input files for the input homology groups
+ * @param ignoreUniqueLimit, still write unique sequences when true
+ * @return updated list where groups with 1 member are removed
+ */
+ private ArrayList<String> createInputMsaPerGroup(boolean ignoreUniqueLimit) {
+ retrieveHmGroups(); //sets hmNodeList
+ ArrayList<String> updatedHmNodeList = new ArrayList<>(); // exclude homology groups with only 1 sequence
+ long totalHmgroups = hmNodeList.size();
+ int groupCounter = 0, notUniqueCounter = 0;
+ if (progress) {
+ System.out.println();
+ }
+ int printThreshold = 100;
+ if (totalHmgroups < 500) {
+ printThreshold = 10;
+ }
+
+ for (Node hmNode : hmNodeList) {
+ groupCounter++;
+ if ((groupCounter % printThreshold == 0 || groupCounter == totalHmgroups || groupCounter < 50) && progress) {
+ System.out.print("\rCreating input sequences: " + groupCounter + "/" + totalHmgroups);
+ }
+
+ checkIfHmIsCorrectGrouping(hmNode);
+
+ String path = outDirMsa + hmNode.getId();
+ String inputPath = path + "/input/";
+ String outputPath = path + "/output/";
+ new File(inputPath).mkdirs(); // create directory
+ new File(outputPath).mkdirs(); // create directory
+
+ if (!checkIfSkippingIsCorrect(inputPath)) {
+ if (LOG) {
+ System.out.println("Skipping is incorrect, removing old files.");
+ }
+ delete_directory(inputPath);
+ delete_directory(outputPath);
+ new File(inputPath).mkdirs(); // create directory
+ new File(outputPath).mkdirs(); // create directory
+ }
+
+ boolean passProt = check_if_file_exists(inputPath + "prot.fasta");
+ boolean passNuc = check_if_file_exists(inputPath + "nuc.fasta");
+ if (!alignNucleotide) {
+ passNuc = true;
+ }
+ if (!alignProtein) {
+ passProt = true;
+ }
+ if (passProt && passNuc) {
+ updatedHmNodeList.add(Long.toString(hmNode.getId()));
+ continue;
+ }
+
+ int numMembers = (int) hmNode.getProperty("num_members"); // number of sequences in group
+ if (numMembers == 1 && !ignoreUniqueLimit) { // do not create files for groups with 1 sequence
+ SELECTED_HMGROUPS = SELECTED_HMGROUPS.replace(hmNode.getId() +",", "");
+ continue;
+ }
+ updatedHmNodeList.add(Long.toString(hmNode.getId()));
+ notUniqueCounter++;
+
+ writeMsaInputFiles(hmNode, inputPath); //
+ }
+
+ int totalNonUniqueHms = countNotUniqueHmGroups();
+ if (totalNonUniqueHms <= notUniqueCounter && alignNucleotide && alignProtein) {
+ // this file is used to skip this function completely
+ write_string_to_file_full_path("all sequences were extracted", outDirMsa + "extract_sequences_done");
+ }
+
+ if (progress) {
+ if (updatedHmNodeList.size() < hmNodeList.size()) {
+ System.out.println("\rNumber of selected groups lowered from " + hmNodeList.size() + " to " + updatedHmNodeList.size() +
+ " due having only 1 sequence in the group");
+ } else {
+ System.out.println();
+ }
+ }
+ return updatedHmNodeList;
+ }
+
+ /**
+ * Creates input for msa_of_multiple_groups
+ * @return name of groups that are aligned (currently a list consisting of one string)
+ */
+ private ArrayList<String> createInputMsaMultipleGroups() {
+ retrieveHmGroups(); //sets hmNodeList
+ ArrayList<String> hmStringList = new ArrayList<>();
+ ArrayList<String> outputHmStringList = new ArrayList<>();
+
+ for (Node hmNode : hmNodeList) {
+ checkIfHmIsCorrectGrouping(hmNode);
+ hmStringList.add(String.valueOf(hmNode.getId()));
+ }
+ String hmString = String.join("_", hmStringList);
+ outputHmStringList.add(hmString);
+ if (progress) {
+ System.out.println();
+ }
+
+ String path = outDirMsa + hmString;
+ String inputPath = path + "/input/";
+ String outputPath = path + "/output/";
+ new File(inputPath).mkdirs(); // create directory
+ new File(outputPath).mkdirs(); // create directory
+
+ if (!checkIfSkippingIsCorrect(inputPath)) {
+ if (LOG) {
+ System.out.println("Skipping is incorrect, removing old files.");
+ }
+ delete_directory(inputPath);
+ delete_directory(outputPath);
+ new File(inputPath).mkdirs(); // create directory
+ new File(outputPath).mkdirs(); // create directory
+ }
+
+ boolean passProt = check_if_file_exists(inputPath + "prot.fasta");
+ boolean passNuc = check_if_file_exists(inputPath + "nuc.fasta");
+ if (!alignNucleotide) {
+ passNuc = true;
+ }
+ if (!alignProtein) {
+ passProt = true;
+ }
+ if (passProt && passNuc) {
+ return outputHmStringList;
+ }
+
+ writeMultiMsaInputFiles(hmNodeList, inputPath);
+
+ return outputHmStringList;
+ }
+
+ /**
+ * Create input for MSA of regions
+ * @return name of the input file that is used as identifier for the alignment (list of one currently)
+ */
+ private ArrayList<String> createInputMsaRegions() {
+ if (target_genome != null || skip_genomes != null) { //stop if --ref or --skip is used
+ System.out.println("'--method regions' is unable to use --reference/-ref or --skip. You should exclude these genomes from your --regions-file\n");
+ System.exit(1);
+ }
+ if (alignProtein && !alignNucleotide) { //stop if only protein should be aligned
+ System.out.println("Cannot run MSA for regions with protein sequence.");
+ System.exit(1);
+ }
+
+ //making sure only nucleotide sequences are used
+ this.alignProtein = false;
+ Mode = "NUCLEOTIDE";
+
+ //read regions (TODO put this in a util class)
+ String[] regionsToSearch = Classification.read_regions_file();
+
+ //create name for region (basename of file currently)
+ ArrayList<String> outputRegionsStringList = new ArrayList<>();
+ String[] regionsFileNameSplit = PATH_TO_THE_REGIONS_FILE.replace(".", "_").split("/");
+ String regionsName = regionsFileNameSplit[regionsFileNameSplit.length - 1];
+ outputRegionsStringList.add(regionsName);
+
+ String path = outDirMsa + regionsName;
+ String inputPath = path + "/input/";
+ String outputPath = path + "/output/";
+
+ new File(inputPath).mkdirs(); // create directory
+ new File(outputPath).mkdirs(); // create directory
+ writeRegionsMsaInputFiles(regionsToSearch, inputPath);
+
+ return outputRegionsStringList;
+ }
+
+ /**
+ * Creates input for MSA of functions
+ * @return list with names of functions that are aligned
+ */
+ private ArrayList<String> createInputMsaFunctions() {
+ if (SELECTED_NAME == null) { //TODO use all functions
+ System.out.println("No functions selected. Please use --name with a comma-separated list of function names.");
+ System.exit(1);
+ }
+
+ ArrayList<String> outputFunctionsStringList = new ArrayList<>();
+ ArrayList<Node> functionNodeList = Classification.find_functional_annotation_node();
+
+ long totalFunctions = functionNodeList.size();
+ int functionCounter = 0;
+ int printThreshold = 100;
+ if (totalFunctions < 500) {
+ printThreshold = 10;
+ }
+
+ for (Node functionNode : functionNodeList) {
+ functionCounter++;
+ if ((functionCounter % printThreshold == 0 || functionCounter == totalFunctions || functionCounter < 50) && progress) {
+ System.out.print("\rCreating input sequences: " + functionCounter + "/" + totalFunctions);
+ }
+
+ String function = (String) functionNode.getProperty("id");
+ function = function.replace(":", "");
+
+ String path = outDirMsa + function;
+ String inputPath = path + "/input/";
+ String outputPath = path + "/output/";
+ new File(inputPath).mkdirs(); // create directory
+ new File(outputPath).mkdirs(); // create directory
+
+ if (!checkIfSkippingIsCorrect(inputPath)) {
+ if (LOG) {
+ System.out.println("Skipping is incorrect, removing old files.");
+ }
+ delete_directory(inputPath);
+ delete_directory(outputPath);
+ new File(inputPath).mkdirs(); // create directory
+ new File(outputPath).mkdirs(); // create directory
+ }
+
+ boolean passProt = check_if_file_exists(inputPath + "prot.fasta");
+ boolean passNuc = check_if_file_exists(inputPath + "nuc.fasta");
+ if (!alignNucleotide) {
+ passNuc = true;
+ }
+ if (!alignProtein) {
+ passProt = true;
+ }
+ if (passProt && passNuc) {
+ outputFunctionsStringList.add(function);
+ continue;
+ }
+ writeFunctionsMsaInputFiles(functionNode, inputPath);
+ outputFunctionsStringList.add(function);
+ }
+
+ return outputFunctionsStringList;
+ }
+
+ /**
+ * Retrieves the names of homology groups and puts them in hmNodeList (private variable to this class)
+ *
+ * Three options
+ * 1. Read the input file given through -hm
+ * 2. Read homology group identifiers from the 'SELECTED_HMGROUPS' string
+ * 3. Retrieve all homology groups with more than 1 sequence
+ *
+ * NB: hmFile means whether or not to read from a file
+ */
+ private void retrieveHmGroups() {
+ if (LOG) {
+ System.out.println("SELECTED_HMGROUPS: " + SELECTED_HMGROUPS);
+ System.out.println("hmFile: " + hmFile);
+ }
+
+ if (SELECTED_HMGROUPS != null && hmFile) { // 1. read input file
+ hmNodeList = readHmGroupInputFile();
+ } else if (SELECTED_HMGROUPS != null && !hmFile) { // 2. hmgroup ids are placed in the SELECTED_HMGROUPS string, not in a file
+ hmNodeList = retrieveHmGroupsOfMatchingInputString();
+ } else { // 3. if no --homology-groups are given, retrieve all of them
+ hmNodeList = retrieveAllHmGroups();
+ }
+ }
+
+ /**
+ * Reads homology group names from an input file
+ * @return list of homology group nodes that are in the input file
+ */
+ private ArrayList<Node> readHmGroupInputFile() {
+ String hmGroupStr = "";
+ String[] hmGroupArray;
+ if (SELECTED_HMGROUPS == null) {
+ System.out.println("\nNo homology groups were provided via --homology-groups/-hm.\n");
+ System.exit(1);
+ }
+
+ try (BufferedReader in = new BufferedReader(new FileReader(SELECTED_HMGROUPS))) {
+ String tempHmgroupStr = "";
+ for (int c = 0; in.ready();) {
+ hmGroupStr = in.readLine().trim();
+ if (hmGroupStr.equals("")) {
+ continue;
+ } else if (hmGroupStr.startsWith("Genome")) {
+ // do nothing
+ } else if (!hmGroupStr.contains(" genomes") && !hmGroupStr.contains("Phenotype") && !hmGroupStr.contains("#")) { // accessory hmgroups were provided
+ tempHmgroupStr += hmGroupStr + ", ";
+ }
+ }
+ tempHmgroupStr = tempHmgroupStr.replaceFirst(".$","").replaceFirst(".$","");
+ hmGroupStr = tempHmgroupStr;
+ if (hmGroupStr.contains("/")) {
+ System.out.println("Homology group input not correctly formatted");
+ System.exit(1);
+ }
+ } catch (IOException ioe) {
+ System.out.println("\nUnable to open the groups provided via --homology-groups or -hm. Stopping now\n");
+ System.exit(1);
+ }
+ hmGroupStr = hmGroupStr.replace(", ",",").replace(" ,",",");
+ if (hmGroupStr.equals("")) {
+ System.out.println("\nThere seems to be no identifiers in the provided --homology-groups / -hm file\n");
+ System.exit(1);
+ }
+ if (hmGroupStr.endsWith(",")) {
+ hmGroupStr = hmGroupStr.replaceFirst(".$","");
+ }
+
+ if (hmGroupStr.contains(", ")) {
+ hmGroupArray = hmGroupStr.split(", ");
+ } else if (hmGroupStr.contains(",")) {
+ hmGroupArray = hmGroupStr.split(",");
+ } else {
+ hmGroupArray = new String[]{hmGroupStr};
+ }
+
+ ArrayList<Node> hmNodeList = new ArrayList<>();
+ for (String hmGroup : hmGroupArray) {
+ long hmNodeId = Long.parseLong(hmGroup);
+ Node hmNode= graphDb.getNodeById(hmNodeId);
+ hmNodeList.add(hmNode);
+ }
+ return hmNodeList;
+ }
+
+ /**
+ * Get all currently active homology groups
+ * @return list of homology group nodes that have more than one member
+ */
+ private ArrayList<Node> retrieveAllHmGroups() {
+ ArrayList<Node> hmList = new ArrayList<>();
+ if (progress) {
+ System.out.print("\rNo homology groups were provided via --homology-groups or -hm, using all ");
+ }
+ ResourceIterator<Node> hmNodes = graphDb.findNodes(homology_group_label);
+ int counter = 0;
+ while (hmNodes.hasNext()) {
+ Node hmNode = hmNodes.next();
+ if (counter > 5) {
+ //continue;
+ }
+ int numMembers = (int) hmNode.getProperty("num_members");
+ if (numMembers == 1) {
+ continue;
+ }
+ hmList.add(hmNode);
+ counter ++;
+ }
+ if (progress) {
+ System.out.println(hmList.size() + " groups with more than one sequence");
+ }
+ return hmList;
+ }
+
+ /**
+ * Get all homology group identifiers are given in the SELECTED_HMGROUP string (, not in a file)
+ * @return list of homology group nodes that are in SELECTED_HMGROUP
+ */
+ private ArrayList<Node> retrieveHmGroupsOfMatchingInputString() {
+ ArrayList<Node> allHmList = new ArrayList<>();
+ String[] groupsArray = SELECTED_HMGROUPS.split(",");
+ for (String groupIdStr : groupsArray) {
+ long groupId = Long.parseLong(groupIdStr);
+ Node hmNode = graphDb.getNodeById(groupId);
+ test_if_correct_label(hmNode, homology_group_label, true);
+ allHmList.add(hmNode);
+ }
+ return allHmList;
+ }
+
+ /**
+ * Check if node has 'homology_group' label
+ * @param hmNode node to be checked
+ *
+ * NB: does not return a boolean, but will exit if incorrect grouping
+ */
+ private void checkIfHmIsCorrectGrouping(Node hmNode) {
+ boolean correct = test_if_correct_label(hmNode, homology_group_label, false);
+ if (!correct) {
+ correct = test_if_correct_label(hmNode, inactive_homology_group_label, false);
+ if (!correct) {
+ System.out.println(hmNode + " is not an homology group");
+ } else {
+ int groupVersion = (int) hmNode.getProperty("group_version");
+ System.out.println("\n" + hmNode + " is an inactive homology group! Grouping " + grouping_version +
+ " is active while this homology group is version " + groupVersion);
+ }
+ System.exit(1);
+ }
+ }
+
+ /**
+ * Counts the number of not unique homology groups of all homology groups
+ * @return integer of the number of not unique homology groups
+ */
+ private int countNotUniqueHmGroups() {
+ int counter = 0;
+ ResourceIterator<Node> hmNodes = graphDb.findNodes(homology_group_label);
+ while (hmNodes.hasNext()) {
+ Node hmNode = hmNodes.next();
+ int numMembers = (int) hmNode.getProperty("num_members");
+ if (numMembers == 1) {
+ continue;
+ }
+ counter++;
+ }
+ return counter;
+ }
+
+ /**
+ * Writes several input files for the input homology groups
+ * prot.fasta, protein sequences (if alignProtein)
+ * nuc.fasta, nucleotide sequences (if alignNucleotide)
+ * genome_order.info, list of genome number and identifiers
+ * sequences.info, relevant information for user
+ * skipped_genomes.info, skip array for current alignment
+ *
+ * @param hmNode node for which to write input files
+ * @param inputPath path to where to write input files
+ */
+ private void writeMsaInputFiles(Node hmNode, String inputPath) {
+ StringBuilder proteinFastaFile = new StringBuilder();
+ StringBuilder nucleotideFastaFile = new StringBuilder();
+ StringBuilder genomeNrsBuilder = new StringBuilder();
+ ArrayList<Integer> presentGenomes = new ArrayList<>();
+ StringBuilder infoBuilderHeader = new StringBuilder("#Information about sequences in homology group\n#Occurance in genomes\n");
+ StringBuilder infoBuilder = new StringBuilder("#genome, gene/mRNA name, mRNA identifier, node identifier, address, strand\n");
+ if (PROTEOME) {
+ infoBuilder = new StringBuilder("#genome, protein identifier, protein node id\n");
+ }
+ int[] copies = new int[total_genomes];
+
+ //needed to get the sequence with getSequence(mrnaNode)
+ if (!PROTEOME) {
+ indexSc = new IndexScanner(indexDb);
+ genomeSc = new SequenceScanner(genomeDb, 1, 1, K_SIZE, indexSc.get_pre_len());
+ }
+
+ Iterable<Relationship> allRelations = hmNode.getRelationships(RelTypes.has_homolog);
+ for (Relationship rel : allRelations) {
+ Node mrnaNode = rel.getEndNode();
+ String mrnaProtein = getSequence(mrnaNode, "protein");
+ mrnaProtein = splitSeqOnLength(mrnaProtein, 80);
+ int genomeNr = (int) mrnaNode.getProperty("genome");
+ if (skip_array[genomeNr-1]) {
+ continue;
+ }
+ copies[genomeNr-1] += 1;
+ int copyNr = copies[genomeNr-1];
+ presentGenomes.add(genomeNr);
+ String proteinId = (String) mrnaNode.getProperty("protein_ID");
+ if (proteinId.contains(":") || proteinId.contains(";") || proteinId.contains("|")) { // not allowed in newick format
+ proteinId = proteinId
+ .replace(":",".")
+ .replace(";",".")
+ .replace("|",".");
+ }
+ String newId = genomeNr + "_" + copyNr + "_" + proteinId;
+
+ long mrnaNodeId = mrnaNode.getId();
+ genomeNrsBuilder.append(genomeNr).append(",").append(newId).append("\n");
+ if (!PROTEOME) {
+ int[] address = (int[]) mrnaNode.getProperty("address");
+ String strand = (String) mrnaNode.getProperty("strand");
+ String name = (String) mrnaNode.getProperty("name");
+ if (name.equals("")) {
+ name = "-";
+ }
+
+ String nucSequence = getSequence(mrnaNode, "CDS"); //can be mRNA as well, but then no protein can be given
+ nucSequence = splitSeqOnLength(nucSequence, 80);
+
+ if (alignProtein) {
+ proteinFastaFile.append(">").append(newId).append(" ").append(address[0]).append("_").append(address[1]).append("_").append(address[2]).append("_").append(address[3]).append("\n")
+ .append(mrnaProtein).append("\n");
+ }
+ if (alignNucleotide) {
+ nucleotideFastaFile.append(">").append(newId).append(" ").append(address[0]).append("_").append(address[1]).append("_").append(address[2]).append("_").append(address[3]).append("\n")
+ .append(nucSequence).append("\n");
+ }
+ infoBuilder.append(genomeNr).append(", ").append(name).append(", ").append(newId).append(", ").append(mrnaNodeId).append(", ")
+ .append(address[0]).append(" ").append(address[1]).append(" ").append(address[2]).append(" ").append(address[3]).append(", ").append(strand).append("\n");
+ } else {
+ proteinFastaFile.append(">").append(newId).append("\n").append(mrnaProtein).append("\n"); //we could check, but this is always alignProtein = true
+ infoBuilder.append(genomeNr).append(", ").append(newId).append(mrnaNodeId).append(", ").append("\n");
+ }
+
+ if (variation) {
+ //get nucleotide sequences of accessions
+ System.out.println("Not yet implemented");
+ System.exit(1);
+ }
+
+ }
+
+ TreeSet<Integer> absent = getMissingGenomesInArrayList(presentGenomes);
+ String genomeFreqs = determineFrequencyListInt(presentGenomes);
+ infoBuilderHeader.append("Present: ").append(genomeFreqs)
+ .append("\nAbsent: ").append(absent.toString().replace("[","").replace("]","").replace(",","")).append("\n\n");
+ write_SB_to_file_full_path(infoBuilderHeader.append(infoBuilder), inputPath + "sequences.info");
+ if (alignProtein) {
+ write_SB_to_file_full_path(proteinFastaFile, inputPath + "prot.fasta");
+ }
+ if (alignNucleotide) {
+ write_SB_to_file_full_path(nucleotideFastaFile, inputPath + "nuc.fasta");
+ }
+ write_SB_to_file_full_path(genomeNrsBuilder, inputPath + "genome_order.info");
+ }
+
+ /**
+ * Writes several input files for the input homology groups
+ * prot.fasta, protein sequences (if alignProtein)
+ * nuc.fasta, nucleotide sequences (if alignNucleotide)
+ * genome_order.info, list of genome number and identifiers
+ * itol_tree_template_groups.txt, iTOL templates for input data
+ * sequences.info, relevant information for user
+ * skipped_genomes.info, skip array for current alignment
+ *
+ * @param hmNodeList list of nodes for which to write input files
+ * @param inputPath path to where to write input files
+ */
+ private void writeMultiMsaInputFiles(ArrayList<Node> hmNodeList, String inputPath) {
+ StringBuilder protFasta = new StringBuilder();
+ StringBuilder nucFasta = new StringBuilder();
+ StringBuilder genomeOrder = new StringBuilder();
+ StringBuilder itolHmTemplate = new StringBuilder("DATASET_COLORSTRIP\nSEPARATOR COMMA\nDATASET_LABEL,label1\nCOLOR,#ff0000\n"
+ + "STRIP_WIDTH,40\nSHOW_INTERNAL,1\n\nDATA\n");
+ StringBuilder itolPhenoTemplate = new StringBuilder("DATASET_COLORSTRIP\nSEPARATOR COMMA\nDATASET_LABEL,label1\nCOLOR,#ff0000\n"
+ + "STRIP_WIDTH,40\nSHOW_INTERNAL,1\n\nDATA\n");
+ StringBuilder infoBuilder = new StringBuilder("#Information about sequences in homology group\n#Occurance in genomes\n");
+ StringBuilder infoBuilderPart2 = new StringBuilder("##genome, mRNA name, mRNA id, node id, address, gene length, gene copy number within the group\n");
+ if (PROTEOME) {
+ infoBuilderPart2 = new StringBuilder("##genome, protein id, node id, protein length, protein copy number within the group\n");
+ }
+ ArrayList<Integer> protLengths = new ArrayList<>();
+ ArrayList<Integer> nucLengths = new ArrayList<>();
+ HashMap<String, Integer> phenoCounterMap = new HashMap<>();
+ ArrayList<String> phenotypesList = new ArrayList<>();
+ int totalSequences = 0, totalGroups = 0;
+ AtomicInteger phenotypeCounter = new AtomicInteger(0);
+ StringBuilder hmColorInfo = new StringBuilder("#Colors used for homology groups\n\n");
+
+ //needed to get the sequence with getSequence(mrnNode)
+ if (!PROTEOME) {
+ indexSc = new IndexScanner(indexDb);
+ genomeSc = new SequenceScanner(genomeDb, 1, 1, K_SIZE, indexSc.get_pre_len());
+ }
+
+ try (Transaction tx = graphDb.beginTx()) { // start database transaction
+ for (Node hmNode : hmNodeList) {
+ totalGroups ++;
+ long hmNodeId = hmNode.getId();
+ String color = COLORCODES[totalGroups];
+ ArrayList<Integer> presentGenomes = new ArrayList<>();
+ int[] genomeCounts = new int[total_genomes];
+
+ hmColorInfo.append("#").append(hmNodeId).append(" ").append(color).append(" ").append(COLORNAMES[totalGroups]).append("\n");
+ infoBuilderPart2.append("#").append(hmNodeId).append("\n");
+
+ for (Relationship rel : hmNode.getRelationships()) {
+ Node mrnaNode = rel.getEndNode();
+ int genomeNr = (int) mrnaNode.getProperty("genome");
+ String proteinId = (String) mrnaNode.getProperty("protein_ID");
+ long mrnaNodeId = mrnaNode.getId();
+
+ if (skip_array[genomeNr-1]) {
+ continue;
+ }
+ genomeCounts[genomeNr-1] += 1;
+ int copyNr = genomeCounts[genomeNr-1];
+ totalSequences ++;
+
+ if (progress) {
+ System.out.print("\rGathering sequences: " + totalGroups + "/" + hmNodeList.size() + " homology groups. " + totalSequences + " sequences");
+ }
+
+ if (proteinId.contains(":") || proteinId.contains(";") || proteinId.contains("|")) { // not allowed in newick format
+ proteinId = proteinId
+ .replace(":",".")
+ .replace(";",".")
+ .replace("|",".");
+ }
+ String newId = genomeNr + "_" + copyNr + "_" + proteinId;
+
+ genomeOrder.append(genomeNr).append(",").append(newId).append("\n");
+ itolHmTemplate.append(genomeNr).append("_").append(newId).append(",").append(color).append("\n");
+
+ if (alignProtein) {
+ String proteinSequence = getSequence(mrnaNode, "protein");
+ proteinSequence = splitSeqOnLength(proteinSequence, 80);
+ protLengths.add(proteinSequence.length());
+ protFasta.append(">").append(newId).append("\n").append(proteinSequence).append("\n");
+ infoBuilderPart2.append(genomeNr).append(", ").append(newId).append(", ").append(mrnaNodeId).append(", ")
+ .append(proteinSequence.length()).append(", ").append(copyNr).append("\n");
+ }
+ if (alignNucleotide) {
+ String mrnaName = (String) mrnaNode.getProperty("name");
+ if (mrnaName.equals("-")) {
+ mrnaName = hmNodeId + "";
+ }
+ int[] address = (int[]) mrnaNode.getProperty("address");
+
+ String mrnaSequence = getSequence(mrnaNode, "CDS");
+ mrnaSequence = splitSeqOnLength(mrnaSequence, 80);
+ nucLengths.add(mrnaSequence.length());
+ nucFasta.append(">").append(newId).append("\n").append(mrnaSequence).append("\n");
+ infoBuilderPart2.append(genomeNr).append(", ").append(mrnaName).append(", ").append(newId).append(", ").append(mrnaNodeId)
+ .append(", ").append(genomeNr).append(" ").append(address[1]).append(" ").append(address[2]).append(" ").append(address[3]).append(", ")
+ .append(mrnaSequence.length()).append(", ").append(copyNr).append("\n");
+ }
+
+ appendMsaMultiPhenoTemplate(genomeNr, phenoCounterMap, phenotypeCounter, phenotypesList, itolPhenoTemplate, newId);
+ }
+ String genomeFreqs = Classification.determine_frequency_list_int(presentGenomes);
+ TreeSet<Integer> absent = getMissingGenomesInArrayList(presentGenomes);
+ infoBuilder.append("#").append(hmNodeId).append("\nPresent: ").append(genomeFreqs)
+ .append("\nAbsent: ").append(absent).append("\n\n");
+ infoBuilderPart2.append("\n");
+ }
+ tx.success(); // transaction successful, commit changes
+ }
+ if (progress) {
+ System.out.println();
+ }
+ new File(inputPath + "similarity_identity").mkdirs(); // create directory
+ new File(inputPath + "var_inf_positions").mkdirs(); // create directory
+
+ write_string_to_file_full_path(genomeOrder.toString(), inputPath + "genome_order.info");
+ write_SB_to_file_full_path(hmColorInfo.append(itolHmTemplate), inputPath + "itol_tree_template_groups.txt");
+ createMsaMultiPhenoTemplate(phenotypesList, itolPhenoTemplate, inputPath);
+
+ if (alignProtein) {
+ write_string_to_file_full_path(protFasta.toString(), inputPath + "prot.fasta");
+ String protLengthsStr = Classification.determine_frequency_list_int(protLengths);
+ write_string_to_file_full_path("Protein lengths: " + protLengthsStr + "\n\n"
+ + infoBuilder + infoBuilderPart2, inputPath + "prot_sequences.info");
+ }
+ if (alignNucleotide) {
+ write_string_to_file_full_path(nucFasta.toString(), inputPath + "nuc.fasta");
+ String nucLengthsStr = Classification.determine_frequency_list_int(nucLengths);
+ write_string_to_file_full_path("Nucleotide lengths: " + nucLengthsStr + "\n\n"
+ + infoBuilder + infoBuilderPart2, inputPath + "nuc_sequences.info");
+ }
+ }
+
+ /**
+ * Writes several input files for the input homology groups
+ * nuc.fasta, nucleotide sequences
+ * genome_order.info, list of genome number and identifiers
+ *
+ * @param regionsToSearch regions to search for
+ * @param inputPath path to where to write input files
+ */
+ private void writeRegionsMsaInputFiles(String[] regionsToSearch, String inputPath) {
+ StringBuilder fastaBuilder = new StringBuilder();
+ StringBuilder genomeNrsBuilder = new StringBuilder();
+
+ //needed to get the sequence with getRegion()
+ if (!PROTEOME) {
+ indexSc = new IndexScanner(indexDb);
+ genomeSc = new SequenceScanner(genomeDb, 1, 1, K_SIZE, indexSc.get_pre_len());
+ }
+
+ long totalRegions = regionsToSearch.length;
+ int regionCounter = 0;
+ int printThreshold = 100;
+ if (totalRegions < 500) {
+ printThreshold = 10;
+ }
+ for (String regionStr : regionsToSearch) {
+ regionCounter++;
+ if ((regionCounter % printThreshold == 0 || regionCounter == totalRegions || regionCounter < 50) && progress) {
+ System.out.print("\rCreating input sequences: " + regionCounter + "/" + totalRegions);
+ }
+
+ String[] regionArray = regionStr.split(" ");
+ int genomeNr;
+ int sequenceNr;
+ int startPos;
+ int endPos;
+ try {
+ genomeNr = Integer.parseInt(regionArray[0]);
+ sequenceNr = Integer.parseInt(regionArray[1]);
+ startPos = Integer.parseInt(regionArray[2]);
+ endPos = Integer.parseInt(regionArray[3]);
+ } catch (NumberFormatException nfe) {
+ System.out.println("Unable to correctly retrieve four numbers in: " + regionStr);
+ continue;
+ }
+
+ boolean reverse = false;
+ String rev_complement = "";
+ if (regionStr.endsWith("-")) {
+ reverse = true;
+ regionStr = regionStr.replace(" -","");
+ rev_complement = "_rvComplement";
+ }
+
+ if (genomeNr > total_genomes) {
+ System.out.println("A genome with number " + genomeNr + " does not exists! Only " + total_genomes + " genomes in pangenome\n");
+ System.exit(1);
+ }
+ if (endPos < startPos) {
+ System.out.println("The start position is lower as the end position. " + regionStr + " (for reverse complement, please use a '-')\n");
+ System.exit(1);
+ }
+
+ regionStr = regionStr.replace(" ","_"); // 1 1 1 1000 becomes 1_1_1_1000
+ String region;
+ if (!reverse) {
+ region = getRegion(genomeNr, sequenceNr, startPos-1, endPos-1, true);
+ } else {
+ region = getRegion(genomeNr, sequenceNr, startPos-1, endPos-1, false);
+ }
+ fastaBuilder.append(">").append(regionStr).append(rev_complement).append("\n")
+ .append(region).append("\n");
+
+ genomeNrsBuilder.append(genomeNr).append(",").append(regionStr).append(rev_complement).append("\n");
+ if (region.length() < 10) {
+ System.out.println("The length of " + regionStr + " is below 10 characters.");
+ System.exit(1);
+ }
+ }
+ if (progress) {
+ System.out.println();
+ }
+
+ write_string_to_file_full_path(fastaBuilder.toString(), inputPath + "/nuc.fasta");
+ write_string_to_file_full_path(genomeNrsBuilder.toString(), inputPath + "/genome_order.info");
+ }
+
+ /**
+ * Writes several input files for the input homology groups
+ * prot.fasta, protein sequences (if alignProtein)
+ * nuc.fasta, nucleotide sequences (if alignNucleotide)
+ * genome_order.info, list of genome number and identifiers
+ * sequences.info, relevant information for user
+ * skipped_genomes.info, skip array for current alignment
+ *
+ * @param functionNode function node for which to create input files
+ * @param inputPath path to where to write input files
+ */
+ private void writeFunctionsMsaInputFiles(Node functionNode, String inputPath) {
+
+ // get all relationships of functionNode
+ Iterable<Label> nodeLabels = functionNode.getLabels();
+ Node pangenomeNode = graphDb.findNodes(pangenome_label).next();
+ Iterable<Relationship> allRelations = pangenomeNode.getRelationships(); // all_rels must be initialized already
+ for (Label label1 : nodeLabels) {
+ String label_str = label1.toString();
+ switch (label_str) {
+ case "GO":
+ allRelations = functionNode.getRelationships(RelTypes.has_go);
+ break;
+ case "interpro":
+ allRelations = functionNode.getRelationships(RelTypes.has_interpro);
+ break;
+ case "pfam":
+ allRelations = functionNode.getRelationships(RelTypes.has_pfam);
+ break;
+ case "tigrfam":
+ allRelations = functionNode.getRelationships(RelTypes.has_tigrfam);
+ break;
+ default:
+ System.out.println(functionNode + " is not a function node.");
+ System.exit(1);
+ }
+ }
+
+ StringBuilder proteinFastaFile = new StringBuilder();
+ StringBuilder nucleotideFastaFile = new StringBuilder();
+ StringBuilder genomeNrsBuilder = new StringBuilder();
+ ArrayList<Integer> presentGenomes = new ArrayList<>();
+ StringBuilder infoBuilderHeader = new StringBuilder("#Information about sequences in homology group\n#Occurance in genomes\n");
+ StringBuilder infoBuilder = new StringBuilder("#genome, gene/mRNA name, mRNA identifier, node identifier, address, strand\n");
+ if (PROTEOME) {
+ infoBuilder = new StringBuilder("#genome, protein identifier, protein node id\n");
+ }
+ int numMembers = 0; // number of sequences in group
+ int[] copies = new int[total_genomes];
+
+ //needed to get the sequence with getSequence(mrnaNode)
+ if (!PROTEOME) {
+ indexSc = new IndexScanner(indexDb);
+ genomeSc = new SequenceScanner(genomeDb, 1, 1, K_SIZE, indexSc.get_pre_len());
+ }
+
+ for (Relationship rel : allRelations) {
+ Node mrnaNode = rel.getStartNode();
+ String mrnaProtein = getSequence(mrnaNode, "protein");
+ mrnaProtein = splitSeqOnLength(mrnaProtein, 80);
+ int genomeNr = (int) mrnaNode.getProperty("genome");
+ if (skip_array[genomeNr-1]) {
+ continue;
+ }
+ copies[genomeNr-1] += 1;
+ int copyNr = copies[genomeNr-1];
+ presentGenomes.add(genomeNr);
+ String proteinId = (String) mrnaNode.getProperty("protein_ID");
+ if (proteinId.contains(":") || proteinId.contains(";") || proteinId.contains("|")) { // not allowed in newick format
+ proteinId = proteinId
+ .replace(":",".")
+ .replace(";",".")
+ .replace("|",".");
+ }
+ String newId = genomeNr + "_" + copyNr + "_" + proteinId;
+
+ long mrnaNodeId = mrnaNode.getId();
+ genomeNrsBuilder.append(genomeNr).append(",").append(newId).append("\n");
+ if (!PROTEOME) {
+ int[] address = (int[]) mrnaNode.getProperty("address");
+ String strand = (String) mrnaNode.getProperty("strand");
+ String name = (String) mrnaNode.getProperty("name");
+ if (name.equals("")) {
+ name = "-";
+ }
+
+ String nucSequence = getSequence(mrnaNode, "CDS"); //can be mRNA as well, but then no protein can be given
+ nucSequence = splitSeqOnLength(nucSequence, 80);
+
+ if (alignProtein) {
+ proteinFastaFile.append(">").append(newId).append(" ").append(address[0]).append("_").append(address[1]).append("_").append(address[2]).append("_").append(address[3]).append("\n")
+ .append(mrnaProtein).append("\n");
+ }
+ if (alignNucleotide) {
+ nucleotideFastaFile.append(">").append(newId).append(" ").append(address[0]).append("_").append(address[1]).append("_").append(address[2]).append("_").append(address[3]).append("\n")
+ .append(nucSequence).append("\n");
+ }
+ infoBuilder.append(genomeNr).append(", ").append(name).append(", ").append(newId).append(", ").append(mrnaNodeId).append(", ")
+ .append(address[0]).append(" ").append(address[1]).append(" ").append(address[2]).append(" ").append(address[3]).append(", ").append(strand).append("\n");
+ } else {
+ proteinFastaFile.append(">").append(newId).append("\n").append(mrnaProtein).append("\n"); //we could check, but this is always alignProtein = true
+ infoBuilder.append(genomeNr).append(", ").append(newId).append(mrnaNodeId).append(", ").append("\n");
+ }
+
+ if (variation) {
+ //get nucleotide sequences of accessions
+ System.out.println("Not yet implemented");
+ System.exit(1);
+ }
+
+ numMembers++;
+ }
+
+ TreeSet<Integer> absent = getMissingGenomesInArrayList(presentGenomes);
+ String genomeFreqs = determineFrequencyListInt(presentGenomes);
+ infoBuilderHeader.append("Present: ").append(genomeFreqs)
+ .append("\nAbsent: ").append(absent.toString().replace("[","").replace("]","").replace(",","")).append("\n\n");
+ write_SB_to_file_full_path(infoBuilderHeader.append(infoBuilder), inputPath + "sequences.info");
+ if (alignProtein) {
+ write_SB_to_file_full_path(proteinFastaFile, inputPath + "prot.fasta");
+ }
+ if (alignNucleotide) {
+ write_SB_to_file_full_path(nucleotideFastaFile, inputPath + "nuc.fasta");
+ }
+ write_SB_to_file_full_path(genomeNrsBuilder, inputPath + "genome_order.info");
+ }
+
+ /**
+ * Gets sequence for a mRNA node
+ * @param mrnaNode mRNA Node
+ * @param feature annotation file feature belonging to gene (can currently accept CDS and protein)
+ * @return sequence belonging to feature of mrnaNode
+ */
+ private String getSequence(Node mrnaNode, String feature) {
+ String sequence = "";
+
+ switch (feature) {
+// case "mRNA":
+// break;
+ case "CDS":
+ Object value = mrnaNode.getProperty("sequence"); // old PT version
+ if (value instanceof String) {
+ sequence = String.valueOf(value);
+ } else {
+ if (mrnaNode.hasProperty("nucleotide_sequence")) {
+ sequence = (String) mrnaNode.getProperty("nucleotide_sequence");
+ } else {
+ sequence = (String) mrnaNode.getProperty("dna_sequence"); // old version, can be removed soon
+ }
+ }
+ break;
+ case "protein":
+ if (mrnaNode.hasProperty("protein")) {
+ sequence = (String) mrnaNode.getProperty("protein", "");
+ } else {
+ sequence = (String) mrnaNode.getProperty("protein_sequence", "");
+ }
+ break;
+ default:
+ System.out.println("Only CDS or protein sequence can currently be retrieved");
+ System.exit(1);
+ }
+
+ return sequence;
+ }
+
+ /**
+ * Retrieve the genomic region from the genome database
+ * @param genome genome number
+ * @param sequence sequence number
+ * @param begin start of region
+ * @param end end of region
+ * @param forward whether or not to give the forward strand
+ * @return sequence in specified region
+ */
+ private static String getRegion(int genome, int sequence, int begin, int end, boolean forward) {
+ if (begin > end) {
+ System.out.println("\nStart location of this region is higher than its end location -> " + genome + " " + sequence + " " + begin + " " +end );
+ System.exit(1);
+ }
+ StringBuilder seq = new StringBuilder();
+ genomeSc.get_sub_sequence(seq, genome, sequence, begin, end - begin + 1, forward);
+ return seq.toString();
+ }
+
+ /**
+ * creates phenotype template for multiple_groups MSA
+ * @param phenotypesList
+ * @param itolPhenoTemplate
+ * @param outputPath path to write files to
+ */
+ private void createMsaMultiPhenoTemplate(ArrayList<String> phenotypesList, StringBuilder itolPhenoTemplate, String outputPath) {
+ if (PHENOTYPE == null) {
+ return;
+ }
+ int sequenceNr = 0;
+ StringBuilder phenoColorInfo = new StringBuilder("Colors used for '" + PHENOTYPE +"' phenotype\n\n");
+ for (String pheno : phenotypesList) {
+ phenoColorInfo.append("#").append(pheno).append(" ").append(COLORCODES[sequenceNr]).append(" ").append(COLORNAMES[sequenceNr]).append("\n");
+ sequenceNr ++;
+ }
+ write_string_to_file_in_DB(phenoColorInfo + "\n" + itolPhenoTemplate.toString(), outputPath + "itol_tree_template_phenotype.txt");
+ }
+
+ /**
+ *
+ * @param genomeNr
+ * @param phenoCounterMap
+ * @param phenotypeCounter
+ * @param phenotypesList
+ * @param itolPhenoTemplate
+ * @param proteinId
+ */
+ private void appendMsaMultiPhenoTemplate(int genomeNr, HashMap<String, Integer> phenoCounterMap, AtomicInteger phenotypeCounter,
+ ArrayList<String> phenotypesList, StringBuilder itolPhenoTemplate, String proteinId) {
+ if (PHENOTYPE == null) {
+ return;
+ }
+ String currentPheno = geno_pheno_map.get(genomeNr);
+ if (currentPheno.equals("?")) {
+ return;
+ }
+ String color;
+ if (phenoCounterMap.containsKey(currentPheno)) {
+ int phenoCount = phenoCounterMap.get(currentPheno);
+ color = COLORCODES[phenoCount];
+ } else {
+ color = COLORCODES[phenotypeCounter.get()];
+ phenotypesList.add(currentPheno);
+ phenoCounterMap.put(currentPheno, phenotypeCounter.get());
+ phenotypeCounter.getAndIncrement();
+ }
+ itolPhenoTemplate.append(genomeNr).append("_").append(proteinId).append(",").append(color).append("\n");
+ }
+
+ /**
+ * Replaces an iTOL template
+ * @param itolTemplate iTOL template file
+ * @param newIdentifiers ArrayList of new identifiers
+ */
+ private void replaceItolTemplate(String itolTemplate, ArrayList<String> newIdentifiers) {
+ StringBuilder newTemplate = new StringBuilder();
+ try (BufferedReader in = new BufferedReader(new FileReader(itolTemplate))) {
+ boolean print = false;
+ int counter = 0;
+ for (int c = 0; in.ready();) {
+ String line = in.readLine().trim();
+ if (line.equals("DATA")) {
+ print = true;
+ newTemplate.append(line).append("\n");
+ continue;
+ }
+ if (print) {
+ String[] lineArray = line.split(",");
+ newTemplate.append(newIdentifiers.get(counter)).append(",").append(lineArray[lineArray.length-1]).append("\n");
+ counter ++ ;
+ } else {
+ newTemplate.append(line).append("\n");
+ }
+ }
+ } catch (IOException ioe) {
+ System.out.println("\nUnable to read: " + itolTemplate + "\n");
+ System.exit(1);
+ }
+ write_SB_to_file_full_path(newTemplate, itolTemplate);
+ }
+
+ /**
+ * Splits sequences based on length
+ * @param sequence sequence
+ * @param length length to split sequence on
+ * @return splitted sequence
+ */
+ private String splitSeqOnLength(String sequence, int length) {
+ String newString = "";
+ for (int i = 0; i < sequence.length(); i++) {
+ char c = sequence.charAt(i);
+ newString += c;
+ if ((i+1) % length == 0) {
+ newString += "\n";
+ }
+ }
+ if (newString.endsWith("*")) {
+ newString = newString.replaceFirst(".$","");
+ }
+ return newString;
+ }
+
+ /**
+ * Gets missing genomes in an ArrayList
+ * @param presentGenomes genomes that are present
+ * @return missing genomes
+ */
+ private TreeSet<Integer> getMissingGenomesInArrayList(ArrayList<Integer> presentGenomes) {
+ TreeSet<Integer> absent = new TreeSet<>();
+ for (int i = 1; i <= total_genomes; ++i) {
+ if (skip_array[i-1]) {
+ continue;
+ }
+ if (!presentGenomes.contains(i)) {
+ absent.add(i);
+ }
+ }
+ return absent;
+ }
+
+ /**
+ * //TODO integrate this function with removeDuplicatesFromALInt
+ * @param sizeList
+ * @return
+ */
+ private String determineFrequencyListInt(ArrayList<Integer> sizeList) {
+ ArrayList<Integer> distinctSizeList = removeDuplicatesFromALInt(sizeList);
+ StringBuilder output = new StringBuilder();
+ for (int size : distinctSizeList) {
+ int occurrences = Collections.frequency(sizeList, size);
+ output.append(size).append("(").append(occurrences).append("x), ");
+ }
+ return output.toString().replaceFirst(".$", "").replaceFirst(".$", ""); // remove last character (2x)
+ }
+
+ /**
+ * //TODO integrate this function with determineFrequencyListInt
+ * @param list
+ * @return
+ */
+ private ArrayList<Integer> removeDuplicatesFromALInt(ArrayList<Integer> list) {
+ List<Integer> newList = list.stream()
+ .distinct()
+ .collect(Collectors.toList());
+ Collections.sort(newList);
+ ArrayList tester = new ArrayList<>(newList);
+ return tester;
+ }
+
+
+
+
+
+
+
+
+
+
+ /**
+ * By default aligns sequences twice, once normal and second round with trimmed input.
+ * @param trim can output be used for trimming?
+ * @param stats
+ *
+ * NB: the global variable TRIMMING exists as well, this is used to run this function only once instead of trim.
+ */
+ public void alignSequences(boolean trim, boolean stats) {
+ //TODO check which input exists and align that input
+
+ check_if_program_exists_stderr("FastTree -h", 100, "Fasttree", true); // check if program is set to the $PATH
+ check_if_program_exists_stderr("mafft -h", 100, "MAFFT", true); // check if program is set to the $PATH
+
+ boolean pass = false; // pass when all alignment (& tree) files exists
+ int loopCounter = 0;
+ while (!pass) {
+ if (LOG) {
+ System.out.println("Checking if MSA is complete for: " + msaNames);
+ }
+ ArrayList<String> toBeAlignedList = checkIfMsaIsComplete(msaNames, !trim);
+ if (toBeAlignedList.isEmpty()) {
+ pass = true;
+ continue;
+ }
+
+ runParallelMafft(msaNames, !trim);
+ if (!FAST) {
+ runParallelFasttree(msaNames, !trim);
+ }
+
+
+ if (progress) {
+ System.out.println();
+ }
+ loopCounter ++;
+ if (loopCounter == 3) {
+ System.out.print("\nFailed to align " + toBeAlignedList.size() + " groups: ");
+ for (String groupNode : toBeAlignedList) {
+ System.out.print(groupNode + ", ");
+ }
+ System.out.println("");
+ System.exit(1);
+ }
+ }
+
+ if (TRIMMING && trim) { // when run from commandline: trim and restart to align the trimmed sequences
+ trimPrealignedProteins(); //trims sequences + sets msaNames to current set
+ alignSequences(false, stats); // restarting this function to align the trimmed sequences
+ } else if (stats) { // this only happens when this function calls itself
+ try {
+ if (TRIMMING) {
+ Classification.create_write_msa_trimmed_output(msaNames, outDirMsa);
+ } else {
+ Classification.create_write_msa_no_trimming_output(msaNames, outDirMsa);
+ }
+ } catch (ArrayIndexOutOfBoundsException e) {
+ e.printStackTrace();
+ System.out.println("This error is likely caused by skipping different genomes for this run compared to a previous run.");
+ System.exit(1);
+ }
+ if (progress) {
+ printResultsMsa();
+ }
+ Classification.include_identity_similarity_to_relations(msaNames, trim);
+ }
+ if (progress) {
+ System.out.println();
+ }
+ }
+
+ /**
+ * Check if the required output files of a multiple sequence alignment exist.
+ * @param hmNodeList arraylist with strings of homology group node (identifiers) that still need to be aligned
+ * @param trim trimmed input?
+ * @return arraylist of homology group nodes still to be aligned
+ */
+ private ArrayList<String> checkIfMsaIsComplete(ArrayList<String> hmNodeList, boolean trim) {
+ ArrayList<String> toBeAlignedList = new ArrayList<>();
+ String dot = ".";
+ if (trim) {
+ dot = dot.replace(".","_trimmed.");
+ }
+
+ int doneCount = 0, notDoneCount = 0;
+ for (String hmgroup : hmNodeList) {
+ String path = outDirMsa + hmgroup + "/output/";
+ boolean pass1, pass2;
+
+ if (FAST) {
+ pass1 = check_if_file_exists(path + "nuc" + dot + "fasta");
+ pass2 = check_if_file_exists(path + "prot" + dot + "fasta");
+ } else {
+ pass1 = check_if_file_exists(path + "nuc" + dot + "newick");
+ pass2 = check_if_file_exists(path + "prot" + dot + "newick");
+ }
+
+ if (!alignProtein) {
+ pass2 = true;
+ }
+ if (!alignNucleotide) {
+ pass1 = true;
+ }
+
+ if (!pass1 || !pass2) {
+ toBeAlignedList.add(hmgroup);
+ notDoneCount ++;
+ } else {
+ doneCount ++;
+ }
+
+ if (((notDoneCount + doneCount) % 100 == 0 || (notDoneCount + doneCount) == hmNodeList.size()) && progress) {
+ System.out.print("\r Checking MSA completeness -> " + notDoneCount + " not done, " + doneCount + " done ");
+ }
+ }
+
+ if (progress) {
+ System.out.print("\r "); // spaces are intentional
+ }
+ return toBeAlignedList;
+ }
+
+
+ /**
+ * MAFFT is run in parallel using ExecutorService
+ * @param hmNodeList arraylist of homology group IDs
+ * @param trim whether input sequences are trimmed or not
+ */
+ private void runParallelMafft(ArrayList<String> hmNodeList, boolean trim) {
+ String dot = ".";
+ if (trim) {
+ dot = dot.replace(".","_trimmed.");
+ }
+
+ //create threadpool for parallel running of MAFFT
+ ExecutorService es = Executors.newFixedThreadPool(THREADS);
+ List<Future<?>> futures = new ArrayList<>();
+
+ for (String hmNode : hmNodeList) {
+ String path = outDirMsa + hmNode + "/";
+ String inPath = path + "input/";
+ String outPath = path + "output/";
+
+ if (alignNucleotide) {
+ String input = inPath + "nuc" + dot + "fasta";
+ String output = outPath + "nuc" + dot + "afa";
+
+ if (!check_if_file_exists(outPath + "nuc" + dot + "afa")) {
+ Future<?> f = es.submit(new runMafft(input, output));
+ futures.add(f);
+ }
+ }
+
+ if (alignProtein) {
+ String input = inPath + "prot" + dot + "fasta";
+ String output = outPath + "prot" + dot + "afa";
+
+ if (!check_if_file_exists(outPath + "prot" + dot + "afa")) {
+ Future<?> f = es.submit(new runMafft(input, output));
+ futures.add(f);
+ }
+ }
+ }
+
+ //actually run mafft
+ int counter = 1;
+ int total = futures.size();
+ for (Future<?> future : futures) {
+ try {
+ future.get();
+ if (progress) {
+ System.out.print("\rAligning sequences: " + counter + "/" + total);
+ }
+ counter++;
+ } catch (InterruptedException | ExecutionException e) {
+ e.printStackTrace();
+ }
+ }
+ es.shutdownNow(); //shutdown ExecutorService
+ if (progress) {
+ System.out.println();
+ }
+ }
+
+ /**
+ * FastTree is run in parallel using ExecutorService
+ * @param hmNodeList arraylist of homology group IDs
+ * @param trim whether input is trimmed or not
+ */
+ private void runParallelFasttree(ArrayList<String> hmNodeList, boolean trim) {
+ String dot = ".";
+ if (trim) {
+ dot = dot.replace(".","_trimmed.");
+ }
+
+ //create threadpool for parallel running of fasttree
+ ExecutorService es = Executors.newFixedThreadPool(THREADS);
+ List<Future<?>> futures = new ArrayList<>();
+
+ for (String groupId : hmNodeList) {
+ String path = outDirMsa + groupId + "/";
+ String outPath = path + "output/";
+
+ if (alignNucleotide) { //
+ String input = outPath + "nuc" + dot + "fasta";
+ String output = outPath + "nuc" + dot + "newick";
+
+ if (!check_if_file_exists(output)) {
+ Future<?> f = es.submit(new runFasttree(input, output, true));
+ futures.add(f);
+ }
+ }
+
+ if (alignProtein) { //
+ String input = outPath + "prot" + dot + "fasta";
+ String output = outPath + "prot" + dot + "newick";
+
+ if (!check_if_file_exists(output)) {
+ Future<?> f = es.submit(new runFasttree(input, output, false));
+ futures.add(f);
+ }
+ }
+ }
+
+ //actually run fasttree
+ int counter = 1;
+ int total = futures.size();
+ for (Future<?> future : futures) {
+ try {
+ future.get();
+ if (progress) {
+ System.out.print("\rPhylogeny inference: " + counter + "/" + total);
+ }
+ counter++;
+ } catch (InterruptedException | ExecutionException e) {
+ e.printStackTrace();
+ }
+ }
+ es.shutdownNow(); //shutdown ExecutorService
+ if (progress) {
+ System.out.println();
+ }
+ }
+
+ /**
+ * Converts afa format to fasta format
+ * @param inputFasta original fasta file
+ * @param inputAfa aligned fasta file in afa format
+ *
+ * Requires original fasta input file and aligned output from mafft
+ * mafft is run with a setting so that the original order of sequences remains
+ */
+ private void convertAfaToAlignedFasta(String inputFasta, String inputAfa) {
+ HashMap<Integer, StringBuilder> sequenceMap = new HashMap<>();
+ ArrayList<String> sequenceList = new ArrayList<>();
+ int totalSequences = 0;
+ try (BufferedReader in = new BufferedReader(new FileReader(inputFasta))) { // read original fasta files
+ for (int c = 0; in.ready();) {
+ String line = in.readLine().trim();
+ if (line.startsWith(">")) {
+ totalSequences++;
+ String key = line.replace(">","");
+ StringBuilder builder = new StringBuilder();
+ sequenceMap.put(totalSequences, builder);
+ sequenceList.add(key);
+ }
+ }
+ } catch (IOException ioe) {
+ System.out.println("\nUnable to read the input fasta : " + inputFasta + "\n");
+ System.exit(1);
+ }
+
+ try (BufferedReader in = new BufferedReader(new FileReader(inputAfa))) {
+ int lineCounter = 0, seqCounter = 0;
+ for (int c = 0; in.ready();) {
+ String line = in.readLine().trim();
+ lineCounter ++;
+ if (lineCounter == 1) {
+ if (!line.startsWith("CLUSTAL")) {
+ System.out.println(inputAfa);
+ System.exit(1);
+ }
+ }
+ if (lineCounter < 4) {
+ continue;
+ }
+ seqCounter ++;
+ if (seqCounter == totalSequences+1) { // first row after sequences with **
+ continue;
+ }
+ if (seqCounter == totalSequences+2) { // always an empty line
+ seqCounter = 0;
+ continue;
+ }
+ String[] lineArray = line.split(" ");
+ StringBuilder seqBuilder = sequenceMap.get(seqCounter);
+ seqBuilder.append(lineArray[lineArray.length-1]).append("\n");
+ sequenceMap.put(seqCounter, seqBuilder);
+ }
+ } catch (IOException ioe) {
+ System.out.println("\nUnable to read the input alignment: " + inputAfa + "\n");
+ System.exit(1);
+ }
+
+ String outputFile = inputAfa.replace(".afa", ".fasta");
+ try (BufferedWriter out1 = new BufferedWriter(new FileWriter(outputFile))) {
+ for (int i = 1; i <= totalSequences; i++) {
+ StringBuilder value = sequenceMap.get(i);
+ out1.write(">" + sequenceList.get(i-1) + "\n" +value.toString());
+ }
+ } catch (IOException ioe) {
+ System.out.println("\nUnable to read: " + outputFile + "\n");
+ System.exit(1);
+ }
+ }
+
+ /**
+ * Trim nucleotide and protein input sequences based on the first PROTEIN alignment.
+ *
+ * 1. Read the protein alignment, find the longest gap at the end and start (countAaToTrim)
+ * 2
+ *
+ * NB: Should be correct for both nucleotide and protein now
+ */
+ private void trimPrealignedProteins() {
+ int groupCounter = 0;
+ ArrayList<String> suitableGroups = new ArrayList<>();
+ ArrayList<String> excludedGroups = new ArrayList<>();
+ for (String groupId : msaNames) {
+ groupCounter ++;
+ String path = outDirMsa + groupId + "/";
+ String inPath = path + "input/";
+ String outPath = path + "output/" ;
+ if ((groupCounter % 10 == 0 || groupCounter == msaNames.size()) && progress) {
+ System.out.print("\rCreating trimmed sequences: " + groupCounter + "/" + msaNames.size());
+ }
+ boolean pass = checkIfGroupIsTrimmed(groupId, inPath, suitableGroups, excludedGroups);
+ if (pass) { // group is already trimmed
+ continue;
+ }
+
+ HashMap<String, int[]> seqTrimMap = new HashMap<>();
+ int[] longestStartEndGap;
+ // key is the fasta header, value is array with number of aa at the start and end of the sequence that need to be trimmed
+ if (alignProtein) { //if protein alignment exists, use that one
+ longestStartEndGap = countAaToTrim(outPath + "/prot.fasta", seqTrimMap); // gaps at start, gaps at end, alignment length
+ if (longestStartEndGap[0] + longestStartEndGap[1] < longestStartEndGap[2]) {
+ suitableGroups.add(groupId);
+ trimSequences(seqTrimMap, groupId, inPath + "/prot.fasta", false);
+ if (alignNucleotide) { //valid when both prot and nuc are aligned
+ trimSequences(seqTrimMap, groupId, inPath + "/nuc.fasta", true);
+ }
+ } else {
+ excludedGroups.add(groupId);
+ }
+ } else { //otherwise, base on nucleotide alignment
+ longestStartEndGap = countAaToTrim(outPath + "/nuc.fasta", seqTrimMap); // gaps at start, gaps at end, alignment length
+ if (longestStartEndGap[0] + longestStartEndGap[1] < longestStartEndGap[2]) {
+ suitableGroups.add(groupId);
+ if (alignNucleotide) {
+ trimSequences(seqTrimMap, groupId, inPath + "/nuc.fasta", false); //we act as if it is protein sequence, such that we don't divide by three
+ }
+ } else {
+ excludedGroups.add(groupId);
+ }
+ }
+ createTrimmedInfoFile(longestStartEndGap, groupId, seqTrimMap, inPath);
+ }
+
+ if (excludedGroups.size() > 0) { // one ore multiple groups were excluded due to trimmed edges overlapping
+ write_string_to_file_full_path(excludedGroups.toString().replace("[","").replace("]","").replace(" ",""),
+ outDirMsa + "/groups_excluded_based_on_trimming.txt");
+ if (progress) {
+ System.out.println("\rCreating trimmed sequences: " + groupCounter + "/" + msaNames.size()
+ + "; Excluded " + excludedGroups.size() + " alignments. "
+ + "See " + outDirMsa + "/groups_excluded_based_on_trimming.txt");
+ }
+ } else if (progress) {
+ System.out.println("\rCreating trimmed sequences: " + groupCounter + "/" + msaNames.size() + "; Excluded 0 alignments");
+ }
+
+ if (suitableGroups.isEmpty()) {
+ if (progress) {
+ System.out.println("\n\nNone of the trimmed alignments can be used for the second alignment round. "
+ + "Use '--mode no-trimming' to further analyze them\n");
+ }
+ } else {
+ // msaNames is a global variable and is read by this function again after restarting
+ this.msaNames = suitableGroups;
+ }
+ }
+
+ /**
+ * Check if a alignments is trimmed
+ * @param groupId alignments ID
+ * @param inPath input path
+ * @param suitableGroups alignments suitable for trimming
+ * @param excludedGroups alignments not suitable for trimming
+ * @return
+ */
+ private boolean checkIfGroupIsTrimmed(String groupId, String inPath, ArrayList<String> suitableGroups, ArrayList<String> excludedGroups) {
+ boolean pass2 = check_if_file_exists(inPath + "/not_trimmed");
+ if (pass2) {
+ excludedGroups.add(groupId); // long + str to convert to a string
+ return true;
+ }
+ boolean pass1 = false;
+ if (alignProtein && alignNucleotide) { // both nucleotide and protein sequences
+ boolean passA = check_if_file_exists(inPath + "/prot_trimmed.fasta");
+ boolean passB = check_if_file_exists(inPath + "/nuc_trimmed.fasta");
+ if (passA && passB){
+ pass1 = true;
+ }
+ } else if (alignProtein) { // proteins only
+ pass1 = check_if_file_exists(inPath + "/prot_trimmed.fasta");
+ } else if (alignNucleotide) { // nucleotides only
+ pass1 = check_if_file_exists(inPath + "/nuc_trimmed.fasta");
+ }
+
+ if (pass1) {
+ suitableGroups.add(groupId);
+ }
+ return pass1;
+ }
+
+ /**
+ * This function finds how many amino acids per sequence needs to be removed based on the longest start and stop gap lengths
+ * 1. identify longest start and end gap in any sequence
+ * 2. count number of gaps in all sequences according to the longest gaps
+ *
+ * @param protFastaFile
+ * @param seqTrimMap
+ * @return int[] array of length 3: gaps at start, gaps at end, alignment length
+ */
+ private int[] countAaToTrim(String protFastaFile, HashMap<String, int[]> seqTrimMap) {
+ HashMap<String, String> sequenceMap = new HashMap<>(); // key is a fasta header, value is the sequence
+ int alignmentLength = readFastaForSequenceAndGaps(protFastaFile, seqTrimMap, sequenceMap );
+ int longestStartGap = 0, longestEndGap = 0;
+ for (String sequenceName : seqTrimMap.keySet()) {
+ int[] gaps = seqTrimMap.get(sequenceName);
+ if (gaps[0] > longestStartGap) {
+ longestStartGap = gaps[0];
+ }
+ if (gaps[1] > longestEndGap) {
+ longestEndGap = gaps[1];
+ }
+ }
+ for (String sequenceName : seqTrimMap.keySet()) {
+ int[] finalStartEndGaps = findNumberOfGapsWithoutBreak(sequenceMap.get(sequenceName),
+ longestStartGap, longestEndGap); // only find gaps in longest start and end gap
+ seqTrimMap.put(sequenceName, finalStartEndGaps);
+ }
+ return new int[] {longestStartGap, longestEndGap, alignmentLength}; // gaps at start, gaps at end, alignment length
+ }
+
+ /**
+ * Based on the longest start and end gaps that were found earlier, count the number of gaps for each sequence
+ * @param sequence sequence
+ * @param posUntilStartGap number of positions until start gap
+ * @param posUntilEndGap number of positions until end gap
+ * @return
+ */
+ private int[] findNumberOfGapsWithoutBreak(String sequence, int posUntilStartGap, int posUntilEndGap) {
+ int startGapCounter = 0, endGapCounter = 0;
+ for (int i = 0; i < posUntilStartGap; i++) {
+ char aa = sequence.charAt(i);
+ if (aa != '-') {
+ startGapCounter ++;
+ }
+ }
+
+ int endPosition = sequence.length()-1-posUntilEndGap;
+ for (int i = sequence.length()-1; i > endPosition; i--) {
+ char aa = sequence.charAt(i);
+ if (aa != '-') {
+ endGapCounter ++;
+ }
+ }
+ return new int[]{startGapCounter, endGapCounter};
+ }
+
+ /**
+ * find the longest start and end gap for each sequence
+ *
+ * @param protFastaFile
+ * @param seqTrimMap
+ * @param sequenceMap
+ * @return
+ */
+ private int readFastaForSequenceAndGaps(String protFastaFile, HashMap<String, int[]> seqTrimMap, HashMap<String, String> sequenceMap) {
+ int alignmentLength = 0;
+ try {
+ BufferedReader in = new BufferedReader(new FileReader(protFastaFile));
+ String prevSeq = "", sequence = "";
+ //startEndGapArray = {0,0};
+ while (in.ready()) {
+ String line = in.readLine().trim();
+ if (line.equals("")) {
+ continue;
+ }
+ if (line.contains(">")) {
+ if (!prevSeq.equals("")) {
+ int[] startEndGapArray = findNumberOfGaps(sequence, sequence.length(), sequence.length());
+ seqTrimMap.put(prevSeq, startEndGapArray);
+ sequenceMap.put(prevSeq, sequence);
+ }
+ prevSeq = line;
+ sequence = "";
+ } else {
+ sequence += line;
+ }
+ }
+ // when done, add the last sequence
+ int[] startEndGapArray = findNumberOfGaps(sequence, sequence.length(), sequence.length());
+ alignmentLength = sequence.length();
+ seqTrimMap.put(prevSeq, startEndGapArray);
+ sequenceMap.put(prevSeq, sequence);
+ } catch (IOException e) {
+ System.out.println(e.getMessage());
+ System.exit(1);
+ }
+ return alignmentLength;
+ }
+
+ /**
+ * From the start and the end of the sequence, iterate over the sequence until no gap is found
+ * @param sequence sequence
+ * @param posUntilStartGap number of positions until start gap
+ * @param posUntilEndGap number of positions until end gap
+ * @return
+ */
+ private int[] findNumberOfGaps(String sequence, int posUntilStartGap, int posUntilEndGap) {
+ int startGapCounter = 0, endGapCounter = 0;
+ for (int i = 0; i < posUntilStartGap; i++) {
+ char aa = sequence.charAt(i);
+ if (aa == '-') {
+ startGapCounter ++;
+ } else {
+ break;
+ }
+ }
+ for (int i = sequence.length()-1; i > 0; i--) {
+ char aa = sequence.charAt(i);
+ if (aa == '-') {
+ endGapCounter ++;
+ } else{
+ break;
+ }
+ }
+ return new int []{startGapCounter, endGapCounter};
+ }
+
+ /**
+ * Trims sequences
+ * @param seqTrimMap
+ * @param geneName
+ * @param path
+ * @param nucleotide whether we are trimming a nucleotide sequence
+ */
+ private void trimSequences(HashMap<String, int[]> seqTrimMap, String geneName, String path, boolean nucleotide) {
+ StringBuilder outputBuilder = new StringBuilder();
+ String newPath = path.replace(".fasta", "_trimmed.fasta");
+ int longestTrim = 0, shortestTrim = 999999;
+ try {
+ BufferedReader in = new BufferedReader(new FileReader(path));
+ String sequence = "", prevSeq = "";
+ while (in.ready()) {
+ String line = in.readLine().trim();
+ if (line.equals("")) {
+ continue;
+ }
+
+ if (line.contains(">")) {
+ //System.out.println("prev seq " + prevSeq + "." );
+ if (prevSeq.length() > 1) {
+ int[] trimArray = seqTrimMap.get(prevSeq);
+ int trimSum = trimArray[0] + trimArray[1];
+ if (trimSum < shortestTrim && trimSum != 0) {
+ shortestTrim = trimSum;
+ }
+ if (trimSum > longestTrim) {
+ longestTrim = trimSum;
+ }
+ outputBuilder.append(prevSeq).append("\n");
+ trimSequence(sequence, trimArray, outputBuilder, nucleotide);
+ }
+ prevSeq = line;
+ sequence = "";
+ } else {
+ sequence += line;
+ }
+ }
+
+ int[] trimArray = seqTrimMap.get(prevSeq);
+ int trimSum = trimArray[0] + trimArray[1];
+ if (trimSum < shortestTrim && trimSum != 0) {
+ shortestTrim = trimSum;
+ }
+ if (trimSum > longestTrim) {
+ longestTrim = trimSum;
+ }
+ outputBuilder.append(prevSeq).append("\n");
+ trimSequence(sequence, trimArray, outputBuilder, nucleotide);
+ } catch (IOException e) {
+ System.out.println("\n" + e.getMessage());
+ System.exit(1);
+ }
+
+ if (nucleotide) {
+ longestTrim = longestTrim*3;
+ shortestTrim = shortestTrim*3;
+ }
+ if (longestTrim < shortestTrim) {
+ shortestTrim = longestTrim;
+ }
+ write_SB_to_file_full_path(outputBuilder, newPath);
+ }
+
+ /**
+ * @param sequence
+ * @param trimArray
+ * @param outputBuilder
+ * @param nucleotide
+ */
+ private void trimSequence(String sequence, int[] trimArray, StringBuilder outputBuilder, boolean nucleotide) {
+ int nucCount = 1, nucCountLoop = 0;
+ int removeNucsStart = trimArray[0];
+ int removeNucsEnd = trimArray[1];
+ if (nucleotide) {
+ removeNucsStart = removeNucsStart*3;
+ removeNucsEnd = removeNucsEnd*3;
+ }
+ removeNucsEnd = sequence.length() - removeNucsEnd; // adjust the ending with the number of nucleotides
+ //System.out.println(removeNucsStart + " " + removeNucsEnd);
+ String trimmedSeq = "";
+ for (int i = 0; i < sequence.length(); i++) {
+ char aa = sequence.charAt(i);
+ nucCountLoop ++;
+ if (nucCount <= removeNucsStart) {
+
+ } else if (nucCount > removeNucsEnd) {
+
+ } else {
+ trimmedSeq += aa;
+ }
+ nucCount ++;
+ if (nucCountLoop == 3) {
+ nucCountLoop = 0;
+ }
+ }
+ trimmedSeq = splitSeqOnLength(trimmedSeq, 80);
+ outputBuilder.append(trimmedSeq).append("\n");
+ }
+
+ /**
+ * Creates 'trimmed.info' and 'notTrimmed' when the group must be excluded
+ *
+ * @param longestStartEndGap
+ * @param hmgroup
+ * @param seqTrimMap
+ * @param inPath
+ */
+ private void createTrimmedInfoFile(int[] longestStartEndGap, String hmgroup, HashMap<String, int[]> seqTrimMap, String inPath) {
+ String trimmed = "Protein alignment length: " + longestStartEndGap[2]
+ + "\nLongest start gap: " + longestStartEndGap[0]
+ + "\nLongest end gap: " + longestStartEndGap[1];
+
+ if (longestStartEndGap[0] + longestStartEndGap[1] < longestStartEndGap[2]) {
+ trimmed += "\n\nTotal number of trimmed positions at the start and end of each protein sequence."
+ + " Multiply the number by three to obtain the number of positions in for the nucleotide sequences.\n";
+ for (String sequenceName : seqTrimMap.keySet()) {
+ int[] trimmedProtPositions = seqTrimMap.get(sequenceName);
+ String[] seqArray = sequenceName.split(" ");
+ trimmed += seqArray[0].replace(">","") + ": " + trimmedProtPositions[0] + ", " + trimmedProtPositions[1] + "\n";
+ }
+ } else {
+ write_string_to_file_full_path("sequences to short", inPath + "/not_trimmed");
+ trimmed += "\nNo trimmed sequence could be created";
+ }
+ write_string_to_file_full_path(trimmed, inPath + "/trimmed.info");
+ }
+
+ /**
+ * Prints MSA results
+ */
+ private void printResultsMsa() {
+ System.out.println("\nOutput written to:\n" + outDirMsa + "\n");
+ if (PHENOTYPE == null) {
+ System.out.println("Provide a phenotype to find phenotype specific variants! (--phenotype)");
+ } else {
+ System.out.println("\n\nPhenotype output written to:\n"
+ + " " + outDirMsa + "groups_with_phenotype_specific_changes.txt");
+
+ if (alignNucleotide) { // nucleotide sequences
+ System.out.print(" " + outDirMsa + "phenotype_specific_changes_nuc.txt\n");
+ }
+ if (alignProtein) { // protein sequences
+ System.out.print(" " + outDirMsa + "phenotype_specific_changes_prot.txt\n");
+ }
+ System.out.println();
+ }
+ }
+
+ /**
+ * Gives the private variable hmNodeList
+ * @return private variable hmNodeList
+ *
+ * NB: this list IS NOT updated with trimming results!
+ */
+ public ArrayList<Node> getHmNodeList() {
+ return hmNodeList;
+ }
+
+ /**
+ * Gives the private variable msaNames
+ * @return private variable msaNames
+ *
+ * NB: this list IS updated with trimming results!
+ */
+ public ArrayList<String> getMsaNames() {
+ return msaNames;
+ }
+
+ /**
+ * Whether we align nucleotide or protein sequence
+ * @return nuc or prot
+ *
+ * NB: preference for prot!
+ */
+ public String getNucOrProt() {
+ if (alignProtein) {
+ return "prot";
+ } else {
+ return "nuc";
+ }
+ }
+
+ /**
+ * Small inner class for running MAFFT in a parallel fashion
+ */
+ private class runMafft implements Callable<String> {
+ private final String input;
+ private final String output;
+
+ public runMafft(String input, String output) {
+ this.input = input;
+ this.output = output;
+ }
+
+ public String call() {
+ String mafftCommand = "mafft --auto --anysymbol --quiet --thread 1 --clustalout " +
+ "--bl " + BLOSUM + " " +
+ input +
+ " 1> " +
+ output;
+
+ if (LOG) {
+ System.out.println(mafftCommand);
+ }
+
+ runCommand(mafftCommand); //run MAFFT
+ convertAfaToAlignedFasta(input, output); //convert output of MAFFT to fasta format
+
+ return "Starting alignment of " + input;
+ }
+
+ private void runCommand(String command) {
+ List<String> cmd = new ArrayList<>();
+ cmd.add("sh");
+ cmd.add("-c");
+ cmd.add(command);
+ ProcessBuilder pb = new ProcessBuilder(cmd);
+ try {
+ Process p = pb.start();
+ p.waitFor();
+ } catch (IOException | InterruptedException e) {
+ e.printStackTrace();
+ System.exit(1);
+ }
+ }
+ }
+
+ /**
+ * Small inner class for running FastTree in a parallel fashion
+ */
+ private class runFasttree implements Callable<String> {
+ private final String input;
+ private final String output;
+ private final boolean isNucleotide;
+ private final String log;
+
+ public runFasttree(String input, String output, boolean isNucleotide) {
+ this.input = input;
+ this.output = output;
+ this.isNucleotide = isNucleotide;
+ this.log = output + ".log";
+ }
+
+ public String call() {
+ String fasttree = "FastTree ";
+ if (isNucleotide) {
+ fasttree += "-nt ";
+ }
+ String fasttreeCommand = fasttree + input +
+ " 1> " + output +
+ " 2> " + log;
+
+ if (LOG) {
+ System.out.println(fasttreeCommand);
+ }
+
+ runCommand(fasttreeCommand); //run FastTree
+
+ if (!LOG) {
+ delete_file_full_path(log);
+ }
+
+ return "Starting alignment of " + input;
+ }
+
+ private void runCommand(String command) {
+ List<String> cmd = new ArrayList<>();
+ cmd.add("sh");
+ cmd.add("-c");
+ cmd.add(command);
+ ProcessBuilder pb = new ProcessBuilder(cmd);
+ try {
+ Process p = pb.start();
+ p.waitFor();
+ } catch (IOException | InterruptedException e) {
+ e.printStackTrace();
+ System.exit(1);
+ }
+ }
+ }
+}
diff --git a/src/pangenome/Phylogeny.java b/src/main/java/nl/wur/bif/pantools/pangenome/Phylogeny.java
similarity index 70%
rename from src/pangenome/Phylogeny.java
rename to src/main/java/nl/wur/bif/pantools/pangenome/Phylogeny.java
index 2bfbc349d98c3b13939f5f649899c5172b9f48fb..77156f8b8a11f067b0782bbc775e4ccd90ae03b4 100644
--- a/src/pangenome/Phylogeny.java
+++ b/src/main/java/nl/wur/bif/pantools/pangenome/Phylogeny.java
@@ -3,127 +3,25 @@
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
-package pangenome;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.Map;
-import static pantools.Pantools.Mode;
-import org.neo4j.graphdb.Node;
-import org.neo4j.graphdb.Relationship;
-import org.neo4j.graphdb.ResourceIterator;
-import org.neo4j.graphdb.Transaction;
-import java.io.BufferedReader;
-import static pantools.Pantools.total_genomes;
-import static pantools.Pantools.WORKING_DIRECTORY;
-import static pantools.Pantools.LOG;
-import static pantools.Pantools.remove_first_position_array;
-import java.io.FileReader;
-import org.neo4j.graphdb.Direction;
-import java.io.IOException;
-import static pantools.Pantools.adj_total_genomes;
-import org.neo4j.graphdb.NotFoundException;
-import static pantools.Pantools.gene_label;
-import java.io.File;
-import java.util.Arrays;
-import java.util.HashSet;
-import java.util.Set;
-import static pantools.Pantools.PATH_TO_THE_ANNOTATIONS_FILE;
+package nl.wur.bif.pantools.pangenome;
+
+import nl.wur.bif.pantools.index.IndexScanner;
+import nl.wur.bif.pantools.sequence.SequenceScanner;
import org.apache.commons.lang.ArrayUtils;
-import pantools.Pantools.RelTypes;
-import static pantools.Pantools.SELECTED_NAME;
-import static pantools.Pantools.PHENOTYPE;
-import static pantools.Pantools.NODE_VALUE;
-import static pantools.Pantools.graphDb;
-import static pantools.Pantools.pangenome_label;
-import static pantools.Pantools.homology_group_label;
-import static pantools.Pantools.skip_array;
-
-import static pantools.Pantools.target_genome;
-import java.util.*;
-import static pangenome.Classification.get_average_from_AL_int;
-import static pangenome.Classification.convert_afa_to_aligned_fasta;
-import static pangenome.Classification.count_aa_to_trim;
-import static pangenome.Classification.count_var_inf_sites_in_msa;
-import static pangenome.Classification.create_similarity_matrices;
-import static pangenome.Classification.determine_frequency_list_int;
-import static pangenome.Classification.get_phenotype_for_genome;
-import static pangenome.Classification.get_annotation_identifiers;
-import static pangenome.Classification.get_nucleotide_sequence;
-import static pangenome.Classification.get_protein_sequence;
-import static alignment.BoundedLocalSequenceAlignment.initialize_BLOSUM_matrix;
-import static pangenome.Classification.remove_duplicates_from_AL_int;
-import static pangenome.Classification.trim_sequences;
-import static pangenome.Classification.try_incr_AL_hashmap;
-import static pangenome.Classification.try_incr_SB_hashmap;
-import static pangenome.Classification.retrieve_hmgroups;
-import static pantools.Pantools.THREADS;
-import static pantools.Pantools.report_number_of_threads;
-import static pantools.Pantools.WD_full_path;
-import static pantools.Pantools.geno_pheno_map;
-import static pantools.Pantools.check_if_graphDb_is_available;
-import static pantools.Pantools.connect_pangenome;
-import static pantools.Pantools.create_directory_in_DB;
-import static pantools.Pantools.delete_directory;;
-import static pantools.Pantools.K_SIZE;
-import static pantools.Pantools.indexDb;
-import static pantools.Pantools.append_string_to_file_full_path;
-import static pantools.Pantools.pantools_path;
-import static pantools.Pantools.write_SB_to_file_in_DB;
-import static pantools.Pantools.write_string_to_file_in_DB;
-import static pantools.Pantools.write_SB_to_file_full_path;
-import static pantools.Pantools.append_SB_to_file_full_path;
-import static pantools.Pantools.check_if_file_exists;
-import static pantools.Pantools.delete_file_in_DB;
-import static pantools.Pantools.delete_file_full_path;
-import static pantools.Pantools.check_if_program_exists_stdout;
-import static pantools.Pantools.check_if_program_exists_stderr;
-import static pangenome.create_skip_arrays.create_skip_arrays;
-import static pantools.Pantools.retrieve_phenotypes;
-import static pantools.Pantools.count_nodes;
-import static pantools.Pantools.stop_if_panproteome;
-import static pantools.Pantools.classification;
-import static pantools.Pantools.genome_label;
-import static pantools.Pantools.phenotype_label;
-import java.io.BufferedWriter;
-import java.io.FileWriter;
-import java.util.Date;
-import java.text.SimpleDateFormat;
-import static pantools.Pantools.genomeDb;
-import static pantools.Pantools.genomeSc;
-import static pantools.Pantools.indexSc;
+import org.neo4j.cypher.internal.compiler.v2_3.executionplan.builders.NodeFetchStrategy;
+import org.neo4j.graphdb.*;
+
+import java.io.*;
import java.text.DecimalFormat;
-import java.util.concurrent.BlockingQueue;
-import java.util.concurrent.ExecutorService;
-import java.util.concurrent.Executors;
-import java.util.concurrent.LinkedBlockingQueue;
-import java.util.concurrent.TimeUnit;
+import java.util.*;
+import java.util.concurrent.*;
import java.util.concurrent.atomic.AtomicInteger;
import java.util.concurrent.atomic.AtomicLong;
-import static pangenome.Classification.check_if_msa_is_complete;
-import static pangenome.Classification.divide;
-import static pangenome.Classification.stop_with_less_than_X_genomes;
-import static pangenome.Classification.trim_prealigned_proteins;
-import static pangenome.Classification.try_incr_hashset_hashmap;
-import static pangenome.Classification.try_incr_hashmap;
-import static pangenome.Classification.check_if_informative_position;
-import static pangenome.Classification.get_full_protein_identifiers;
-import static pangenome.Classification.read_genome_order_file;
-import static pangenome.Classification.read_mafft_alignment;
-import static pantools.Pantools.INPUT_FILE;
-import static pantools.Pantools.SELECTED_HMGROUPS;
-import static pantools.Pantools.annotation_identifiers;
-import static pantools.Pantools.check_current_grouping_version;
-import static pantools.Pantools.check_if_panproteome;
-import static pantools.Pantools.check_r_libraries_environment;
-import static pantools.Pantools.grouping_version;
-import static pantools.Pantools.write_fasta;
-import static pantools.Pantools.write_string_to_file_full_path;
-import static pantools.Pantools.PROTEOME;
-import static pantools.Pantools.FAST;
-import static pantools.Pantools.print_runtime;
-import sequence.SequenceScanner;
-import index.IndexScanner;
+
+import static nl.wur.bif.pantools.alignment.BoundedLocalSequenceAlignment.initialize_BLOSUM_matrix;
+import static nl.wur.bif.pantools.pangenome.Classification.*;
+import static nl.wur.bif.pantools.pangenome.create_skip_arrays.create_skip_arrays;
+import static nl.wur.bif.pantools.pantools.Pantools.*;
/**
*
@@ -134,20 +32,22 @@ public class Phylogeny {
private static AtomicLong atomic_counter1;
private static AtomicLong atomic_counter2;
private static int warning_counter = 0;
- public static boolean mlsa_function; // mlsa_find_gene can be used with or without the goal to use the sequences for a MLSA. Output directories are different
+ public static boolean mlsa_function; // mlsa_find_gene can be used with or without the goal to use the sequences for a MLSA. Output directories are different
final static public String[] COLOR_CODES = new String[]{"#fabebe","#bfef45","#42d4f4","#ffd8b1","#aaffc3","#fffac8","#e6beff","#469990","#e6194B","#f58231", "#ffe119",
"#3cb44b","#4363d8","#911eb4","#a9a9a9","#800000","#808000","#9A6324","#000075","#f032e6"};
-
+ final static public String[] COLORBLIND_CODES = new String[]{"#E69F00", "#56B4E9", "#009E73", "#0072B2", "#D55E00",
+ "#CC79A7", "#999999", "#F0E442", "#000000"}; // colourblind friendly palette up to 8 colors (9th value is black)
+
/**
* Function for mlsa_find_genes() and find_genes_by_name()
- * Requires
+ * Requires
* -dp
* --name
- *
+ *
* Optional
* --skip
* --reference
- * --mode extensive
+ * --mode extensive
* @param mlsa_function_boolean
*/
public void mlsa_find_genes(boolean mlsa_function_boolean) {
@@ -157,7 +57,7 @@ public class Phylogeny {
} else {
System.out.println("\nFinding genes in pangenome\n");
}
-
+
if (Mode.equals("0")) {
System.out.println("--mode extensive was NOT included. Can only find exact (and case insensitive) matches!");
} else if (Mode.equals("EXTENSIVE")) {
@@ -166,11 +66,11 @@ public class Phylogeny {
Mode = "0";
System.out.println("--mode was not recognized. Can only find exact (case insensitive) matches!");
}
- if (SELECTED_NAME == null) {
+ if (SELECTED_NAME == null) {
System.out.println("\nNo gene name was provided via --name\n");
System.exit(1);
- }
-
+ }
+
check_if_graphDb_is_available(); // starts up the graph database if needed
check_if_program_exists_stderr("mafft -h", 100, "MAFFT", true); // check if program is set to $PATH
try (Transaction tx = graphDb.beginTx()) {
@@ -181,9 +81,9 @@ public class Phylogeny {
tx.success(); // transaction successful, commit changes
} catch (NotFoundException nfe) {
System.out.println("Unable to start the database");
- return;
+ System.exit(1);
}
-
+
if (mlsa_function) {
create_directory_in_DB("mlsa/input/protein");
create_directory_in_DB("mlsa/input/nucleotide");
@@ -191,7 +91,7 @@ public class Phylogeny {
create_directory_in_DB("find_genes/by_name/protein_sequences");
create_directory_in_DB("find_genes/by_name/nucleotide_sequences");
}
-
+
try (Transaction tx = graphDb.beginTx()) { // start database transaction
if (mlsa_function) {
int hm_nodes = (int) count_nodes(homology_group_label);
@@ -207,35 +107,36 @@ public class Phylogeny {
tx.success(); // transaction successful, commit changes
}
if (mlsa_function) {
- System.out.println("\nStored sequences in\n "
- + WORKING_DIRECTORY + "mlsa/input/nucleotide/\n "
+ System.out.println("\nStored sequences in\n "
+ + WORKING_DIRECTORY + "mlsa/input/nucleotide/\n "
+ WORKING_DIRECTORY + "mlsa/input/protein/\n\n"
- + "Log file:\n "
+ + "Log file:\n "
+ WORKING_DIRECTORY + "mlsa/mlsa_find_genes.log\n");
if (warning_counter > 0) {
System.out.println("Important! " + warning_counter + " warnings were found! Check the log file!\n");
}
} else {
- System.out.println("\nOutput written to:\n "
+ System.out.println("\nOutput written to:\n "
+ WORKING_DIRECTORY + "find_genes/by_name/find_genes_by_name.log\n "
- + WORKING_DIRECTORY + "find_genes/by_name/nucleotide_sequences/\n "
+ + WORKING_DIRECTORY + "find_genes/by_name/nucleotide_sequences/\n "
+ WORKING_DIRECTORY + "find_genes/by_name/protein_sequences/\n");
}
}
-
+
/**
- *
+ *
* @param gene_names
* @param found_genes_map
- * @param case_insenstive
+ * @param case_insenstive
*/
public void find_gene_nodes_for_given_names(ArrayList<String> gene_names, HashMap<String, ArrayList<Node>> found_genes_map, boolean case_insenstive) {
ResourceIterator<Node> all_gene_nodes = graphDb.findNodes(gene_label);
int gene_nodes = (int) count_nodes(gene_label);
int gene_node_counter = 0;
+ System.out.print("\rSearching for gene names in gene nodes: ");
while (all_gene_nodes.hasNext()) {
- gene_node_counter ++;
- if (gene_node_counter % 100 == 0 || gene_nodes == gene_node_counter) {
+ gene_node_counter++;
+ if (gene_node_counter % 10000 == 0 || gene_nodes == gene_node_counter ) {
System.out.print("\rSearching for gene names in gene nodes: " + gene_node_counter + "/" + gene_nodes + " ");
}
Node gene_node = all_gene_nodes.next();
@@ -250,21 +151,37 @@ public class Phylogeny {
target_gene_name = target_gene_name.toLowerCase();
gene_name = gene_name.toLowerCase();
gene_name_key += "#case_insensitive";
- }
+ }
if (Mode.equals("EXTENSIVE") && gene_name.startsWith(target_gene_name)) {
try_incr_AL_hashmap(found_genes_map, gene_name_key, gene_node);
} else if (gene_name.equals(target_gene_name)) {
try_incr_AL_hashmap(found_genes_map, gene_name_key, gene_node);
}
}
+
+ String gene_id = (String) gene_node.getProperty("id");
+ for (String target_gene_name : gene_names) {
+ String gene_name_key = target_gene_name;
+ if (case_insenstive) {
+ target_gene_name = target_gene_name.toLowerCase();
+ gene_id = gene_id.toLowerCase();
+ gene_name_key += "#case_insensitive";
+ }
+ if (Mode.equals("EXTENSIVE") && gene_id.startsWith(target_gene_name)) {
+ try_incr_AL_hashmap(found_genes_map, gene_name_key, gene_node);
+ } else if (gene_id.equals(target_gene_name)) {
+ try_incr_AL_hashmap(found_genes_map, gene_name_key, gene_node);
+ }
+ }
+
}
System.out.print("\r ");
}
-
+
/**
- *
+ *
* @param gene_names
- * @return
+ * @return
*/
public HashMap<String, ArrayList<Node>> find_genes_by_name(ArrayList<String> gene_names) {
HashMap<String, ArrayList<Node>> found_genes_map = new HashMap<>();
@@ -281,22 +198,22 @@ public class Phylogeny {
}
if (!genes_without_hit.isEmpty()) { // search again but now case insensitive for genes without a hit
find_gene_nodes_for_given_names(genes_without_hit, found_genes_map, true);
- }
+ }
return found_genes_map;
}
-
+
/**
- *
+ *
* @param gene_names
- * @param found_genes_map
+ * @param found_genes_map
*/
public void report_found_genes(ArrayList<String> gene_names, HashMap<String, ArrayList<Node>> found_genes_map) {
StringBuilder log_builder = new StringBuilder();
System.out.println("\rgene name -> total hits/total genomes, range of gene lengths");
for (String gene_name : gene_names) {
SELECTED_NAME = gene_name;
- log_builder.append("#gene name ").append(gene_name).append(", genome, gene node id, mRNA node id, homology group id, gene length,"
- + " protein length, gene address\n");
+ log_builder.append("#gene name ").append(gene_name).append("; genome; gene node id; mRNA node id; homology group id; gene length;"
+ + " protein length; gene address\n");
ArrayList<Node> gene_list = found_genes_map.get(gene_name);
if (!gene_list.isEmpty()) {
retrieve_gene_seq_check_presence_hmgroup(gene_list, log_builder);
@@ -310,44 +227,45 @@ public class Phylogeny {
retrieve_gene_seq_check_presence_hmgroup(gene_list, log_builder);
}
}
- }
+ }
+
if (mlsa_function) {
- write_SB_to_file_in_DB(log_builder, "mlsa/mlsa_find_genes.log");
+ write_SB_to_file_in_DB(log_builder, "mlsa/mlsa_find_genes.log");
} else {
write_SB_to_file_in_DB(log_builder, "find_genes/by_name/find_genes_by_name.log");
}
}
-
+
/**
* SELECTED_NAME is by the user set via --name
- * @return
+ * @return
*/
public ArrayList<String> parse_gene_names() {
- ArrayList<String> gene_list = new ArrayList<>();
+ ArrayList<String> gene_list = new ArrayList<>();
if (SELECTED_NAME.contains(",")) {
String[] names = SELECTED_NAME.split(",");
for (String name : names) {
gene_list.add(name);
}
} else {
- gene_list.add(SELECTED_NAME);
+ gene_list.add(SELECTED_NAME);
}
System.out.println("\rSearching for " + SELECTED_NAME + " gene(s)");
return gene_list;
}
-
+
/**
- *
+ *
* First run mlsa_find_genes()
- * Requires
+ * Requires
* -dp
* -name gene,names,seperated,by,commas
- *
+ *
* Optional
* -skip
* -phenotype
- *
- */
+ *
+ */
public void mlsa_concatenate() {
System.out.println("\nMLSA Step 2/3. Concatenate sequences\n");
if (SELECTED_NAME == null) {
@@ -362,7 +280,7 @@ public class Phylogeny {
}
report_number_of_threads(true, true); // prints how many threads were selected by user
check_if_graphDb_is_available(); // starts up the graph database if needed
- try (Transaction tx = graphDb.beginTx()) { // start database transaction
+ try (Transaction tx = graphDb.beginTx()) { // start database transaction
Node pangenome_node = graphDb.findNodes(pangenome_label).next();
stop_if_panproteome(pangenome_node, "MLSA_concatenate"); // stops the progam when run on a panproteome, retrieves K_size & total_genomes
create_skip_arrays(false, true); // create skip array if --skip/-ref is provided by user
@@ -370,15 +288,16 @@ public class Phylogeny {
tx.success(); // transaction successful, commit changes
} catch (NotFoundException nfe) {
System.out.println("Unable to start the database");
+ System.exit(1);
}
graphDb.shutdown();
gene_names = concatenate_pre_alignment(gene_names);
concatenate_seq_in_dir(gene_names);
- System.out.println("\nOutput written to:\n "
+ System.out.println("\nOutput written to:\n "
+ WORKING_DIRECTORY + "mlsa/input/concatenated.fasta\n\n"
+ "Log file:\n " + WORKING_DIRECTORY + "mlsa/mlsa.info\n");
}
-
+
/*
--mode 1, skip over IQ-tree (this option is hidden in the manual)
*/
@@ -396,112 +315,134 @@ public class Phylogeny {
tx.success(); // transaction successful, commit changes
} catch (NotFoundException nfe) {
System.out.println("\rUnable to start the database");
- return;
+ System.exit(1);
}
if (Mode.equals("1") || Mode.contains("SKIP")) {
System.out.println("\r--mode skip selected. Skipping over IQtree");
}
-
+
read_concatenated_fasta_for_genome_order();
graphDb.shutdown();
check_if_program_exists_stderr("mafft -h", 100, "MAFFT", true);
- check_if_program_exists_stdout("iqtree -h", 100, "IQtree");
+ check_if_program_exists_stdout("iqtree -h", 100, "IQtree");
String path = WORKING_DIRECTORY + "mlsa/";
- if (!check_if_file_exists(WORKING_DIRECTORY+ "mlsa/input/concatenated.fasta")) {
- System.out.println("\rPlease run 'MLSA_concatenate' first!"
- + "\nNo sequences found in " + WORKING_DIRECTORY + "mlsa/input/concatenated.fasta\n");
- System.exit(1);
- }
-
+
System.out.print("\rStep 1/3. Aligning sequences using MAFFT");
run_alignment_for_mlsa();
-
-
+
System.out.println("\nStep 2/3. Identifying SNPs in the alignment.");
HashMap<String, Integer> shared_snps_map = new HashMap<>();
StringBuilder pheno_specific_output = new StringBuilder("# Each row contains: position in the alignment,"
- + " reference letter/other letters found, phenotype, "
- + "number of sequences with the phenotype and letter/total sequences with phenotype\n");
+ + " reference letter/other letters found, phenotype, "
+ + "number of sequences with the phenotype and letter/total sequences with phenotype\n");
HashMap<String, Integer> pheno_specific_group_sites = new HashMap<>();
if (PHENOTYPE == null) {
pheno_specific_output = null;
pheno_specific_group_sites = null;
- }
- int[] var_inf_sites = count_var_inf_sites_in_msa(shared_snps_map, pheno_specific_output,
+ }
+ int[] var_inf_sites = count_var_inf_sites_in_msa(shared_snps_map, pheno_specific_output,
pheno_specific_group_sites, path + "output/mlsa.afa", "MLSA", "nucleotide", path + "input/genome_order.info"); // variable, informative, shared between all
System.out.println("\nTotal variable/informative sites: " + var_inf_sites[0] + "/" + var_inf_sites[1]);
classification.create_shared_site_matrices(shared_snps_map, path + "output/var_inf_positions/", var_inf_sites[0], "", "nuc", path + "input/genome_order.info");
classification.create_shared_site_matrices(shared_snps_map, path + "output/var_inf_positions/", var_inf_sites[1], "#inf", "nuc", path + "input/genome_order.info");
delete_file_full_path(WORKING_DIRECTORY + "mlsa/input/genome_order.info");
-
-
+
+
System.out.println("\nStep 3/3. Running IQtree");
if (!Mode.equals("1") && !Mode.contains("SKIP") && var_inf_sites[1] > 0) { // these two modes were only created for development, not shown in manual
- LOG = true; // to print the iq-tree log output to the screen
+ LOG = true; // to print the iq-tree log output to the screen
String[] iq_command = {"iqtree", "-nt", threads_str, "-s", path + "output/mlsa.fasta","-redo","-bb", "1000"};
ExecCommand.ExecCommand(iq_command);
}
-
+
System.out.print("\nOutput written to:\n "
- + path + "output/\n "
- + path + "output/mlsa.afa\n "
+ + path + "output/\n "
+ + path + "output/mlsa.afa\n "
+ path + "output/mlsa.fasta\n "
- + path + "output/nuc_alignment.info\n ");
-
+ + path + "output/nuc_alignment.info\n ");
+
if (PHENOTYPE != null) {
- System.out.print(path + "output/nuc_phenotype_specific_changes.info\n ");
+ System.out.print(path + "output/nuc_phenotype_specific_changes.info\n ");
}
if (!Mode.equals("1") && !Mode.contains("SKIP")) { // these two modes were only created for development, not shown in manual
System.out.print(path + "output/mlsa.fasta.treefile\n "
+ path + "output/mlsa.fasta.contree\n "
+ path + "output/mlsa.fasta.iqtree\n");
- }
-
+ }
+
System.out.print("\n " + path + "output/var_inf_positions/variable_nuc_distance.csv\n "
- + path + "output/var_inf_positions/variable_nuc_site_counts.csv\n ");
+ + path + "output/var_inf_positions/variable_nuc_site_counts.csv\n ");
if (var_inf_sites[1] > 0) {
System.out.print(path + "output/var_inf_positions/informative_nuc_distance.csv\n "
- + path + "output/var_inf_positions/informative_nuc_site_counts.csv\n\n");
+ + path + "output/var_inf_positions/informative_nuc_site_counts.csv\n\n");
} else {
System.out.println("The alignment does not contains parsimony informative sites.\n"
+ "Unable to infer a phylogeny!\n");
}
- }
-
+ }
+
/**
* Creates a genome_order.info file, used by the functions that count SNPs in the alignment
+ * When a --phenotype is included, create a new fasta with phenotype info in the headers
*/
public void read_concatenated_fasta_for_genome_order() {
StringBuilder genome_order = new StringBuilder();
StringBuilder target_genomes = new StringBuilder();
- try (BufferedReader in = new BufferedReader(new FileReader(WORKING_DIRECTORY + "mlsa/input/concatenated.fasta"))) {
+ StringBuilder new_fasta = new StringBuilder();
+
+ if (!check_if_file_exists(WORKING_DIRECTORY+ "mlsa/input/concatenated.fasta")) {
+ System.out.println("\rPlease run 'MLSA_concatenate' first!"
+ + "\nNo sequences found in " + WORKING_DIRECTORY + "mlsa/input/concatenated.fasta\n");
+ System.exit(1);
+ }
+
+ try (BufferedReader in = new BufferedReader(new FileReader(WORKING_DIRECTORY + "mlsa/input/concatenated.fasta"))) {
for (int c = 0; in.ready();) {
String line = in.readLine().trim();
if (line.startsWith(">")) {
String[] line_array = line.split("_");
String genome_nr = line_array[0].replace(">","");
- genome_order.append(genome_nr).append(",").append(genome_nr).append("\n");
+
target_genomes.append(genome_nr).append(",");
+ if (PHENOTYPE != null) {
+ String current_pheno = geno_pheno_map.get(Integer.parseInt(genome_nr));
+ new_fasta.append(line_array[0]).append("_").append(current_pheno).append("\n");
+ genome_order.append(genome_nr).append(",").append(genome_nr + "_" + current_pheno ).append("\n");
+ } else {
+ genome_order.append(genome_nr).append(",").append(genome_nr).append("\n");
+ }
+ } else if (PHENOTYPE != null) {
+ new_fasta.append(line).append("\n");
}
}
} catch (IOException ioe) {
System.out.println("\nUnable to read: " + WORKING_DIRECTORY + "mlsa/input/concatenated.fasta\n");
System.exit(1);
}
-
+
+ delete_file_in_DB("mlsa/input/concatenated_pheno.fasta");
+ if (PHENOTYPE != null) {
+ write_SB_to_file_in_DB(new_fasta, "mlsa/input/concatenated_pheno.fasta");
+ }
+
+
String target_genomes_str = target_genomes.toString().replaceFirst(".$","");
target_genome = target_genomes_str;
create_skip_arrays(false, false); // create skip array if --skip/-ref is provided by user
write_SB_to_file_in_DB(genome_order, "mlsa/input/genome_order.info");
}
-
+
/**
- * Run MAFFT against concatenated.fasta (created by 'mlsa_concatenate')
+ * Run MAFFT against concatenated.fasta
*/
public void run_alignment_for_mlsa() {
- boolean pass = false;
+ String input_fasta = "concatenated.fasta";
+ if (PHENOTYPE != null) {
+ input_fasta = "concatenated_pheno.fasta";
+ }
+ boolean pass = false;
while (!pass) {
- String[] command = {"mafft","--auto", "--anysymbol", "--thread", THREADS +"", "--clustalout", WORKING_DIRECTORY + "mlsa/input/concatenated.fasta"};
+ String[] command = {"mafft","--auto", "--anysymbol", "--thread", THREADS +"", "--clustalout", WORKING_DIRECTORY + "mlsa/input/" + input_fasta};
String mafft_output = ExecCommand.ExecCommand(command);
if (!mafft_output.equals("")) {
pass = true;
@@ -509,13 +450,13 @@ public class Phylogeny {
}
}
System.out.print(".");
- convert_afa_to_aligned_fasta(WORKING_DIRECTORY + "mlsa/input/concatenated.fasta", WORKING_DIRECTORY + "mlsa/output/mlsa.afa");
- }
-
+ convert_afa_to_aligned_fasta(WORKING_DIRECTORY + "mlsa/input/" + input_fasta, WORKING_DIRECTORY + "mlsa/output/mlsa.afa");
+ }
+
/**
- *
+ *
* @param gene_name
- * @param path
+ * @param path
*/
public static void run_alignment_for_mlsa_concatenate(String gene_name, String path) {
boolean pass = false;
@@ -528,21 +469,21 @@ public class Phylogeny {
}
}
}
-
+
/**
* 1. Align protein sequences
- * 2. Find longest start and end gap in protein prealignment. Multiply by aa by 3 to trim nucleotide input sequences.
+ * 2. Find longest start and end gap in protein prealignment. Multiply by aa by 3 to trim nucleotide input sequences.
* 3. Align trimmed nucleotide sequences
- * 4. Report variable & informative sites
- * @param gene_names
- * @return
+ * 4. Report variable & informative sites
+ * @param gene_names
+ * @return
*/
public String[] concatenate_pre_alignment(String[] gene_names) {
String new_gene_names = ""; // exclude the genes that cannot be used
initialize_BLOSUM_matrix(62);
- System.out.println("\rGene name: Maximum bases trimmed from START/END of nucleotide sequences -> "
- + "variable/informative sites in protein prealignment -> variable/informative sites in trimmed nucleotide alignment");
-
+ System.out.println("\rGene name: Maximum bases trimmed from START/END of nucleotide sequences -> " +
+ "Parsimony informative sites in trimmed nucleotide alignment");
+
boolean incorrect_input = false;
for (String gene_name : gene_names) {
if (!check_if_file_exists(WORKING_DIRECTORY + "mlsa/input/protein/" + gene_name + ".fasta")) {
@@ -556,34 +497,34 @@ public class Phylogeny {
continue;
}
new_gene_names += gene_name + ",";
-
String info = "\r" + gene_name + ": ";
System.out.print(info + "Running initial alignment");
- run_alignment_for_mlsa_concatenate(gene_name, WORKING_DIRECTORY + "mlsa/input/protein/");
- convert_afa_to_aligned_fasta(WORKING_DIRECTORY + "mlsa/input/protein/" + gene_name + ".fasta",
- WORKING_DIRECTORY + "mlsa/input/protein/" + gene_name + "_aligned.afa");
+ run_alignment_for_mlsa_concatenate(gene_name, WORKING_DIRECTORY + "mlsa/input/protein/");
+ convert_afa_to_aligned_fasta(WORKING_DIRECTORY + "mlsa/input/protein/" + gene_name + ".fasta",
+ WORKING_DIRECTORY + "mlsa/input/protein/" + gene_name + "_aligned.afa");
String prot_file = WORKING_DIRECTORY + "mlsa/input/protein/" + gene_name + "_aligned.fasta";
HashMap<String, Integer> shared_snps_map = new HashMap<>();
- int[] prot_var_inf_sites = count_var_inf_sites_in_msa(shared_snps_map, null, null,
+ int[] prot_var_inf_sites = count_var_inf_sites_in_msa(shared_snps_map, null, null,
WORKING_DIRECTORY + "mlsa/input/protein/" + gene_name + "_aligned.afa",
- "Multiple sequence alignment", "protein",
+ "Multiple sequence alignment", "protein",
WORKING_DIRECTORY + "mlsa/input/protein/" + gene_name + ".order"); // variable, informative, shared between all
- HashMap<String, int[]> seq_trim_map = new HashMap<>();
- int[] longest_start_end_gap = count_aa_to_trim(prot_file, seq_trim_map);
- info += longest_start_end_gap[0]*3 + "/" + longest_start_end_gap[1]*3 + " -> " + prot_var_inf_sites[0] + "/" + prot_var_inf_sites[1];
+
+ HashMap<String, int[]> seq_trim_map = new HashMap<>();
+ int[] longest_start_end_gap = count_aa_to_trim(prot_file, seq_trim_map);
+ info += longest_start_end_gap[0] * 3 + "/" + longest_start_end_gap[1] * 3;
System.out.print(info + ". Running second alignment ");
if (longest_start_end_gap[0] + longest_start_end_gap[1] > longest_start_end_gap[2]) {
System.out.print(" No sequence left after trimming!\n");
continue;
- }
+ }
trim_sequences(seq_trim_map, gene_name, WORKING_DIRECTORY + "mlsa/input/nucleotide/" + gene_name + ".fasta", true);
run_alignment_for_mlsa_concatenate(gene_name +"_trimmed", WORKING_DIRECTORY + "mlsa/input/nucleotide/");
shared_snps_map = new HashMap<>();
-
- int[] nuc_var_inf_sites = count_var_inf_sites_in_msa(shared_snps_map, null, null,
- WORKING_DIRECTORY + "mlsa/input/nucleotide/" + gene_name + "_trimmed_aligned.afa", "Multiple sequence alignment", "nucleotide",
+
+ int[] nuc_var_inf_sites = count_var_inf_sites_in_msa(shared_snps_map, null, null,
+ WORKING_DIRECTORY + "mlsa/input/nucleotide/" + gene_name + "_trimmed_aligned.afa", "Multiple sequence alignment", "nucleotide",
WORKING_DIRECTORY + "mlsa/input/protein/" + gene_name + ".order"); // variable, informative, shared between all
- info += " -> " + nuc_var_inf_sites[0] + "/" + nuc_var_inf_sites[1];
+ info += " -> " + nuc_var_inf_sites[1];
System.out.println(info + " ");
delete_file_full_path(WORKING_DIRECTORY + "mlsa/input/protein/" + gene_name + ".order");
delete_file_full_path(WORKING_DIRECTORY + "mlsa/input/nucleotide/nuc_alignment_info.txt");
@@ -592,21 +533,21 @@ public class Phylogeny {
if (new_gene_names.length() < 2) {
System.out.println("\nNone of the given input genes were appropriate for the MLSA.\n"
+ "1. Use the same genome selection as in 'mlsa_find_genes'\n"
- + "2. If the same selection is used but the problem reoccurs, check the log file of 'mlsa_find_genes' and adjust the input files.\n" );
+ + "2. If the same selection is used but the problem reoccurs, check the log file of 'mlsa_find_genes' and adjust the input files.\n");
System.exit(1);
}
if (incorrect_input) {
System.out.println("\nAt least one of the given input genes had the incorrect number of sequences for the MLSA. If you want to include this gene:\n"
+ "1. Use the same genome selection as in 'mlsa_find_genes'\n"
- + "2. If the same selection is used but the problem reoccurs, check the log file of 'mlsa_find_genes' and adjust the input files.\n" );
+ + "2. If the same selection is used but the problem reoccurs, check the log file of 'mlsa_find_genes' and adjust the input files.\n");
}
return new_gene_names.split(",");
}
-
+
/**
* Create a .order file, required for the SNP extraction function
* @param input
- * @return
+ * @return
*/
public int count_seqs_in_fasta(String input) {
int seq_count = 0;
@@ -618,13 +559,13 @@ public class Phylogeny {
continue;
}
if (line.contains(">")) {
- seq_count ++;
+ seq_count++;
line = line.replace(">","");
String[] line_array = line.split("_gn_");
String[] line_array2 = line_array[1].split("_");
genome_order.append(line_array2[0]).append(",").append(line).append("\n");
}
- }
+ }
} catch (IOException e) {
System.out.println(e.getMessage());
System.exit(1);
@@ -634,27 +575,27 @@ public class Phylogeny {
}
/**
- *
- * @param gene_names
- */
+ *
+ * @param gene_names
+ */
public static void concatenate_seq_in_dir(String[] gene_names) {
String path = WORKING_DIRECTORY + "mlsa/input/nucleotide/";
StringBuilder log_builder = new StringBuilder();
File folder = new File(path);
String[] files = folder.list();
StringBuilder output = new StringBuilder();
- HashMap<String, StringBuilder> dna_seq_map = new HashMap<>();
+ HashMap<String, StringBuilder> dna_seq_map = new HashMap<>();
boolean stop = false;
String stop_info = "";
- for (String file : files) {
- if (!file.contains("_trimmed.fasta")) {
+ for (String file : files) {
+ if (!file.contains("_trimmed.fasta")) {
continue;
}
String gene_name = file.replace("_trimmed.fasta","");
if (!ArrayUtils.contains(gene_names, gene_name)) {
continue;
}
-
+
try {
BufferedReader in = new BufferedReader(new FileReader(path + file));
int line_count = 0;
@@ -665,31 +606,31 @@ public class Phylogeny {
continue;
}
if (line.contains(">")) {
- line_count ++;
+ line_count++;
String[] line_list = line.split("gn_");
String[] line_list2 = line_list[1].split("_");
current_genome = line_list2[0];
- } else {
+ } else {
try_incr_SB_hashmap(dna_seq_map, current_genome, line);
}
}
in.close();
if (line_count < adj_total_genomes) {
- stop = true;
- stop_info = " lines found: " + line_count + ". should be " + adj_total_genomes;
+ stop = true;
+ stop_info = " lines found: " + line_count + ". should be " + adj_total_genomes;
}
} catch (IOException e) {
- System.out.println(e.getMessage());
- System.exit(1);
+ System.out.println(e.getMessage());
+ System.exit(1);
}
}
if (stop) {
System.out.println("Unable to use the concatenated sequence for MLSA!\n" + stop_info);
System.exit(1);
}
-
+
int counter = 0;
- TreeSet<Integer> all_sizes = new TreeSet<>();
+ TreeSet<Integer> all_sizes = new TreeSet<>();
for (String genome_key : dna_seq_map.keySet()) {
int genome_nr = Integer.valueOf(genome_key);
StringBuilder builder = dna_seq_map.get(genome_key);
@@ -697,18 +638,18 @@ public class Phylogeny {
if (skip_array[genome_nr-1]) {
continue;
}
-
+
if (PHENOTYPE != null) {
String pheno = geno_pheno_map.get(genome_nr);
genome_key += "_" + pheno;
}
-
+
log_builder.append(genome_key).append(", ").append(seq_str.length()).append("bp\n");
all_sizes.add(seq_str.length());
output.append(">").append(genome_key).append("\n").append(seq_str).append("\n");
- counter ++;
- }
-
+ counter++;
+ }
+
String info = counter + " genomes\n"
+ "Genes: " + SELECTED_NAME + "\n"
+ "All sizes: " + all_sizes + "\n\n";
@@ -720,18 +661,18 @@ public class Phylogeny {
write_string_to_file_in_DB(info + log_builder.toString(), "mlsa/mlsa.info");
write_SB_to_file_full_path(output, WORKING_DIRECTORY + "mlsa/input/concatenated.fasta");
}
-
+
/**
- *
+ *
* @param gene_list
* @param log_builder
- * @return
- *
- * The functions assumes there is only one mRNA for each gene. Will not work for eukaryotes
+ * @return
+ *
+ * The functions assumes there is only one mRNA for each gene. Will not work for eukaryotes
*/
public boolean retrieve_gene_seq_check_presence_hmgroup(ArrayList<Node> gene_list, StringBuilder log_builder) {
- HashMap<Node, StringBuilder> prot_seqs_per_hmgroup = new HashMap<>();
- HashMap<Node, StringBuilder> dna_seqs_per_hmgroup = new HashMap<>();
+ HashMap<Node, StringBuilder> prot_seqs_per_hmgroup = new HashMap<>(); // key is homology node.
+ HashMap<Node, StringBuilder> nuc_seqs_per_hmgroup = new HashMap<>();
HashMap<Node, ArrayList<Integer>> dna_lengths_per_hmgroup = new HashMap<>();
HashMap<Node, ArrayList<Integer>> prot_lengths_per_hmgroup = new HashMap<>();
StringBuilder prot_seq_builder = new StringBuilder();
@@ -740,14 +681,14 @@ public class Phylogeny {
ArrayList<Integer> protein_length_list = new ArrayList<>();
HashMap<Integer, Integer> gene_genome_map = new HashMap<>();
int [] presence_array = new int[total_genomes];
- for(int i = 1 ; i < total_genomes + 1; ++i) {
- gene_genome_map.put(i, 0);
+ for(int i = 1 ; i <= total_genomes; i++) {
+ gene_genome_map.put(i, 0);
}
- HashMap<String, String> prot_seqs_per_genome = new HashMap<>();
- // key is genome_nr "_" + copy_number. Value is protein sequence used for when multiple copies are found
+ HashMap<String, String> prot_seqs_per_genome = new HashMap<>();
+ // key is genome_nr "_" + copy_number. Value is protein sequence used for when multiple copies are found
HashMap<String, String> nuc_seqs_per_genome = new HashMap<>();
- Set<Node> all_hms = new HashSet<>();
-
+ Set<Node> all_hms = new HashSet<>(); // homology_group nodes
+
String address_str = "";
for (Node gene_node : gene_list) {
int gene_length = 0, protein_length = 0;
@@ -757,14 +698,14 @@ public class Phylogeny {
}
String gene_name = (String) gene_node.getProperty("name");
Iterable<Relationship> rels = gene_node.getRelationships(RelTypes.codes_for);
- String prot_seq = "", nuc_seq = "", seq_header = "", mrna_node_str = "";
- for (Relationship rel : rels) { // for MLSA, the functions assumes there is only one mRNA for each gene. Will not work for eukaryotes
+ String prot_sequence = "", nuc_sequence = "", seq_header = "", mrna_node_str = "", hm_node_str = "no homology group";
+ for (Relationship rel : rels) { // for MLSA, the functions assumes there is only one mRNA for each gene. Will not work for eukaryotes
Node mrna_node = rel.getEndNode();
mrna_node_str = mrna_node.getId() +"";
- if (!mrna_node.hasProperty("protein_ID")) {
+ if (!mrna_node.hasProperty("protein_ID")) {
continue;
}
-
+
String protein_id = (String) mrna_node.getProperty("protein_ID");
gene_length = (int) mrna_node.getProperty("length");
protein_length = (int) mrna_node.getProperty("protein_length");
@@ -772,64 +713,73 @@ public class Phylogeny {
address_str = address[0] + " " + address[1] + " " + address[2] + " " + address[3];
gene_length_list.add(gene_length);
protein_length_list.add(protein_length);
- Relationship hm_rel = mrna_node.getSingleRelationship(RelTypes.has_homolog, Direction.INCOMING);
- String hm_node_str = "";
- if (hm_rel != null) { // mrna is connected to an homology_group node
+ Relationship hm_rel = mrna_node.getSingleRelationship(RelTypes.has_homolog, Direction.INCOMING);
+
+ prot_sequence = get_protein_sequence(mrna_node);
+ nuc_sequence = get_nucleotide_sequence(mrna_node);
+ prot_sequence = split_seq_in_parts_of_80bp(prot_sequence);
+ nuc_sequence = split_seq_in_parts_of_80bp(nuc_sequence);
+ String phenotype = get_phenotype_for_genome(genome_nr, true);
+ if (hm_rel != null) { // mrna is connected to an homology_group node
Node hm_node = hm_rel.getStartNode();
- hm_node_str = hm_node.getId() +"";
+ hm_node_str = hm_node.getId() +"";
+ if (mlsa_function) {
+ seq_header = ">" + protein_id + " " + gene_name + "_gn_" + genome_nr + "_" + gene_node.getId() + "_hmgroup_" + hm_node.getId() + phenotype + "\n";
+ } else {
+ seq_header = ">" + protein_id + " " + gene_name + " " + genome_nr + phenotype + "\n";
+ }
all_hms.add(hm_node);
try_incr_AL_hashmap(dna_lengths_per_hmgroup, hm_node, gene_length);
try_incr_AL_hashmap(prot_lengths_per_hmgroup, hm_node, protein_length);
- try_incr_SB_hashmap(prot_seqs_per_hmgroup, hm_node, seq_header + prot_seq +"\n");
- try_incr_SB_hashmap(dna_seqs_per_hmgroup, hm_node, seq_header + nuc_seq +"\n");
- }
-
- String phenotype = get_phenotype_for_genome(genome_nr, true);
- if (mlsa_function) {
- seq_header = ">" + protein_id + " " + gene_name + "_gn_" + genome_nr + "_" + gene_node.getId() + "_hmgroup_" + hm_node_str + phenotype + "\n";
- } else {
- seq_header = ">" + protein_id + " " + gene_name + " " + genome_nr + phenotype + "\n";
+ try_incr_SB_hashmap(prot_seqs_per_hmgroup, hm_node, seq_header + prot_sequence +"\n");
+ try_incr_SB_hashmap(nuc_seqs_per_hmgroup, hm_node, seq_header + nuc_sequence +"\n");
+ } else { // proteins are not clustered
+ if (mlsa_function) {
+ seq_header = ">" + protein_id + " " + gene_name + "_gn_" + genome_nr + "_" + gene_node.getId() + phenotype + "\n";
+ } else {
+ seq_header = ">" + protein_id + " " + gene_name + " " + genome_nr + phenotype + "\n";
+ }
}
- prot_seq = get_protein_sequence(mrna_node);
- nuc_seq = get_nucleotide_sequence(mrna_node);
-
- }
- if (gene_length == 0) {
- log_builder.append(gene_name).append(", ").append(genome_nr).append(", ").append(gene_node.getId()).append(", ").append(mrna_node_str)
- .append(", Protein sequence is missing! Something wrong with GFF?\n");
- continue;
- }
- presence_array[genome_nr-1] ++;
+ }
+ if (gene_length == 0) {
+ log_builder.append(gene_name).append(", ").append(genome_nr).append(", ").append(gene_node.getId()).append(", ").append(mrna_node_str)
+ .append(", Protein sequence is missing! Something wrong with GFF?\n");
+ continue;
+ }
+ presence_array[genome_nr-1]++;
log_builder.append(gene_name).append("; ").append(genome_nr).append("; ").append(gene_node.getId()).append("; ").append(mrna_node_str).append("; ")
- .append(all_hms.toString()).append("; ").append(gene_length).append("; ").append(protein_length).append("; ").append(address_str).append("\n");
+ .append(hm_node_str).append("; ").append(gene_length).append("; ").append(protein_length).append("; ").append(address_str).append("\n");
int gene_count = gene_genome_map.get(genome_nr);
- gene_count ++;
- gene_genome_map.put(genome_nr, gene_count);
- prot_seqs_per_genome.put(genome_nr + "_" + gene_count + "_header" , seq_header);
- prot_seqs_per_genome.put(genome_nr + "_" + gene_count, prot_seq);
- nuc_seqs_per_genome.put(genome_nr + "_" + gene_count, nuc_seq);
- }
-
- boolean multi_groups = false;
+ gene_count++;
+ gene_genome_map.put(genome_nr, gene_count);
+ prot_seqs_per_genome.put(genome_nr + "_" + gene_count + "_header", seq_header);
+ prot_seqs_per_genome.put(genome_nr + "_" + gene_count, prot_sequence);
+ nuc_seqs_per_genome.put(genome_nr + "_" + gene_count, nuc_sequence);
+ }
+
+ boolean multi_groups = false; // when true, the genes are found in multiple homology groups
if (prot_seqs_per_hmgroup.size() > 1) {
multi_groups = true;
if (mlsa_function) {
create_directory_in_DB("/mlsa/input/protein/" + SELECTED_NAME);
create_directory_in_DB("/mlsa/input/nucleotide/" + SELECTED_NAME);
- } else {
+ } else {
create_directory_in_DB("find_genes/by_name/protein_sequences/" + SELECTED_NAME);
- create_directory_in_DB("find_genes/by_name/nucleotide_sequences/" + SELECTED_NAME);
+ create_directory_in_DB("find_genes/by_name/nucleotide_sequences/" + SELECTED_NAME);
}
for (Node hm_node : prot_seqs_per_hmgroup.keySet()) {
- long hm_node_id = hm_node.getId();
StringBuilder prot_seq = prot_seqs_per_hmgroup.get(hm_node);
- StringBuilder dna_seq = prot_seqs_per_hmgroup.get(hm_node);
+ StringBuilder nuc_seq = nuc_seqs_per_hmgroup.get(hm_node);
if (mlsa_function) {
- write_SB_to_file_in_DB(prot_seq, "/mlsa/input/protein/" + SELECTED_NAME + "/" + hm_node_id + ".fasta");
- write_SB_to_file_in_DB(dna_seq, "/mlsa/input/nucleotide/" + SELECTED_NAME + "/" + hm_node_id + ".fasta");
+ write_SB_to_file_in_DB(prot_seq, "/mlsa/input/protein/" + SELECTED_NAME + "/" + hm_node.getId() + ".fasta");
+ write_SB_to_file_in_DB(nuc_seq, "/mlsa/input/nucleotide/" + SELECTED_NAME + "/" + hm_node.getId() + ".fasta");
+ append_SB_to_file_in_DB(nuc_seq, "/mlsa/input/protein/" + SELECTED_NAME + "/all_sequence.fasta");
+ append_SB_to_file_in_DB(nuc_seq, "/mlsa/input/nucleotide/" + SELECTED_NAME + "/all_sequence.fasta");
} else {
- write_SB_to_file_in_DB(prot_seq, "find_genes/by_name/nucleotide_sequences/" + SELECTED_NAME + "/" + hm_node_id + ".fasta");
- write_SB_to_file_in_DB(dna_seq, "find_genes/by_name/protein_sequences/" + SELECTED_NAME + "/" + hm_node_id + ".fasta");
+ write_SB_to_file_in_DB(prot_seq, "find_genes/by_name/nucleotide_sequences/" + SELECTED_NAME + "/" + hm_node.getId() + ".fasta");
+ write_SB_to_file_in_DB(nuc_seq, "find_genes/by_name/protein_sequences/" + SELECTED_NAME + "/" + hm_node.getId() + ".fasta");
+ append_SB_to_file_in_DB(nuc_seq, "find_genes/by_name/nucleotide_sequences/" + SELECTED_NAME + "/all_sequence.fasta");
+ append_SB_to_file_in_DB(nuc_seq, "find_genes/by_name/protein_sequences/" + SELECTED_NAME + "/all_sequence.fasta");
}
}
}
@@ -841,7 +791,7 @@ public class Phylogeny {
double protein_average = get_average_from_AL_int(protein_length_list);
String prot_avg_str = String.format("%.2f", protein_average);
String protein_lengths = determine_frequency_list_int(protein_length_list);
-
+
log_builder.append("\nAverage gene length: ").append(gene_avg_str)
.append("\nAll gene lengths: ").append(gene_lengths)
.append("\nAverage protein length: ").append(prot_avg_str)
@@ -857,7 +807,7 @@ public class Phylogeny {
absent_genomes += genome_nr + ",";
} else {
present_genomes += genome_nr + ",";
- if (value > 1) {
+ if (value > 1) {
HashSet<Integer> duplicate_set = check_if_duplicate_sequences(value, genome_nr, prot_seqs_per_genome);
if (value - duplicate_set.size() == 1) {
if (duplicate_set.size() == 1) {
@@ -867,16 +817,16 @@ public class Phylogeny {
.append(genome_nr).append(" because they are identical\n");
}
for (int copy_number: duplicate_set) {
- prot_seqs_per_genome.remove(genome_nr + "_" + copy_number);
+ prot_seqs_per_genome.remove(genome_nr + "_" + copy_number);
nuc_seqs_per_genome.remove(genome_nr + "_" + copy_number);
}
- } else { // extra copy
+ } else { // extra copy
multiple_copies += genome_nr + ",";
}
}
}
- }
-
+ }
+
for (Map.Entry<String, String> entry : nuc_seqs_per_genome.entrySet()) {
String genome_str = entry.getKey();
String nuc_seq = entry.getValue();
@@ -885,7 +835,7 @@ public class Phylogeny {
prot_seq_builder.append(header).append(prot_seq).append("\n");
nuc_seq_builder.append(header).append(nuc_seq).append("\n");
}
-
+
absent_genomes = absent_genomes.replaceFirst(".$","");
present_genomes = present_genomes.replaceFirst(".$","");
multiple_copies = multiple_copies.replaceFirst(".$","");
@@ -893,43 +843,47 @@ public class Phylogeny {
// do nothing
} else {
log_builder.append("\nWarning! Gene was not found!\n\n");
- warning_counter ++;
+ warning_counter++;
return false;
}
- String[] present_array = present_genomes.split(",");
+ String[] present_array = present_genomes.split(",");
String size_str = get_size_str(distinct_gene_lengths);
System.out.println(SELECTED_NAME + " -> " + gene_list.size() + "/" + present_array.length + ", " + size_str);
boolean absent = true;
if (absent_genomes.length() > 27) {
log_builder.append(present_genomes).append("\n")
.append(absent_genomes).append("\n");
- warning_counter ++;
+ warning_counter++;
} else {
log_builder.append("Gene was found in every genome!\n");
absent = false;
}
-
+
if (multiple_copies.length() > 29) {
log_builder.append("Warning! ").append(multiple_copies).append("\n");
- warning_counter ++;
- }
+ warning_counter++;
+ }
+
if (all_hms.size() == 1) {
log_builder.append("All genes are part of the same homology group\n");
if (multiple_copies.length() > 29 && !absent) { // 1 group but multiple copies, extra warning!
- log_builder.append("Warning! You must remove duplicate copies from the input files\n ")
- .append(WORKING_DIRECTORY).append("/mlsa/input/nucleotide/").append(SELECTED_NAME).append(".fasta\n ")
- .append(WORKING_DIRECTORY).append("/mlsa/input/protein/").append(SELECTED_NAME).append(".fasta\n");
- warning_counter ++;
+ log_builder.append("Warning! You must remove duplicate copies from the input files\n ")
+ .append(WORKING_DIRECTORY).append("/mlsa/input/nucleotide/").append(SELECTED_NAME).append(".fasta\n ")
+ .append(WORKING_DIRECTORY).append("/mlsa/input/protein/").append(SELECTED_NAME).append(".fasta\n");
+ warning_counter++;
}
} else if (all_hms.size() > 1) {
- log_builder.append("Warning! Genes were found in ").append(all_hms.size()).append(" different homology groups!\n");
- warning_counter ++;
- }else {
+ log_builder.append("Warning! Genes were found in ").append(all_hms.size()).append(" different homology groups! Sequences for are written to:\n")
+ .append(" ").append(WORKING_DIRECTORY).append("mlsa/input/protein/").append(SELECTED_NAME).append("/\n")
+ .append(" ").append(WORKING_DIRECTORY).append("mlsa/input/nucleotide/").append(SELECTED_NAME).append("/\n\n");
+ warning_counter++;
+ } else {
log_builder.append("Warning! No (active) homology grouping is present!\n");
- warning_counter ++;
+ warning_counter++;
}
-
+
StringBuilder hm_builder = new StringBuilder();
+ int perfect_group_counter = 0;
for (Node hm_node : all_hms) {
ArrayList<Integer> dna_lengths_lists = dna_lengths_per_hmgroup.get(hm_node);
ArrayList<Integer> prot_lengths_lists = prot_lengths_per_hmgroup.get(hm_node);
@@ -941,15 +895,20 @@ public class Phylogeny {
hm_builder.append("Homology group ").append(hm_node.getId()).append(", ").append(num_members).append(" members ").append(Arrays.toString(copy_number))
.append("\nGene lengths: ").append(dna_freqs)
.append("\nProtein lengths: ").append(prot_freqs).append("\n");
- if (multi_groups && num_members == total_genomes) {
+
+ if (multi_groups && num_members == total_genomes && perfect_group_counter == 0) {
log_builder.append("Warning! Multiple homology groups are found! Group ").append(hm_node.getId()).append(" is selected for ").append(SELECTED_NAME)
.append(".fasta as the group size matches the number of genomes.\n");
prot_seq_builder = prot_seqs_per_hmgroup.get(hm_node);
- nuc_seq_builder = dna_seqs_per_hmgroup.get(hm_node);
- warning_counter ++;
+ nuc_seq_builder = nuc_seqs_per_hmgroup.get(hm_node);
+ warning_counter++;
+ perfect_group_counter++;
+ } else if (multi_groups && num_members == total_genomes) {
+ log_builder.append("Warning! Group ").append(hm_node.getId()).append(" is also suitable for the analysis for ").append(SELECTED_NAME)
+ .append(". It was not selected because a suitable candidate was already found. \n");
}
}
-
+
log_builder.append("\n").append(hm_builder.toString()).append("\n");
if (mlsa_function) {
write_SB_to_file_in_DB(prot_seq_builder, "/mlsa/input/protein/" + SELECTED_NAME + ".fasta");
@@ -960,11 +919,11 @@ public class Phylogeny {
}
return true;
}
-
+
/**
- *
+ *
* @param distinct_gene_lengths
- * @return
+ * @return
*/
public String get_size_str(ArrayList<Integer> distinct_gene_lengths) {
int size1 = distinct_gene_lengths.get(0);
@@ -972,18 +931,18 @@ public class Phylogeny {
if (distinct_gene_lengths.size() == 1) {
size_str += "bp";
return size_str;
- }
+ }
int size2 = distinct_gene_lengths.get(distinct_gene_lengths.size() - 1);
size_str += "-" + size2 + "bp";
return size_str;
}
/**
- *
+ *
* @param value
* @param genome_nr
* @param prot_seqs_per_genome
- * @return
+ * @return
*/
public HashSet<Integer> check_if_duplicate_sequences(int value, int genome_nr, HashMap<String, String> prot_seqs_per_genome) {
HashSet<Integer> duplicate_set = new HashSet<>();
@@ -1004,21 +963,21 @@ public class Phylogeny {
/**
* Calculates ANI scores for every genome combination. These results should be comparable to JspeciesWS.
- *
- * Requires
- * -dp
- *
+ *
+ * Requires
+ * -dp
+ *
* Optional
* --phenotype
* --mode fastani or mash. uses mash if nothing was selected.
- *
+ *
*/
public void calculate_ani() {
String program = mash_or_fastaANI(); // check --mode argument and checks if required software is set to $PATH
create_directory_in_DB("/databases/genome.db/genomes");
- HashMap<Integer, String> genome_path_map = new HashMap<>();
- HashMap<String,Integer> path_genome_map = new HashMap<>();
-
+ HashMap<Integer, String> genome_path_map = new HashMap<>();
+ HashMap<String,Integer> path_genome_map = new HashMap<>();
+
connect_pangenome(); // starts up the graph database if needed
try (Transaction tx = graphDb.beginTx()) { // start database transaction
Node pangenome_node = graphDb.findNodes(pangenome_label).next();
@@ -1031,52 +990,52 @@ public class Phylogeny {
// index and genomescanner required for reconstructing genomes (if required)
indexSc = new IndexScanner(indexDb);
genomeSc = new SequenceScanner(genomeDb, 1, 1, K_SIZE, indexSc.get_pre_len());
-
+
create_skip_arrays(false, true); // create skip array if -skip/-ref is provided by user
try (Transaction tx = graphDb.beginTx()) { // start database transaction
retrieve_phenotypes(); // Creates and fills geno_pheno_map and phenotype_map when a phenotype was provided by the user
ResourceIterator<Node> genome_nodes = graphDb.findNodes(genome_label);
- while (genome_nodes.hasNext()) { // retrieve genome locations
+ while (genome_nodes.hasNext()) { // retrieve genome locations
Node genome_node = genome_nodes.next();
int genome_nr = (int) genome_node.getProperty("number");
String genome_path = (String) genome_node.getProperty("path");
genome_path = reconstruct_genome_if_not_present(genome_path, genome_nr);
-
+
genome_path_map.put(genome_nr, genome_path);
path_genome_map.put(genome_path, genome_nr);
- }
-
+ }
+
HashMap<String, Double> ani_score_map = calculate_ani_loop(genome_path_map, path_genome_map, program);
boolean typestrains_present = compare_to_typestrains(ani_score_map, program);
create_ani_distance_matrix(program);
create_ani_rscript(program);
- System.out.print("\n\nOutput written to:\n "
- + WORKING_DIRECTORY+ "ANI/" + program + "/ANI_scores.csv\n "
+ System.out.print("\n\nOutput written to:\n "
+ + WORKING_DIRECTORY+ "ANI/" + program + "/ANI_scores.csv\n "
+ WORKING_DIRECTORY + "ANI/" + program + "/ANI_distance_matrix.csv\n "
+ WORKING_DIRECTORY + "ANI/" + program + "/ANI_tree.R\n ");
if (typestrains_present) {
- System.out.print(WORKING_DIRECTORY + "ANI/" + program + "/typestrain_comparison.csv\n\n");
+ System.out.print(WORKING_DIRECTORY + "ANI/" + program + "/typestrain_comparison.csv\n\n");
} else {
- System.out.print("\n");
+ System.out.print("\n");
}
tx.success(); // transaction successful, commit changes
}
graphDb.shutdown();
}
-
+
/**
- *
+ *
* @param genome_path
* @param genome_nr
- * @return
- */
- public static String reconstruct_genome_if_not_present(String genome_path, int genome_nr) {
- if (check_if_file_exists(genome_path)) {
+ * @return
+ */
+ public static String reconstruct_genome_if_not_present(String genome_path, int genome_nr) {
+ if (check_if_file_exists(genome_path)) {
return genome_path;
}
- StringBuilder seq = new StringBuilder();
+ StringBuilder seq = new StringBuilder();
try (BufferedWriter out = new BufferedWriter(new FileWriter(WORKING_DIRECTORY + "/databases/genome.db/Genome_" + genome_nr + ".fasta"))) {
- for (int sequence = 1; sequence <= genomeDb.num_sequences[genome_nr]; ++sequence) {
+ for (int sequence = 1; sequence <= genomeDb.num_sequences[genome_nr]; sequence++) {
out.write(">" + genomeDb.sequence_titles[genome_nr][sequence] + "\n");
int begin = 0;
int end = (int) genomeDb.sequence_length[genome_nr][sequence] - 1;
@@ -1093,18 +1052,18 @@ public class Phylogeny {
String[] wd_array = WORKING_DIRECTORY.split("/");
return wd_array[wd_array.length-1] + "/databases/genome.db/Genome_" + genome_nr + ".fasta";
}
-
+
/**
- *
+ *
* @param genome_path_map
* @param path_genome_map
* @param program is 'MASH' or 'fastANI'
- * @return
+ * @return
*/
- public static HashMap<String, Double> calculate_ani_loop(HashMap<Integer, String> genome_path_map,
- HashMap<String, Integer> path_genome_map, String program) {
-
- StringBuilder header = new StringBuilder("Genome,");
+ public static HashMap<String, Double> calculate_ani_loop(HashMap<Integer, String> genome_path_map,
+ HashMap<String, Integer> path_genome_map, String program) {
+
+ StringBuilder header = new StringBuilder("Genome,");
for (int i = 1; i <= total_genomes; i++) {
if (skip_array[i-1]){
continue;
@@ -1112,9 +1071,9 @@ public class Phylogeny {
String phenotype = get_phenotype_for_genome(i, true);
header.append(i).append(phenotype).append(",");
}
-
+
StringBuilder table_build = new StringBuilder(header.toString().replaceFirst(".$","")); //remove last character
- HashMap<String, Double> ani_score_map = new HashMap<>();
+ HashMap<String, Double> ani_score_map = new HashMap<>();
if (Mode.equals("FASTANI")) {
calculate_ani_loop_fastani(genome_path_map);
read_fastani_output(path_genome_map, ani_score_map, table_build);
@@ -1123,99 +1082,99 @@ public class Phylogeny {
}
write_SB_to_file_in_DB(table_build, "ANI/" + program + "/ANI_scores.csv");
return ani_score_map;
- }
-
+ }
+
/**
- *
+ *
* @param table_build
* @param genome_path_map
- * @param ani_score_map
+ * @param ani_score_map
*/
public static void calculate_ani_loop_mash(StringBuilder table_build, HashMap<Integer, String> genome_path_map, HashMap<String, Double> ani_score_map) {
double ani;
for (int i = 1; i <= total_genomes; i++) {
- create_directory_in_DB("ANI/MASH/calculations/" + i);
+ create_directory_in_DB("ANI/MASH/calculations/" + i);
}
-
+
for (int i = 1; i <= total_genomes; i++) {
System.out.print("\rCalculating ANI: " + i + "/" + total_genomes);
- if (skip_array[i-1]) {
- continue;
+ if (skip_array[i-1]) {
+ continue;
}
String phenotype = get_phenotype_for_genome(i, true);
table_build.append("\n").append(i).append(phenotype).append(",");
String path1 = genome_path_map.get(i);
for (int j = 1; j <= total_genomes; j++) {
- if (skip_array[j-1]) {
+ if (skip_array[j-1]) {
continue;
}
if (j < i) { // get ani score from earlier loop
- ani = ani_score_map.get(j + " " + i);
+ ani = ani_score_map.get(j + " " + i);
table_build.append(ani * 100);
- write_string_to_file_in_DB(ani +"", "ANI/MASH/calculations/" + j + "/" + i + "_" + j);
+ write_string_to_file_in_DB(ani +"", "ANI/MASH/calculations/" + j + "/" + i + "_" + j);
} else if (j == i) {
table_build.append("100");
} else {
String ani_file = WORKING_DIRECTORY + "/ANI/MASH/calculations/" + i + "/" + i + "_" + j;
if (check_if_file_exists(ani_file)) {
ani = read_ani_from_file(ani_file);
- ani_score_map.put(i + " " + j, ani);
+ ani_score_map.put(i + " " + j, ani);
table_build.append(ani * 100);
} else {
String path2 = genome_path_map.get(j);
- ani = run_mash(path1, path2, i, j);
+ ani = run_mash(path1, path2, i, j);
table_build.append(ani * 100);
ani_score_map.put(i + " " + j, ani);
- write_string_to_file_in_DB(ani +"", "ANI/MASH/calculations/" + i + "/" + i + "_" + j);
- write_string_to_file_in_DB(ani +"", "ANI/MASH/calculations/" + j + "/" + i + "_" + j);
+ write_string_to_file_in_DB(ani +"", "ANI/MASH/calculations/" + i + "/" + i + "_" + j);
+ write_string_to_file_in_DB(ani +"", "ANI/MASH/calculations/" + j + "/" + i + "_" + j);
}
}
if (j != total_genomes) {
table_build.append(",");
}
-
+
}
}
}
-
+
/**
* Runs MASH between two genomes and returns the ANI score as a Double
* @param path1
* @param path2
* @param genome1_nr
* @param genome2_nr
- * @return ani score
- */
+ * @return ani score
+ */
public static double run_mash(String path1, String path2, int genome1_nr, int genome2_nr) {
String[] mash_command = new String[] {"mash", "dist", path1, path2};
String mash_output = ExecCommand.ExecCommand(mash_command);
if (mash_output.equals("")) {
- System.out.println("\nCalculation between genome " + genome1_nr + " and " + genome2_nr + " failed. Please run the following command to identify the issue \n"
+ System.out.println("\nCalculation between genome " + genome1_nr + " and " + genome2_nr + " failed. Please run the following command to identify the issue \n"
+ "mash dist " + path1 + " " + path2 + "\n");
System.exit(1);
}
String[] output_array = mash_output.split("\t");
- double distance = Double.parseDouble(output_array[2]);
+ double distance = Double.parseDouble(output_array[2]);
double ani = 1 - distance;
return ani;
}
-
+
/**
- * Runs fastANI software
- * @param genome_path_map
+ * Runs fastANI software
+ * @param genome_path_map
*/
public static void calculate_ani_loop_fastani(HashMap<Integer, String> genome_path_map) {
StringBuilder files = new StringBuilder();
for (int i = 1; i <= total_genomes; i++) {
String path1 = genome_path_map.get(i);
files.append(path1).append("\n");
- }
-
+ }
+
write_SB_to_file_in_DB(files, "ANI/fastANI/references.txt");
String path = WORKING_DIRECTORY + "ANI/fastANI/";
for (int i = 1; i <= total_genomes; i++) {
- if (skip_array[i-1]) {
- continue;
+ if (skip_array[i-1]) {
+ continue;
}
System.out.print("\r Running fastANI: " + i + "/" + total_genomes + " genomes");
String query = genome_path_map.get(i);
@@ -1223,21 +1182,21 @@ public class Phylogeny {
String[] ani_command = {"fastANI", "-q", query, "--threads", THREADS +"", "--rl", path + "references.txt", "-o", path + "calculations/" + i}; // one vs all
ExecCommand.ExecCommand(ani_command);
}
- }
+ }
delete_file_full_path(path + "references.txt");
}
-
+
/**
- *
+ *
* @param path_genome_map
* @param ani_score_map
- * @param table_build
+ * @param table_build
*/
public static void read_fastani_output(HashMap<String, Integer> path_genome_map, HashMap<String, Double> ani_score_map, StringBuilder table_build) {
for (int i = 1; i <= total_genomes; i++) {
- if (skip_array[i-1]) {
+ if (skip_array[i-1]) {
continue;
- }
+ }
try (BufferedReader in = new BufferedReader(new FileReader(WORKING_DIRECTORY + "ANI/fastANI/calculations/" + i))) {
ArrayList<Integer> present_genomes = new ArrayList<>();
while (in.ready()) {
@@ -1251,21 +1210,21 @@ public class Phylogeny {
ani_score_map.put(i + " " + genome2, d);
} else if (genome2 < i) {
ani_score_map.put(genome2 + " " + i, d);
- } else { // if the same
+ } else { // if the same
ani_score_map.put(genome2 + " " + i, 1.0);
}
- }
-
+ }
+
if (present_genomes.size() != total_genomes) { // no ANI score means the score is below 0.80
for (int j = 1; j <= total_genomes; j++) {
- if (present_genomes.contains(j)) {
+ if (present_genomes.contains(j)) {
continue;
- }
+ }
if (j > i) {
ani_score_map.put(i + " " + j, 0.70);
} else {
ani_score_map.put(j + " " + i, 0.70);
- }
+ }
}
}
} catch (IOException ioe) {
@@ -1273,17 +1232,17 @@ public class Phylogeny {
System.exit(1);
}
}
-
- for (int i = 1; i <= total_genomes; i++) {
- if (skip_array[i-1]) {
+
+ for (int i = 1; i <= total_genomes; i++) {
+ if (skip_array[i-1]) {
continue;
- }
+ }
String phenotype = get_phenotype_for_genome(i, true);
table_build.append("\n").append(i).append(phenotype);
for (int j = 1; j <= total_genomes; j++) {
- if (skip_array[j-1]) {
+ if (skip_array[j-1]) {
continue;
- }
+ }
double ani;
if (j > i) {
ani = ani_score_map.get(i + " " + j);
@@ -1291,10 +1250,10 @@ public class Phylogeny {
ani = ani_score_map.get(j + " " + i);
}
table_build.append(",").append(ani * 100);
- }
+ }
}
}
-
+
/**
* @param program is 'MASH' or 'fastANI'
*/
@@ -1303,7 +1262,7 @@ public class Phylogeny {
try (BufferedReader in = new BufferedReader(new FileReader(WORKING_DIRECTORY + "/ANI/" + program + "/ANI_scores.csv"))) {
boolean first = true;
while (in.ready()) {
- String line = in.readLine().trim();
+ String line = in.readLine().trim();
if (first) { // header is the same
rev_ani_builder.append(line).append("\n");
first = false;
@@ -1335,7 +1294,7 @@ public class Phylogeny {
}
write_SB_to_file_in_DB(rev_ani_builder, "ANI/" + program + "/ANI_distance_matrix.csv");
}
-
+
/**
* ANI NJ tree
* @param program is 'MASH' or 'fastANI'
@@ -1358,23 +1317,23 @@ public class Phylogeny {
.append("cat(\"\\nANI tree written to: ").append(WD_full_path).append("ANI/").append(program).append("/ANI.newick\\n\\n\")");
write_SB_to_file_in_DB(rscript, "ANI/" + program + "/ANI_tree.R");
}
-
+
/**
- *
+ *
* @param genome_list
* @param genome_ts_map
- * @return
+ * @return
*/
public static String create_name_string_for_ani(ArrayList<Integer> genome_list, HashMap<Integer, String> genome_ts_map) {
String output = "";
for (int genome_nr : genome_list) {
- if (skip_array[genome_nr-1]) {
+ if (skip_array[genome_nr-1]) {
continue;
- }
+ }
String name = genome_ts_map.get(genome_nr);
output += genome_nr + " " + name + "/";
}
- return output.replaceFirst(".$",""); // remove last character
+ return output.replaceFirst(".$",""); // remove last character
}
/**
@@ -1386,19 +1345,19 @@ public class Phylogeny {
double ani = 0;
try (BufferedReader in = new BufferedReader(new FileReader(ani_file))) {
while (in.ready()) {
- String line = in.readLine().trim();
- ani = Double.valueOf(line);
- }
+ String line = in.readLine().trim();
+ ani = Double.valueOf(line);
+ }
} catch (IOException ioe) {
System.out.println("\nFailed to read: " + ani_file + "\n");
System.exit(1);
}
return ani;
}
-
+
/**
* Return true when 'typestrain' property is present in the phenotype node of genome 1
- * @return
+ * @return
*/
public static boolean check_if_typestrain_present() {
boolean present = false;
@@ -1407,13 +1366,13 @@ public class Phylogeny {
Node pheno_node = pheno_nodes.next();
if (pheno_node.hasProperty("typestrain")) {
present = true;
- }
+ }
}
return present;
}
-
+
/**
- * Creates a table with the ANI scores to the available type strains in the pangenome
+ * Creates a table with the ANI scores to the available type strains in the pangenome
* Only when phenotype nodes have the 'typestrain' phenotype
* @param ani_score_map
* @param program is 'MASH' or 'fastANI'
@@ -1426,13 +1385,13 @@ public class Phylogeny {
}
ResourceIterator<Node> pheno_nodes = graphDb.findNodes(phenotype_label);
ArrayList<Integer> genomes_with_typestrains = new ArrayList<>();
- HashMap<Integer, String> genome_ts_map = new HashMap<>();
+ HashMap<Integer, String> genome_ts_map = new HashMap<>();
while (pheno_nodes.hasNext()) { //retrieve all 'typestrain' phenotypes from phenotype nodes
Node pheno_node = pheno_nodes.next();
int genome_nr = (int) pheno_node.getProperty("genome");
- if (skip_array[genome_nr-1]) {
+ if (skip_array[genome_nr-1]) {
continue;
- }
+ }
String typestrain = (String) pheno_node.getProperty("typestrain");
if (!typestrain.equals("?")) {
genomes_with_typestrains.add(genome_nr);
@@ -1443,32 +1402,32 @@ public class Phylogeny {
System.out.println("Even though the 'typestrain' property is present, no typestrains were found!");
return false;
}
-
+
String header = "";
for (int genome_nr : genomes_with_typestrains) {
String name = genome_ts_map.get(genome_nr);
header += genome_nr + " " + name + ",";
}
- StringBuilder output_builder;
+ StringBuilder output_builder;
if (PHENOTYPE == null) {
output_builder = new StringBuilder("Genome number,Highest score,Closest type strain,Above 95%,," + header.replaceFirst(".$","") +"\n");
} else {
- output_builder = new StringBuilder("Genome number,Current phenotype,Highest score,Closest type strain,Above 95%,,"
- + header.replaceFirst(".$","") +"\n");
+ output_builder = new StringBuilder("Genome number,Current phenotype,Highest score,Closest type strain,Above 95%,,"
+ + header.replaceFirst(".$","") +"\n");
}
for (int genome1 = 1; genome1 <= total_genomes; genome1++) {
- if (skip_array[genome1-1]) {
- continue;
+ if (skip_array[genome1-1]) {
+ continue;
}
- HashMap<Double, ArrayList<Integer>> score_genome_map = new HashMap<>();
+ HashMap<Double, ArrayList<Integer>> score_genome_map = new HashMap<>();
Double highest = 0.0;
String all_scores = "";
for (int genome2 : genomes_with_typestrains) {
- if (skip_array[genome2-1]) {
+ if (skip_array[genome2-1]) {
continue;
- }
+ }
String key = genome1 + " " + genome2;
- if (genome1 > genome2) {
+ if (genome1 > genome2) {
key = genome2 + " " + genome1;
}
Double score = ani_score_map.get(key);
@@ -1481,7 +1440,7 @@ public class Phylogeny {
highest = score;
}
}
-
+
boolean close_enough = true;
if (highest < 0.95) {
close_enough = false;
@@ -1495,31 +1454,31 @@ public class Phylogeny {
pheno = "";
}
output_builder.append(genome1).append(",").append(pheno).append(highest).append(",").append(highest_str).append(",")
- .append(close_enough).append(",,").append(all_scores.replaceFirst(".$","")).append("\n");
+ .append(close_enough).append(",,").append(all_scores.replaceFirst(".$","")).append("\n");
}
write_SB_to_file_in_DB(output_builder, "ANI/" + program + "/typestrain_comparison.csv");
return true;
}
-
+
/**
* Create appropriate directories for selected ANI calculation tool
* Two options: MASH or FASTANI
- * @return
+ * @return
*/
- public static String mash_or_fastaANI() {
+ public static String mash_or_fastaANI() {
String program = "MASH";
if (Mode.equals("0")) { // default value of Mode
System.out.println("\nCalculate ANI scores\n");
- create_directory_in_DB("ANI/MASH/calculations");
+ create_directory_in_DB("ANI/MASH/calculations");
check_if_program_exists_stdout("mash -h", 100, "MASH"); // check if program is set to $PATH
System.out.println("No --mode provided. Using MASH (default)");
Mode = "MASH";
} else if (Mode.startsWith("MASH")) {
- create_directory_in_DB("ANI/MASH/calculations");
+ create_directory_in_DB("ANI/MASH/calculations");
check_if_program_exists_stdout("mash -h", 100, "MASH"); // check if program is set to $PATH
System.out.println("\nCalculate ANI scores using MASH\n");
- } else if (Mode.startsWith("FASTANI")) {
- create_directory_in_DB("ANI/fastANI/calculations");
+ } else if (Mode.startsWith("FASTANI")) {
+ create_directory_in_DB("ANI/fastANI/calculations");
System.out.println("\nCalculate ANI scores using fastANI\n");
program = "fastANI";
check_if_program_exists_stderr("fastANI -h", 100, "fastANI", true); // check if program is set to $PATH
@@ -1530,31 +1489,31 @@ public class Phylogeny {
}
return program;
}
-
+
/**
- * Create overview of the color hex codes.
+ * Create overview of the color hex codes.
*/
public void create_color_code_text_file() {
- String color_codes = "https://sashat.me/2017/01/11/list-of-20-simple-distinct-colors/ \n\n"
- + "Pink - #fabebe\nLime - #bfef45\nCyan - #42d4f4\nApricot - #ffd8b1\nMint - #aaffc3\nBeige - #fffac8\nLavender - #e6beff\nTeal - #469990\nRed - #e6194B\n"
- + "Orange - #f58231\nYellow - #ffe119\nGreen - #3cb44b\nBlue - #4363d8\nPurple - #911eb4\nGrey - #a9a9a9\nMaroon - #800000\nOlive - #808000\nBrown - #9A6324\n"
- + "Navy - #000075\nMagenta - #f032e6\n\nUnused colors\nLight grey #E8E8E8";
+ String color_codes = "https://sashat.me/2017/01/11/list-of-20-simple-distinct-colors/ \n\n"
+ + "Pink - #fabebe\nLime - #bfef45\nCyan - #42d4f4\nApricot - #ffd8b1\nMint - #aaffc3\nBeige - #fffac8\nLavender - #e6beff\nTeal - #469990\nRed - #e6194B\n"
+ + "Orange - #f58231\nYellow - #ffe119\nGreen - #3cb44b\nBlue - #4363d8\nPurple - #911eb4\nGrey - #a9a9a9\nMaroon - #800000\nOlive - #808000\nBrown - #9A6324\n"
+ + "Navy - #000075\nMagenta - #f032e6\n\nUnused colors\nLight grey #E8E8E8";
write_string_to_file_in_DB(color_codes, "tree_templates/color_code_guide.txt");
}
-
- /**
- Create ITOL templates
- https://sashat.me/2017/01/11/list-of-20-simple-distinct-colors/
-
- Requires
- -dp
-
- Optional
- --phenotype or -ph
- --value the number of genomes a phenotype should have before a color is assigned
+
+ /**
+ Create ITOL templates
+ https://sashat.me/2017/01/11/list-of-20-simple-distinct-colors/
+
+ Requires
+ -dp
+
+ Optional
+ --phenotype or -ph
+ --value the number of genomes a phenotype should have before a color is assigned
--mode no-numbers
-
- */
+
+ */
public void create_tree_templates() {
System.out.println("\nCreating templates for phylogenetic trees in ITOL\n");
create_directory_in_DB("tree_templates/label/");
@@ -1568,7 +1527,7 @@ public class Phylogeny {
tx.success(); // transaction successful, commit changes
} catch (NotFoundException nfe) {
System.out.println("Unable to start the database\n");
- return;
+ System.exit(1);
}
boolean print_header = true;
HashMap<String, HashSet<String>> pheno_property_map = new HashMap<>();
@@ -1581,7 +1540,7 @@ public class Phylogeny {
} catch (NumberFormatException no) {
System.out.println("'" + NODE_VALUE + "' is not a numerical value\n");
System.exit(1);
- }
+ }
System.out.println("\rSelected --value is " + NODE_VALUE + ". A phenotype must have this many genomes before a color is assigned");
} else {
System.out.println("\rNo --value was selected. A color is assigned to phenotype values present in least 2 genomes");
@@ -1591,11 +1550,11 @@ public class Phylogeny {
if (PHENOTYPE != null) {
if (Mode.contains("NO-NUMBERS")) {
System.out.println("The phenotype '" + PHENOTYPE + "' was included and genome numbers are exluded! "
- + "The created templates will match trees where nodes only contain a phenotype value.\n");
+ + "The created templates will match trees where nodes only contain a phenotype value.\n");
} else {
System.out.println("The phenotype '" + PHENOTYPE + "' was included. "
- + "The created templates will match trees where nodes have genome numbers combined with the '" + PHENOTYPE + "' phenotype values! "
- + "Include the --mode no-numbers argument to EXCLUDE genome numbers from templates\n");
+ + "The created templates will match trees where nodes have genome numbers combined with the '" + PHENOTYPE + "' phenotype values! "
+ + "Include the --mode no-numbers argument to EXCLUDE genome numbers from templates\n");
}
retrieve_phenotypes(); // Creates and fills geno_pheno_map and phenotype_map when a phenotype was provided by the user
create_directory_in_DB("tree_templates/label/" + PHENOTYPE);
@@ -1614,39 +1573,39 @@ public class Phylogeny {
HashSet<String> phenotype_values = pheno_property_map.get(phenotype);
AtomicInteger counter = new AtomicInteger(0);
String[] label_ring_output = create_label_ring_templates(phenotype, phenotype_values, genomes_per_phenotype_map, counter, required_genomes);
- print_header = write_label_ring_output(label_ring_output, counter.get(), print_header, phenotype, phenotype_values, to_many_pheno_values);
- }
+ print_header = write_label_ring_output(label_ring_output, counter.get(), print_header, phenotype, phenotype_values, to_many_pheno_values);
+ }
tx.success(); // transaction successful, commit changes
}
-
+
String to_many_pheno_val_str = to_many_pheno_values.toString();
if (to_many_pheno_val_str.length() > 1) {
- System.out.println("\nPhenotypes with more than the 20 allowed values -> Required colors\n" + to_many_pheno_val_str );
+ System.out.println("\nPhenotypes with more than the 20 allowed values -> Required colors\n" + to_many_pheno_val_str);
}
if (PHENOTYPE != null) {
- System.out.println("\nTemplate files written to:\n "
+ System.out.println("\nTemplate files written to:\n "
+ WORKING_DIRECTORY + "tree_templates/ring/" + PHENOTYPE +"/\n "
+ WORKING_DIRECTORY + "tree_templates/label/" + PHENOTYPE +"/\n");
} else {
- System.out.println("\nTemplate files written to\n "
+ System.out.println("\nTemplate files written to\n "
+ WORKING_DIRECTORY + "tree_templates/\n");
}
}
-
+
/**
- * Write the template to their files
+ * Write the template to their files
* @param label_ring_output
* @param counter
* @param print_header
* @param phenotype
* @param phenotype_values
* @param to_many_pheno_values
- * @return
+ * @return
*/
- public boolean write_label_ring_output(String[] label_ring_output, int counter, boolean print_header, String phenotype,
- HashSet<String> phenotype_values, StringBuilder to_many_pheno_values) {
+ public boolean write_label_ring_output(String[] label_ring_output, int counter, boolean print_header, String phenotype,
+ HashSet<String> phenotype_values, StringBuilder to_many_pheno_values) {
- if (counter-1 < COLOR_CODES.length) {
+ if (counter-1 < COLOR_CODES.length) {
if (print_header) {
System.out.println("Phenotype name, Different phenotypes -> Used colors");
print_header = false;
@@ -1664,27 +1623,37 @@ public class Phylogeny {
}
return print_header;
}
-
+
/**
* Create the ring and label templates for ITOL
* @param key
* @param phenotypes
* @param genomes_per_phenotype_map
* @param counter
- * @param required_genomes default is 2, can be adjusted by user
- * @return
+ * @param required_genomes default is 2, can be adjusted by user
+ * @return
*/
- public String[] create_label_ring_templates(String key, HashSet<String> phenotypes,
- HashMap<String, ArrayList<Integer>> genomes_per_phenotype_map, AtomicInteger counter, int required_genomes) {
-
+ public String[] create_label_ring_templates(String key, HashSet<String> phenotypes,
+ HashMap<String, ArrayList<Integer>> genomes_per_phenotype_map, AtomicInteger counter, int required_genomes) {
+
String label = key;
if (PHENOTYPE != null) {
label = PHENOTYPE + " colored_by " + key;
}
StringBuilder label_builder = new StringBuilder("TREE_COLORS\nSEPARATOR COMMA\nDATA\n\n");
- StringBuilder ring_builder = new StringBuilder("DATASET_COLORSTRIP\nSEPARATOR COMMA\nDATASET_LABEL," + label
+ StringBuilder ring_builder = new StringBuilder("DATASET_COLORSTRIP\nSEPARATOR COMMA\nDATASET_LABEL," + label
+ "\nCOLOR,#ff0000\nSTRIP_WIDTH,40\nSHOW_INTERNAL,1\nDATA\n\n");
-
+
+ // first loop to check if the number of phenotype colors exceeds 8
+ int requiredColors = 0;
+ for (String value : phenotypes) {
+ ArrayList<Integer> genomes = genomes_per_phenotype_map.get(key + "##" + value);
+ if (genomes.size() < required_genomes) {
+ continue;
+ }
+ requiredColors++;
+ }
+
for (String value : phenotypes) {
String pheno_value = value;
ArrayList<Integer> genomes = genomes_per_phenotype_map.get(key + "##" + value);
@@ -1699,7 +1668,7 @@ public class Phylogeny {
pheno_value = geno_pheno_map.get(genome_nr);
}
phenotype_info = "_" + pheno_value;
- }
+ }
if (Mode.contains("NO-NUMBERS")) {
label_builder.append(pheno_value);
ring_builder.append(pheno_value);
@@ -1707,24 +1676,28 @@ public class Phylogeny {
label_builder.append(genome_nr).append(phenotype_info);
ring_builder.append(genome_nr).append(phenotype_info);
}
-
- label_builder.append(",range,").append(COLOR_CODES[counter.get()]).append(",").append(value).append(",1.0\n");
- ring_builder.append(",").append(COLOR_CODES[counter.get()]).append(",").append(value).append("\n");
+ if (requiredColors < 9) { // use colourblind friendly pallette
+ label_builder.append(",range,").append(COLORBLIND_CODES[counter.get()]).append(",").append(value).append(",1.0\n");
+ ring_builder.append(",").append(COLORBLIND_CODES[counter.get()]).append(",").append(value).append("\n");
+ } else {
+ label_builder.append(",range,").append(COLOR_CODES[counter.get()]).append(",").append(value).append(",1.0\n");
+ ring_builder.append(",").append(COLOR_CODES[counter.get()]).append(",").append(value).append("\n");
+ }
}
}
counter.getAndIncrement();
- }
+ }
return new String[]{label_builder.toString(), ring_builder.toString()};
}
-
+
/**
* Extracts all available phenotypes from 'phenotype' nodes
* @param pheno_property_map
- * @param genomes_per_phenotype_map
+ * @param genomes_per_phenotype_map
*/
- public void retrieve_phenotypes_for_tree_templates(HashMap<String, HashSet<String>> pheno_property_map,
- HashMap<String, ArrayList<Integer>> genomes_per_phenotype_map) {
-
+ public void retrieve_phenotypes_for_tree_templates(HashMap<String, HashSet<String>> pheno_property_map,
+ HashMap<String, ArrayList<Integer>> genomes_per_phenotype_map) {
+
ResourceIterator<Node> phenotype_nodes = graphDb.findNodes(phenotype_label);
while (phenotype_nodes.hasNext()) {
Node pheno_node = phenotype_nodes.next();
@@ -1752,16 +1725,16 @@ public class Phylogeny {
}
}
}
-
+
/**
- * Requires
+ * Requires
* --database-path
* --input-file a phylogenetic tree
- *
- * Optional
+ *
+ * Optional
* --phenotype
- * --mode no-numbers == mode 1
- *
+ * --mode no-numbers == mode 1
+ *
* This function only works on the phylogenetic trees on 1 of the 5 methods. A genome number may only occur once.
*/
public void rename_phylogeny() {
@@ -1779,130 +1752,233 @@ public class Phylogeny {
tx.success(); // transaction successful, commit changes
} catch (NotFoundException nfe) {
System.out.println("Unable to start the database\n");
- return;
+ System.exit(1);
}
boolean exclude_numbers = false;
if (Mode.contains("NO-NUMBERS")) {
if (PHENOTYPE == null) {
- System.out.println("--mode no-numbers can only be used in combination with --phenotype\n");
- return;
+ System.out.println("--mode no-numbers can only be used in combination with --phenotype\n");
+ return;
}
System.out.println("Selected --mode no-numbers. Removing the genome numbers from the leaves");
exclude_numbers = true;
- }
-
+ }
graphDb.shutdown();
-
- String phylogeny = read_newick_file();
- int total_changes = 0;
- boolean correct_tree = true;
- for (int i = 1; i <= total_genomes; i++) {
- int changes_counter = 0; // per genome, this function should make 1 change, if not the case, the tree cannot be used.
- String phenotype = create_phenotype_for_rename_phylo(i);
- if (phylogeny.contains("(" + i + ":")) {
- if (exclude_numbers) {
- phylogeny = phylogeny.replace("(" + i + ":", "(" + phenotype + ":");
- } else {
- phylogeny = phylogeny.replace("(" + i + ":", "(" + i + phenotype + ":");
- }
- changes_counter ++;
- } else if (phylogeny.contains("(" + i + "_")) {
- String[] phylogeny_array = phylogeny.split("\\(" + i + "_");
- if (phylogeny_array.length != 2) {
- correct_tree = false;
- break;
- }
- String str = phylogeny_array[1];
- int index1 = str.indexOf(':');
- if (exclude_numbers) {
- phylogeny = phylogeny_array[0] + "(" + phenotype + str.substring(index1, str.length());
- } else {
- phylogeny = phylogeny_array[0] + "(" + i + phenotype + str.substring(index1, str.length());
- }
- changes_counter ++;
- } else if (phylogeny.contains("(" + i + ",")) {
- if (exclude_numbers) {
- phylogeny = phylogeny.replace("(" + i + ",", "(" + phenotype + ",");
- } else {
- phylogeny = phylogeny.replace("(" + i + ",", "(" + i + phenotype + ",");
- }
- changes_counter ++;
- } else if (phylogeny.contains("," + i + ")")) {
- changes_counter ++;
- if (exclude_numbers) {
- phylogeny = phylogeny.replace("," + i + ")", "," + phenotype + ")");
- } else {
- phylogeny = phylogeny.replace("," + i + ")", "," + i + phenotype + ")");
- }
- } else if (phylogeny.contains("," + i + ":")) {
- changes_counter ++;
- if (exclude_numbers) {
- phylogeny = phylogeny.replace("," + i + ":", "," + phenotype + ":");
- } else {
- phylogeny = phylogeny.replace("," + i + ":", "," + i + phenotype + ":");
+
+ ArrayList<String> lines = readNewickOrNexus(true);
+ if (lines.size() == 1) {
+ String phylogeny = lines.get(0);
+ int total_changes = 0;
+ boolean correct_tree = true;
+ for (int i = 1; i <= total_genomes; i++) {
+ int changes_counter = 0; // per genome, this function should make 1 change, if not the case, the tree cannot be used.
+ String phenotype = create_phenotype_for_rename_phylo(i);
+ if (phylogeny.contains("(" + i + ":")) {
+ if (exclude_numbers) {
+ phylogeny = phylogeny.replace("(" + i + ":", "(" + phenotype + ":");
+ } else {
+ phylogeny = phylogeny.replace("(" + i + ":", "(" + i + phenotype + ":");
+ }
+ changes_counter++;
+ } else if (phylogeny.contains("(" + i + "_")) {
+ String[] phylogeny_array = phylogeny.split("\\(" + i + "_");
+ if (phylogeny_array.length != 2) {
+ correct_tree = false;
+ break;
+ }
+ String str = phylogeny_array[1];
+ int index1 = str.indexOf(':');
+ if (exclude_numbers) {
+ phylogeny = phylogeny_array[0] + "(" + phenotype + str.substring(index1, str.length());
+ } else {
+ phylogeny = phylogeny_array[0] + "(" + i + phenotype + str.substring(index1, str.length());
+ }
+ changes_counter++;
+ } else if (phylogeny.contains("(" + i + ",")) {
+ if (exclude_numbers) {
+ phylogeny = phylogeny.replace("(" + i + ",", "(" + phenotype + ",");
+ } else {
+ phylogeny = phylogeny.replace("(" + i + ",", "(" + i + phenotype + ",");
+ }
+ changes_counter++;
+ } else if (phylogeny.contains("," + i + ")")) {
+ changes_counter++;
+ if (exclude_numbers) {
+ phylogeny = phylogeny.replace("," + i + ")", "," + phenotype + ")");
+ } else {
+ phylogeny = phylogeny.replace("," + i + ")", "," + i + phenotype + ")");
+ }
+ } else if (phylogeny.contains("," + i + ":")) {
+ changes_counter++;
+ if (exclude_numbers) {
+ phylogeny = phylogeny.replace("," + i + ":", "," + phenotype + ":");
+ } else {
+ phylogeny = phylogeny.replace("," + i + ":", "," + i + phenotype + ":");
+ }
+ } else if (phylogeny.contains("," + i + "_")) {
+ changes_counter++;
+ String[] phylogeny_array = phylogeny.split("," + i + "_");
+ if (phylogeny_array.length != 2) {
+ correct_tree = false;
+ break;
+ }
+ String str = phylogeny_array[1];
+ int index1 = str.indexOf(':');
+ if (exclude_numbers) {
+ phylogeny = phylogeny_array[0] + "," + phenotype + str.substring(index1, str.length());
+ } else {
+ phylogeny = phylogeny_array[0] + "," + i + phenotype + str.substring(index1, str.length());
+ }
}
- } else if (phylogeny.contains("," + i + "_")) {
- changes_counter ++;
- String[] phylogeny_array = phylogeny.split("," + i + "_");
- if (phylogeny_array.length != 2) {
+
+ if (changes_counter > 1) { // the function assumes each genome is present only once
correct_tree = false;
break;
+ } else if (changes_counter == 0) { // genome nr is not present in the phylogeny
+ // do nothing
+ } else { // 1 change
+ total_changes++;
}
- String str = phylogeny_array[1];
- int index1 = str.indexOf(':');
- if (exclude_numbers) {
- phylogeny = phylogeny_array[0] + "," + phenotype + str.substring(index1, str.length());
+ }
+
+ if (correct_tree) {
+ String outputFile = addStringBeforeFinalDot(INPUT_FILE, "_RENAMED");
+ write_string_to_file_full_path(phylogeny, outputFile);
+ System.out.println(total_changes + " leaves were changed\n\n" +
+ "New phylogeny written to:\n "
+ + outputFile + "\n");
+ } else {
+ System.out.println("\nThe provided phylogeny is incorrect. Only trees from one PanTools's phylogenetic methods can be used\n");
+ }
+ } else {
+ renameNexusFile(lines, exclude_numbers);
+ }
+ }
+
+ /**
+ * Update a nexus file to include phenotype (optionally remove genome number)
+ * Example part of Nexus file. Part between '' is the label.
+ * IMPORTANT the value within brackets [] is not a genome number!
+ *
+ * file1
+ * #nexus
+ *
+ * BEGIN Taxa;
+ * DIMENSIONS ntax=25;
+ * TAXLABELS
+ * [1] '1'
+ * [2] '2'
+ * [3] '3'
+ * [4] '4'
+ * [5] '5'
+ * ;
+ * END; [Taxa]
+ *
+ * file2
+ * #nexus
+ *
+ * BEGIN Taxa;
+ * DIMENSIONS ntax=12;
+ * TAXLABELS
+ * [1] '1_D._ananassae'
+ * [2] '2_D._erecta'
+ * [3] '3_D._grimshawi'
+ * [4] '4_D._melanogaster'
+ * [5] '5_D._mojavensis'
+ * ;
+ * END; [Taxa]
+ */
+ public void renameNexusFile(ArrayList<String> lines, boolean exclude_numbers) {
+ boolean readLines = false;
+ StringBuilder newNexus = new StringBuilder();
+ for (String line : lines) {
+ if (line.startsWith("TAXLABELS")) {
+ readLines = true;
+ newNexus.append(line).append("\n");
+ } else if (readLines) {
+ if (line.startsWith(";") || line.startsWith("END") ){
+ readLines = false;
+ newNexus.append(line).append("\n");
} else {
- phylogeny = phylogeny_array[0] + "," + i + phenotype + str.substring(index1, str.length());
+ String[] lineArray = line.split(" "); // example line: [1] '1_D._ananassae'
+ try {
+ String genomeNrStr2 = lineArray[1].replace("'","");
+ int genomeNr = Integer.parseInt(genomeNrStr2);
+ String newValue = create_phenotype_for_rename_nexus(genomeNr, exclude_numbers);
+ newNexus.append(lineArray[0]).append(" '").append(newValue).append("'\n");
+ continue;
+ } catch (NumberFormatException nfe) {
+ // file does not only contain a genome number. can still try the next option
+ }
+
+ String[] underscoreArray = lineArray[1].split("_");
+ try {
+ String genomeNrStr = underscoreArray[0].replace("'","");
+ int genomeNr = Integer.parseInt(genomeNrStr);
+ String newValue = create_phenotype_for_rename_nexus(genomeNr, exclude_numbers);
+ newNexus.append(lineArray[0]).append(" '").append(newValue).append("'\n");
+ } catch (NumberFormatException npe) {
+ System.out.println("Was unsuccessful in retrieving a genome number from this line:\n" + line);
+ System.exit(1);
+ }
}
+ } else {
+ newNexus.append(line).append("\n");
}
-
- if (changes_counter > 1) { // the function assumes each genome is present only once
- correct_tree = false;
- break;
- } else if (changes_counter == 0) { // genome nr is not present in the phylogeny
- // do nothing
- } else { // 1 change
- total_changes ++;
- }
- }
-
- if (correct_tree) {
- String output_file = add_string_before_final_dot(INPUT_FILE, "_RENAMED");
- write_string_to_file_full_path(phylogeny, output_file);
- System.out.println(total_changes + " leaves were changed\n\n" +
- "New phylogeny written to:\n "
- + output_file + "\n");
- } else {
- System.out.println("\nThe provided phylogeny is incorrect. Only trees from one PanTools's phylogenetic methods can be used\n");
}
+ String outFileName = addStringBeforeFinalDot(INPUT_FILE, "_RENAMED");
+ write_SB_to_file_full_path(newNexus, outFileName);
+ System.out.println("New phylogeny written to:\n "
+ + outFileName + "\n");
+ }
+
+ /**
+ * Return a phenotype value of a specific genome as a string when a --phenotype is included
+ * @param genomeNr a genome number
+ * @return
+ */
+ public String create_phenotype_for_rename_nexus(int genomeNr, boolean exclude_numbers) {
+ if (PHENOTYPE == null) {
+ return genomeNr +"";
+ }
+ String phenotype = "";
+ if (geno_pheno_map.containsKey(genomeNr)) {
+ phenotype = geno_pheno_map.get(genomeNr);
+ }
+ if (phenotype.equals("?")) {
+ phenotype = "Unknown";
+ }
+ if (exclude_numbers) {
+ return phenotype;
+ }
+ return genomeNr + "_" + phenotype;
}
-
+
/**
* tree.newick becomes tree*STRING*.newick
- *
- * @param original_file
- * @param add
- * @return
- */
- public static String add_string_before_final_dot(String original_file, String add){
- String new_string = "";
- String[] file_array = original_file.split("\\."); // split on .
- for (int i = 0; i < file_array.length; i++) {
- new_string += file_array[i];
- if (i == file_array.length-2){ // add the new string before the final part is added
- new_string += add;
+ *
+ * @param originalFileName
+ * @param add the string to be appended before the final .
+ * @return
+ */
+ public static String addStringBeforeFinalDot(String originalFileName, String add) {
+ StringBuilder newFileName = new StringBuilder();
+ String[] file_array = originalFileName.split("\\."); // split on .
+ for (int i = 0; i < file_array.length; i++) {
+ newFileName.append(file_array[i]);
+ if (i == file_array.length-2) { // add the new string before the final part is added
+ newFileName.append(add);
}
if (i != file_array.length-1) {
- new_string += ".";
- }
+ newFileName.append(".");
+ }
}
- return new_string;
+ return newFileName.toString();
}
-
+
/**
- Create an Rscript to reroot a phylogeny (using APE)
- */
+ Create an Rscript to reroot a phylogeny (using APE)
+ */
public void reroot_phylogeny() {
System.out.println("\nCreate an Rscript to reroot an phylogenetic tree\n");
if (WORKING_DIRECTORY == null) {
@@ -1917,7 +1993,7 @@ public class Phylogeny {
* Stops the program when the value specified by the user does not exist in the phylogeny
*/
public void check_if_node_exists_in_tree() {
- // check if the required files were included
+ // check if the required files were included
boolean stop = false;
if (INPUT_FILE == null){
System.out.println("\nThis function requires a newick file via --input-file/-if\n");
@@ -1934,14 +2010,14 @@ public class Phylogeny {
if (stop) {
System.exit(1);
}
-
+
String phylogeny = read_newick_file();
// Check if node exists in the tree
if (!phylogeny.contains(NODE_VALUE)) { // check if value is present at all
System.out.println(NODE_VALUE + " was not found back in the provided phylogeny!\n");
System.exit(1);
}
-
+
boolean correct = false;
if (phylogeny.contains("(" + NODE_VALUE + ",")) {
correct = true;
@@ -1952,18 +2028,18 @@ public class Phylogeny {
} else if (phylogeny.contains("," + NODE_VALUE + ":")) {
correct = true;
}
-
+
if (!correct) { // not 100% sure if the 4 options cover all posibilities, therefore not stopping the program when not true
System.out.println(NODE_VALUE + " was not found back in the provided phylogeny!");
} else {
- System.out.println(NODE_VALUE + " was succesfully found back in the provided phylogeny!");
- }
+ System.out.println(NODE_VALUE + " was succesfully found back in the provided phylogeny!");
+ }
}
/**
* Rscript that uses APE to reroot a phylogeny
*/
- public void create_reroot_script() {
+ public void create_reroot_script() {
String R_LIB = check_r_libraries_environment();
StringBuilder rscript = new StringBuilder();
rscript.append("#! /usr/bin/env RScript\n")
@@ -1977,9 +2053,59 @@ public class Phylogeny {
write_SB_to_file_in_DB( rscript, "reroot.R");
}
+ /**
+ *
+ * @return 1 line = newick. multiple lines = nexus
+ */
+ public ArrayList<String> readNewickOrNexus(boolean print) {
+ ArrayList<String> lines = new ArrayList<>();
+ boolean beginTaxafound = false;
+ boolean beginSplitsfound = false;
+ int lineCounter = 0;
+ if (INPUT_FILE == null) {
+ System.out.println("Provide a phylogeny through --input-file/-if\n");
+ System.exit(1);
+ }
+ if (!INPUT_FILE.contains(".")) {
+ System.out.println("The file provided through --input-file/-if must have a file extension, .newick for example\n");
+ System.exit(1);
+ }
+
+ try (BufferedReader in = new BufferedReader(new FileReader(INPUT_FILE))) {
+ for (int c = 0; in.ready();) {
+ String line = in.readLine().trim();
+ lines.add(line); // add the regular line before uppercase
+ line = line.toUpperCase();
+ lineCounter++;
+ if (line.startsWith("BEGIN TAXA;")) {
+ beginTaxafound = true;
+ } else if (line.startsWith("BEGIN SPLITS;")) {
+ beginSplitsfound = true;
+ }
+ }
+ } catch (IOException ioe) {
+ System.out.println("Failed to read: " + INPUT_FILE);
+ System.exit(1);
+ }
+
+ if (lineCounter == 1) { // assume file is newick format, no file checks
+ if (print) {
+ System.out.println("Input file was recognized as newick");
+ }
+ } else if (beginTaxafound && beginSplitsfound) {
+ if (print) {
+ System.out.println("Input file was recognized as nexus ");
+ }
+ } else {
+ System.out.println("File could not be recognized as newick or nexus ");
+ System.exit(1);
+ }
+ return lines;
+ }
+
/**
* Read a newick file that was given by the --input-file argument
- * @return
+ * @return
*/
public String read_newick_file() {
if (INPUT_FILE == null) {
@@ -1995,7 +2121,7 @@ public class Phylogeny {
int line_counter = 0;
for (int c = 0; in.ready();) {
phylogeny = in.readLine().trim();
- line_counter ++;
+ line_counter++;
}
if (line_counter > 1) {
System.out.println("\n" + INPUT_FILE + " is not a (correctly formatted) Newick file\n");
@@ -2006,12 +2132,12 @@ public class Phylogeny {
System.exit(1);
}
return phylogeny;
- }
-
+ }
+
/**
* Read a newick file that was given by input argument (Written by Dirk-Jan)
* @param path_to_newick
- * @return
+ * @return
*/
public String read_newick_file(String path_to_newick) {
String phylogeny = "";
@@ -2032,12 +2158,12 @@ public class Phylogeny {
}
}
return phylogeny;
- }
-
+ }
+
/**
- * Return a phenotype value of a specific genome as a string when a --phenotype is included
+ * Return a phenotype value of a specific genome as a string when a --phenotype is included
* @param genome_nr
- * @return
+ * @return
*/
public String create_phenotype_for_rename_phylo(int genome_nr) {
String phenotype = "";
@@ -2055,7 +2181,7 @@ public class Phylogeny {
}
return phenotype;
}
-
+
/**
* Update skip_array with genome numbers that were skipped in the previous 'gene_classification' run
*/
@@ -2063,7 +2189,7 @@ public class Phylogeny {
if (!SELECTED_HMGROUPS.equals(WORKING_DIRECTORY + "gene_classification/single_copy_orthologs.csv")) {
return; // genomes can only be validated when the file above is used.
}
-
+
if (!check_if_file_exists(WORKING_DIRECTORY + "gene_classification/skipped_genomes.info")) {
System.out.println("\nOne of the required input file is missing. Please run 'gene_classification' again.\n");
System.exit(1);
@@ -2072,10 +2198,10 @@ public class Phylogeny {
try (BufferedReader in = new BufferedReader(new FileReader(WORKING_DIRECTORY + "gene_classification/skipped_genomes.info"))) {
while (in.ready()) {
String line = in.readLine().trim();
- if (line.startsWith("None")) { // no genomes were skipped
- // do nothing
+ if (line.startsWith("None")) { // no genomes were skipped
+ // do nothing
} else { // genomes were skipped
- String[] line_array = line.split(",");
+ String[] line_array = line.split(",");
for (String genome_nr_str : line_array) {
int genome_nr = Integer.parseInt(genome_nr_str);
if (!skip_array[genome_nr-1]) {
@@ -2086,12 +2212,12 @@ public class Phylogeny {
}
if (!missed_genome.equals("")) { // more genes were skipped in the previous gene classsification run than were selected by --skip
- missed_genome = missed_genome.replaceFirst(".$","");
+ missed_genome = missed_genome.replaceFirst(".$","");
String genome = "Genome";
if (missed_genome.contains(",")) {
genome += "s";
}
- System.out.println("Important! " + genome + " " + missed_genome +
+ System.out.println("Important! " + genome + " " + missed_genome +
" will be excluded from this analysis because it was skipped during gene_classification.\n");
}
}
@@ -2101,116 +2227,107 @@ public class Phylogeny {
System.exit(1);
}
}
-
+
/**
- *
+ *
* Does not create the phylogeny directly but only prepares the Rscript or IQ-tree command that creates it
- *
+ *
* Requires
- * -dp
- *
+ * -dp
+ *
* Optional arguments
- --mode ML or --mode NJ Maximum likelihood (default) or Neighbour joining.
- --phenotype/-ph Include phenotype information in the output files.
- --skip / --reference
- --homology-groups / -hm . Default is single_copy_orthologs.csv from the previous gene_classification run
+ --mode ML or --mode NJ Maximum likelihood (default) or Neighbour joining.
+ --phenotype/-ph Include phenotype information in the output files.
+ --skip / --reference
+ --homology-groups / -hm . Default is single_copy_orthologs.csv from the previous gene_classification run
*/
public void core_snp_tree() {
- System.out.println("\nCreating core SNP phylogeny from SNPs identified in single-copy-orthologous groups\n");
+ System.out.println("\nInferring core phylogeny from SNPs or Amino acid substitutions identified in single-copy-orthologous groups\n");
check_if_graphDb_is_available(); // starts up the graph database if needed
- FAST = true; // skip fastTree
- String single_copy_input_file = "";
- boolean check_if_single_copy_groups = false;
+ FAST = true; // skip the fastTree phylogeny inference per homology group
+ String singleCopyInputFile = "";
+ boolean checkSingleCopyGroups = false;
if (SELECTED_HMGROUPS == null) {
SELECTED_HMGROUPS = WORKING_DIRECTORY + "gene_classification/single_copy_orthologs.csv";
- System.out.println("No homology groups provided. Using -> " + SELECTED_HMGROUPS + " (was created during the previous 'gene_classification' run)");
+ System.out.println("No homology groups provided. Using " + SELECTED_HMGROUPS + " (was created during the previous 'gene_classification' run)");
if (!check_if_file_exists(SELECTED_HMGROUPS)) {
System.out.println("No single copy orthologs information is available. Please run 'gene_classification'");
System.exit(1);
}
} else {
System.out.println("Homology groups were provided with --hm");
- check_if_single_copy_groups = true;
+ checkSingleCopyGroups = true;
}
- single_copy_input_file = SELECTED_HMGROUPS;
- report_number_of_threads(true, true); // prints how many threads were selected by user
- ArrayList<Node> sco_node_list;
- if (PHENOTYPE == null) {
- System.out.println("No --phenotype was provided, tree will only contain genome numbers");
- }
-
+ singleCopyInputFile = SELECTED_HMGROUPS;
+
try (Transaction tx = graphDb.beginTx()) { // start database transaction
Node pangenome_node = graphDb.findNodes(pangenome_label).next();
check_if_panproteome(pangenome_node); // sets PROTEOME boolean that controls functions, retrieves K_size & total_genomes
check_current_grouping_version(); // check which version of homology grouping is active
create_skip_arrays(false, true); // create skip array if -skip/-ref is provided by user
- stop_with_less_than_X_genomes(4);
+ stopWithLessThanGenomes(4);
retrieve_phenotypes(); // Creates and fills geno_pheno_map and phenotype_map when a phenotype was provided by the user
- sco_node_list = retrieve_hmgroups(true); // this will read the groups from single_copy_orthologs.csv
tx.success(); // transaction successful, commit changes
} catch (NotFoundException nfe) {
- System.out.println("Unable to start the database\n");
- return;
+ System.out.println("Unable to start the database\n");
+ System.exit(1);
}
- if (check_if_single_copy_groups){
- sco_node_list = check_if_single_copy_groups(sco_node_list);
+ graphDb.shutdown();
+
+ System.out.println("\nRunning MSA for all core groups");
+ String msaMethod = "per_group";
+ MultipleSequenceAlignment msa = new MultipleSequenceAlignment(
+ msaMethod,
+ false,
+ true,
+ true
+ );
+ System.out.println();
+
+ ArrayList<Node> hmNodeList = msa.getHmNodeList(); //get hmNodeList, this list is not updated by msa
+ if (checkSingleCopyGroups) {
+ hmNodeList = checkSingleCopyGroups(hmNodeList);
}
+
retrieve_skipped_genomes_during_glassification();
- String alignment_phylogeny_mode = check_mode_for_snp_tree();
- new File(WORKING_DIRECTORY + "alignments/grouping_v" + grouping_version).mkdirs(); // create directory
+ String alignmentPhylogenyMode = checkModeCorePhylogeny();
+ new File(WORKING_DIRECTORY + "alignments/msa_" + msaMethod + "/grouping_v" + grouping_version).mkdirs(); // create directory
new File(WORKING_DIRECTORY + "core_snp_tree").mkdir(); // create directory
- System.out.println("Single copy ortholog genes: " + sco_node_list.size());
- if (sco_node_list.isEmpty()) {
+ System.out.println("Single copy ortholog genes: " + hmNodeList.size());
+ if (hmNodeList.isEmpty()) {
System.out.println("No single copy orthologs. Run 'gene_classification'");
System.exit(1);
- }
-
- int original_threads = THREADS;
- if (sco_node_list.size() < THREADS) {
- THREADS = sco_node_list.size();
}
+
+ msa.alignSequences(true, false); //NB: I do not check for alignment_phylogeny_mode.contains("nucleotide") currently tho
+ ArrayList<String> updatedMsaNames = msa.getMsaNames(); //get msaNames, since this list is updated with trimming results
+
+ initialize_BLOSUM_matrix(BLOSUM);
+ HashMap<String, String> groupInfoMap = gatherInfoCorePhylogenyLog(singleCopyInputFile, hmNodeList);
graphDb.shutdown();
-
- ArrayList<Node> scos_to_be_aligned = check_if_msa_is_complete(sco_node_list, true); // checking if sequences are already 2 times
- if (!scos_to_be_aligned.isEmpty()) { // not every group is aligned two times yet
- FAST = true; // to skip the phylogeny construction
- core_snp_tree_prealign(scos_to_be_aligned); // step 1/4. Align protein/nucleotide sequences
- System.out.println("\n2/4. Trimming sequences");
- sco_node_list = trim_prealigned_proteins(sco_node_list); // step 2/4
- if (alignment_phylogeny_mode.contains("nucleotide")) {
- Mode = "NUCLEOTIDE";
- }
- run_msa_for_core_snp_tree(sco_node_list); // step 3/4
- } else { //
- sco_node_list = trim_prealigned_proteins(sco_node_list); // check which groups were removed and update the list
- }
-
- initialize_BLOSUM_matrix(62);
- HashMap<String, String> group_info_map = gather_info_for_core_snp_tree_log(single_copy_input_file);
- System.out.println("\n4/4. Reading alignments");
- THREADS = original_threads;
- if (alignment_phylogeny_mode.contains("NJ")) { // --mode nj
- prepare_NJ_core_snp_tree_results(sco_node_list, group_info_map);
+
+ if (alignmentPhylogenyMode.contains("NJ")) { // --mode nj
+ prepareNJCorePhylogenyResults(updatedMsaNames, groupInfoMap, msaMethod);
} else { // --mode ml
- prepare_ML_core_snp_tree_results(sco_node_list, group_info_map);
- }
+ prepareMLCorePhylogenyResults(updatedMsaNames, groupInfoMap, msaMethod);
+ }
}
-
+
/**
- * Verify if homology groups are single copy
+ * Verify if homology groups are single copy
* @param sco_node_list
- * @return
+ * @return
*/
- public static ArrayList<Node> check_if_single_copy_groups(ArrayList<Node> sco_node_list) {
+ public static ArrayList<Node> checkSingleCopyGroups(ArrayList<Node> sco_node_list) {
ArrayList<Node> updated_sco_node_list = new ArrayList<>();
try (Transaction tx = graphDb.beginTx()) { // start database transaction
for (Node hm_node : sco_node_list) {
int[] copy_number_array = (int[]) hm_node.getProperty("copy_number");
boolean sco_group = true;
- for (int i = 1; i < copy_number_array.length; ++i) { // walk over the cnv array in the homology node
+ for (int i = 1; i < copy_number_array.length; i++) { // walk over the cnv array in the homology node
if (skip_array[i - 1]) {
continue;
- }
+ }
if (copy_number_array[i] != 1) { // group cannot be single copy ortholog
sco_group = false;
}
@@ -2224,16 +2341,16 @@ public class Phylogeny {
if (updated_sco_node_list.isEmpty()) {
System.out.println("\rNone of the included homology groups are single copy");
} else if (updated_sco_node_list.size() < sco_node_list.size()) {
- System.out.println("\rNot all included homology groups are single copy. Lowered the number of groups from " + sco_node_list.size()
+ System.out.println("\rNot all included homology groups are single copy. Lowered the number of groups from " + sco_node_list.size()
+ " to " + updated_sco_node_list.size());
}
- return updated_sco_node_list;
+ return updated_sco_node_list;
}
-
+
/**
- * Combine multiple temporary files into a single fasta file
+ * Combine multiple temporary files into a single fasta file
* @param variable_or_informative
- * @param path
+ * @param path
*/
public static void concatenate_msa_inputs(String variable_or_informative, String path) {
String output_file = "variable.fasta";
@@ -2254,11 +2371,11 @@ public class Phylogeny {
System.out.println("\nUnable to create: " + path + output_file + "\n");
}
}
-
+
/**
- *
+ *
* @param input
- * @return
+ * @return
*/
public static String read_temp_sequence_input(String input) {
String line = "";
@@ -2270,42 +2387,42 @@ public class Phylogeny {
} catch (IOException e) {
System.out.println("\nUnable to read: " + input + "\n");
System.exit(1);
- }
+ }
return line;
- }
-
+ }
+
/**
* // create 2, 1 informative, 1 variable
* @param in_path
* @param out_path
- * @param first_sequence // create or append the file
+ * @param first_sequence // create or append the file
* @param genome_order
- * @return
+ * @return
*/
public static int[] get_snps_from_msa_and_create_alignments(String in_path, String out_path, boolean first_sequence, String genome_order) {
ArrayList<Integer> genome_order_list = read_genome_order_file(genome_order, false);
String [] sequence_array = new String[genome_order_list.size()]; // sequences are added in next function
ArrayList<Integer> snp_positions = read_mafft_alignment(in_path, sequence_array, genome_order_list.size());
String[][] all_seq_position_array = create_all_seq_position_array(sequence_array, genome_order_list);
- int[] ignored_conserved_sites = retrieve_and_add_var_inf_sites_from_alignment(all_seq_position_array, first_sequence, snp_positions, out_path);
+ int[] ignored_conserved_sites = retrieve_and_add_var_inf_sites_from_alignment(all_seq_position_array, first_sequence, snp_positions, out_path);
return new int[] {snp_positions.size()-1-ignored_conserved_sites[1], snp_positions.size()-1-ignored_conserved_sites[0]-ignored_conserved_sites[1]};
}
-
+
/**
- *
+ *
* @param all_seq_position_array
* @param first_sequence
* @param snp_positions
* @param out_path
- * @return
+ * @return
*/
- public static int[] retrieve_and_add_var_inf_sites_from_alignment(String[][] all_seq_position_array, boolean first_sequence,
- ArrayList<Integer> snp_positions, String out_path) {
-
+ public static int[] retrieve_and_add_var_inf_sites_from_alignment(String[][] all_seq_position_array, boolean first_sequence,
+ ArrayList<Integer> snp_positions, String out_path) {
+
int ignore_positions = 0, conserved_positions = 0; // ignore pos are not parsimony informative positions, conserved pos are the none variable sites
HashMap<String, StringBuilder> nuc_per_genome = new HashMap<>(); // key is genome nr for variable and genome nr + "_inf" for informative sites
- for (int l = 0; l < snp_positions.size()-1; l++) { // -1 because last number is the alignment length
- int snp_pos = snp_positions.get(l);
+ for (int l = 0; l < snp_positions.size()-1; l++) { // -1 because last number is the alignment length
+ int snp_pos = snp_positions.get(l);
HashMap<String, Integer> pos_count_map = new HashMap<>(); // used to determine if position is variable or informative
for (int genome_nr = 1; genome_nr <= total_genomes; genome_nr++) {
if (skip_array[genome_nr-1]) {
@@ -2315,14 +2432,14 @@ public class Phylogeny {
try_incr_hashmap(pos_count_map, nuc, 1);
}
if (pos_count_map.size() == 1) {
- conserved_positions ++;
+ conserved_positions++;
continue;
}
boolean informative = check_if_informative_position(pos_count_map);
if (!informative) {
ignore_positions++;
}
-
+
for (int genome_nr = 1; genome_nr <= total_genomes; genome_nr++) {
if (skip_array[genome_nr-1]) {
continue;
@@ -2332,12 +2449,12 @@ public class Phylogeny {
if (informative) {
try_incr_SB_hashmap(nuc_per_genome, genome_nr + "_inf", nucleotide);
}
- }
+ }
}
-
+
for (String genome_key : nuc_per_genome.keySet()) {
StringBuilder value_builder = nuc_per_genome.get(genome_key);
- if (first_sequence) {
+ if (first_sequence) {
write_SB_to_file_full_path(value_builder, out_path + "/temp/" + genome_key);
} else {
append_SB_to_file_full_path(value_builder, out_path + "/temp/" + genome_key);
@@ -2345,12 +2462,12 @@ public class Phylogeny {
}
return new int[]{ignore_positions, conserved_positions};
}
-
+
/**
- *
+ *
* @param sequence_array
* @param genome_order_list
- * @return
+ * @return
*/
public static String[][] create_all_seq_position_array(String[] sequence_array, ArrayList<Integer> genome_order_list) {
String[][] all_seq_position_array = new String[total_genomes][0];
@@ -2360,80 +2477,19 @@ public class Phylogeny {
if (skip_array[genome_nr-1]) {
continue;
}
- sequence_counter ++;
+ sequence_counter++;
all_seq_position_array[genome_nr-1] = sequence.split(""); // -1 because data in array
}
return all_seq_position_array;
}
-
- /**
- * Step 1 of 4 of the core snp tree. The first alignment of the sequences
- * @param updated_sco_node_list
- */
- public void core_snp_tree_prealign(ArrayList<Node> updated_sco_node_list) {
- System.out.println("\n1/4. Prealigning sequences");
- boolean pass = false; // pass when all alignment files exists
- int loop_counter = 0;
- while (!pass) {
- ArrayList<Node> updated_sco_node_list2 = check_if_msa_is_complete(updated_sco_node_list, false); // checking if trimmed sequences are aligned 1 time
- SELECTED_HMGROUPS = ""; // group identifiers. is read by the 'msa_of_group' function
- if (!updated_sco_node_list2.isEmpty()) {
- int counter = 0;
- for (Node hm_node : updated_sco_node_list2) {
- SELECTED_HMGROUPS += hm_node.getId() + ",";
- counter ++;
- }
- SELECTED_HMGROUPS = SELECTED_HMGROUPS.replaceFirst(".$","");
- System.out.println("");
- classification.msa_of_group(false, false, false);
-
- } else {
- pass = true;
- }
- loop_counter ++;
- if (loop_counter == 4) {
- System.out.println("\nFailed to align " + updated_sco_node_list2.size() + " groups: " + updated_sco_node_list2);
- System.exit(1);
- }
- }
- }
-
- /**
- * Step 3 of 4 of the core snp tree. The second alignment using trimmed sequences
- * @param scos_to_be_aligned
- */
- public void run_msa_for_core_snp_tree(ArrayList<Node> scos_to_be_aligned) {
- boolean pass = false; // pass when all alignment files exists
- int loop_counter = 0;
- while (!pass) {
- SELECTED_HMGROUPS = ""; // group identifiers. is read by 'msa_of_group' function
- System.out.println("\n3/4. Aligning trimmed sequences");
- ArrayList<Node> updated_scos_to_be_aligned = check_if_msa_is_complete(scos_to_be_aligned, true); // checking if trimmed sequences are aligned
- if (!updated_scos_to_be_aligned.isEmpty()) {
- for (Node hm_node : updated_scos_to_be_aligned) {
- SELECTED_HMGROUPS += hm_node.getId() + ",";
- }
- SELECTED_HMGROUPS = SELECTED_HMGROUPS.replaceFirst(".$",""); // remove last character
- classification.msa_of_group(false, true, false);
- } else {
- pass = true;
- }
-
- loop_counter ++;
- if (loop_counter == 4) {
- System.out.println("\nFailed to align " + updated_scos_to_be_aligned.size() + " groups: " + updated_scos_to_be_aligned);
- System.exit(1);
- }
- }
- SELECTED_HMGROUPS = "";
- }
-
+
/**
- *
- * @param sco_node_list homology group node identifiers
+ *
+ * @param sco_string_list homology group node identifiers
* @param group_info_map
+ * @param msaMethod
*/
- public void prepare_ML_core_snp_tree_results(ArrayList<Node> sco_node_list, HashMap<String, String> group_info_map) {
+ public void prepareMLCorePhylogenyResults(ArrayList<String> sco_string_list, HashMap<String, String> group_info_map, String msaMethod) {
String output_path = WORKING_DIRECTORY + "core_snp_tree/";
int group_counter = 0, informative_sites = 0, variable_sites = 0;
String nuc_or_prot = "nuc", gene_or_prot = "gene sizes()";
@@ -2445,15 +2501,14 @@ public class Phylogeny {
";(max) trimmed start;(max) trimmed end;variable positions;informative positions\n");
delete_directory(output_path + "temp/");
new File(output_path + "temp/").mkdir(); // create directory
-
+
boolean first = true;
- for (Node hm_node : sco_node_list) {
- String group_id = hm_node.getId() + "";
- group_counter ++;
- System.out.print("\r Reading alignments: " + group_counter + "/" + sco_node_list.size());
+ for (String group_id : sco_string_list) {
+ group_counter++;
+ System.out.print("\r Reading alignments: " + group_counter + "/" + sco_string_list.size());
int[] var_inf_sites = get_snps_from_msa_and_create_alignments(
- WORKING_DIRECTORY + "alignments/grouping_v" + grouping_version + "/groups/" + group_id + "/output/" + nuc_or_prot + "_trimmed.afa",
- output_path, first, WORKING_DIRECTORY + "alignments/grouping_v" + grouping_version + "/groups/" + group_id + "/input/genome_order.info");
+ WORKING_DIRECTORY + "alignments/msa_" + msaMethod + "/grouping_v" + grouping_version + "/" + group_id + "/output/" + nuc_or_prot + "_trimmed.afa",
+ output_path, first, WORKING_DIRECTORY + "alignments/msa_" + msaMethod + "/grouping_v" + grouping_version + "/" + group_id + "/input/genome_order.info");
informative_sites += var_inf_sites[1];
variable_sites += var_inf_sites[0];
if (variable_sites > 0) {
@@ -2461,39 +2516,41 @@ public class Phylogeny {
}
String info = group_info_map.get(group_id);
gene_info.append(info).append(var_inf_sites[0]).append(";").append(var_inf_sites[1]).append("\n"); // Total variable/informative positions:
- }
+ }
write_SB_to_file_full_path(gene_info, output_path + "sites_per_group.csv");
- System.out.println("\nTotal variable/informative positions: " + variable_sites + "/" + informative_sites);
+ System.out.println("\rTotal variable sites : " + variable_sites + "\n" +
+ "Total informative sites: " + informative_sites);
if (variable_sites == 0) {
- System.out.println("Unable to create a phylogeny as the " + adj_total_genomes + " genomes do not have any variation in the " +
- sco_node_list.size() + " homology groups\n");
+ System.out.println("Unable to create a phylogeny as the " + adj_total_genomes + " genomes do not have any variation in the " +
+ sco_string_list.size() + " homology groups\n");
return;
}
concatenate_msa_inputs("", output_path);
-
- System.out.print("\nOutput written to:\n "
+
+ System.out.print("\nOutput written to:\n "
+ output_path + "sites_per_group.csv\n "
+ output_path + "variable.fasta\n ");
-
+
if (informative_sites > 0) {
- concatenate_msa_inputs("_inf", output_path);
+ concatenate_msa_inputs("_inf", output_path);
System.out.println(output_path + "informative.fasta\n ");
String iqtree_command = "iqtree -nt " + THREADS + " -s " + output_path + "informative.fasta -redo -bb 1000";
- System.out.print("Run IQtree:\n " +
- "iqtree -nt " + THREADS + " -s " + output_path + "informative.fasta -redo -bb 1000\n\n" +
- "When running IQtree, make sure there are no temp files present from a previous IQtree run:\n" +
+ System.out.print("Run IQ-tree:\n " +
+ "iqtree -nt " + THREADS + " -s " + output_path + "informative.fasta -redo -bb 1000\n\n" +
+ "When running IQ-tree, make sure there are no temp files present from a previous run:\n" +
" rm " + output_path + "informative.fasta.*\n\n");
if (PHENOTYPE == null) {
String rename_command = "pantools rename_phylogeny -dp " + WORKING_DIRECTORY + " --phenotype PHENOTYPE -if " + output_path;
System.out.println("Since you did not provide a phenotype, the phylogeny will only contains genome numbers."
- + " When IQtree is done, run the following command to add the phenotypes to the tree\n "
- + rename_command + "informative.fasta.treefile\n");
+ + " When IQ-tree is done, run the following command to add phenotypes to the tree\n "
+ + rename_command + "informative.fasta.treefile\n"
+ + rename_command + "informative.fasta.splits.nex\n");
} else {
System.out.println("");
}
write_string_to_file_full_path(iqtree_command, output_path + "iqtree.sh");
- System.out.println("When using the core SNP tree in your research, please also cite:\n" +
- "Minh, Bui Quang, et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era.\n"
+ System.out.println("When using the core phylogeny in your research, please also cite:\n" +
+ " Minh, Bui Quang, et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era.\n"
+ "Molecular biology and evolution 37.5 (2020): 1530-1534.\n");
} else {
System.out.println("No parsimony informative sites were found in the input sequences. Unable to create a phylogeny.\n");
@@ -2504,122 +2561,108 @@ public class Phylogeny {
/**
* Builds a consensus species phylogeny based on user specified homology groups (written by Dirk-Jan).
* Old function name was phylogeny_using_groups()
+ *
+ * NB: There is more recent version of ASTRAL-Pro available, both at https://github.com/chaoszhang/ASTER and at
+ * https://github.com/chaoszhang/A-pro.git, but both of these do not accept polytomies. Our FastTree trees do
+ * contain polytomies. So we will need to wait until they update ASTRAL-Pro to accept polytomies before updating to
+ * a more recent version of their software.
*/
public void consensus_tree() {
System.out.println("\nBuilding phylogeny using user-specified groups\n"
+ "Using ASTRAL-PRO (https://github.com/chaoszhang/ASTER at commit 2c1c469) for this.\n"
+ + "This version should be the same as v1.1.2 that was described in the accompanying paper.\n\n"
+ "Please cite the original authors:\n"
+ "Chao Zhang, Celine Scornavacca, Erin K Molloy, Siavash Mirarab, ASTRAL-Pro: Quartet-Based Species-\n"
+ "Tree Inference despite Paralogy, Molecular Biology and Evolution, Volume 37, Issue 11, November 2020, \n"
+ "Pages 3292–3307, https://doi.org/10.1093/molbev/msaa139\n\n"
- + "No need to put ASTRAL-PRO in path, it is already in " + pantools_path + "addons/ASTER/\n");
-
- // Set total_genomes, grouping_version, Mode, hm_node_list
- ArrayList<Node> hm_node_list = new ArrayList<>();
+ + "Please make sure the following file is executable: " + pantools_path + "ASTER/astral-pro\n"
+ + "One can compile this file by running: `cd " + pantools_path + "ASTER && g++ -std=gnu++11 -march=native -Ofast -pthread astral.cpp -o astral && g++ -std=gnu++11 -march=native -Ofast -pthread astral-pro.cpp -o astral-pro`\n");
+
+ check_if_program_exists_stderr(pantools_path + "ASTER/astral-pro", 500, "ASTRAL-PRO", true);
+
check_if_graphDb_is_available(); // starts up the graph database if needed
+// graphDb.shutdown();
+// connect_pangenome();
try (Transaction tx = graphDb.beginTx()) { // start database transaction
- Node pangenome_node = graphDb.findNodes(pangenome_label).next();
- check_if_panproteome(pangenome_node); // sets PROTEOME boolean that controls functions, retrieves K_size & total_genomes
- classification.check_mode_for_msa(); // sets Mode for running MSA
+ Node pangenomeNode = graphDb.findNodes(pangenome_label).next();
+
+ check_if_panproteome(pangenomeNode); // sets PROTEOME boolean that controls functions, retrieves K_size & total_genomes
+ create_skip_arrays(false, true); // create skip array if --skip/-ref is provided by user
check_current_grouping_version(); // check which version of homology grouping is active
- hm_node_list = retrieve_hmgroups(true); // sets hm_node_list
+
if (grouping_version < 1) {
System.out.println("\nNo homology grouping is active\n");
System.exit(1);
}
+
tx.success(); // transaction successful, commit changes
} catch (NotFoundException nfe) {
System.out.println("Unable to start the pangenome database\n");
- return;
- }
- if (LOG) {
- System.out.println("Total genomes: " + total_genomes);
- System.out.println("All homology groups to be used for genome tree building: " +
- hm_node_list);
- System.out.println("Current grouping: " + grouping_version + "\n");
+ System.exit(1);
}
-
+
// Set file names and remove old files
create_directory_in_DB("consensus_tree/grouping_v" + grouping_version);
- String all_gene_tree_file = WORKING_DIRECTORY + "consensus_tree/grouping_v" + grouping_version +
+ String all_gene_tree_file = WORKING_DIRECTORY + "consensus_tree/grouping_v" + grouping_version +
"/all_trees.hmgroups.newick";
- String species_tree_file = WORKING_DIRECTORY + "consensus_tree/grouping_v" + grouping_version +
+ String species_tree_file = WORKING_DIRECTORY + "consensus_tree/grouping_v" + grouping_version +
"/consensus_tree.astral-pro.newick";
delete_file_full_path(all_gene_tree_file);
delete_file_full_path(species_tree_file);
-
+
// Check presence of all trees
String gene_tree_file;
- ArrayList<Node> hmgroups_to_be_done = new ArrayList<>();
String trimming = "_trimmed";
- if (Mode.contains("NO-TRIMMING")) {
- System.out.println("--mode no-trimming was included, aligning the groups once");
+ String outDirMsa = WORKING_DIRECTORY + "alignments/msa_per_group";
+ if (!TRIMMING) {
+ System.out.println("\r--no-trimming was included, aligning the groups once");
trimming = "";
} else {
- System.out.println("--mode no-trimming was not included, aligning the groups two times");
- }
- for (Node hm_node : hm_node_list) {
- gene_tree_file = WORKING_DIRECTORY + "alignments/grouping_v" + grouping_version + "/groups/" +
- hm_node.getId() + "/output/prot" + trimming +".newick";
- if (!check_if_file_exists(gene_tree_file)) {
- hmgroups_to_be_done.add(hm_node);
- }
- System.out.print("\rHomology groups to be aligned: " + hmgroups_to_be_done.size() + "/" + hm_node_list.size());
- }
-
- // For all homology groups for which no tree exists, run MSA
- if (!hmgroups_to_be_done.isEmpty()) {
- System.out.println("\rRunning run_msa for all groups that do not yet have a homology group tree");
- if (LOG) {
- System.out.println("Homology groups that do not yet have an output tree: " +
- hmgroups_to_be_done);
- System.out.println("PROTEOME: " + PROTEOME);
- System.out.println("Mode: " + Mode);
- }
-
- check_if_graphDb_is_available(); // starts up the graph database if needed
- try (Transaction tx = graphDb.beginTx()) { // start database transaction
- create_skip_arrays(false, true); // create skip array if -skip/-ref is provided by user
- hmgroups_to_be_done = classification.prepare_msa_sequences(hmgroups_to_be_done, false); // prepare msa
- tx.success(); // transaction successful, commit changes
- } catch (NotFoundException nfe) {
- System.out.println("Unable to start the pangenome database\n");
- return;
- }
- classification.run_msa(hmgroups_to_be_done, false); // Run MSA without trimming
- if (!Mode.contains("NO-TRIMMING")) {
- hmgroups_to_be_done = trim_prealigned_proteins(hmgroups_to_be_done);
- Mode = "PROTEIN,NO-TRIMMING"; // only protein trees are used
- classification.run_msa(hmgroups_to_be_done, true); // Run MSA with trimming
- }
- System.out.println("");
- }
-
+ System.out.println("\r--no-trimming was not included, aligning the groups two times");
+ }
+
+ //run MSA
+ MultipleSequenceAlignment msa = new MultipleSequenceAlignment(
+ "per_group",
+ false,
+ true,
+ false
+ );
+ msa.alignSequences(true, false);
+ ArrayList<Node> hmNodeList = msa.getHmNodeList();
+ String nucOrProt = msa.getNucOrProt();
+ System.out.println();
+
// Concatenate all tree files into one large tree file
String gene_tree;
String gene_tree_reformatted;
-
- System.out.println("Reading in all alignments belonging to user-specified homology groups\n");
+
+ System.out.println("Reading in all alignments belonging to user-specified homology groups");
+ if (ALLOW_POLYTOMIES) {
+ System.out.println("NB: Polytomies allowed for ASTRAL-PRO; accuracy of final tree not guaranteed!");
+ }
+ System.out.println();
int group_counter = 0;
- for (Node hm_node : hm_node_list) {
- group_counter ++;
+ for (Node hm_node : hmNodeList) {
+ group_counter++;
if (group_counter % 1000 == 0) {
- System.out.print("\rReading gene tree: " + group_counter + "/" + hm_node_list.size());
+ System.out.print("\rReading gene tree: " + group_counter + "/" + hmNodeList.size());
}
- gene_tree_file = WORKING_DIRECTORY + "alignments/grouping_v" + grouping_version + "/groups/" +
- hm_node.getId() + "/output/prot" + trimming + ".newick";
+ gene_tree_file = outDirMsa + "/grouping_v" + grouping_version + "/" +
+ hm_node.getId() + "/output/" + nucOrProt + trimming + ".newick";
gene_tree = read_newick_file(gene_tree_file);
- gene_tree_reformatted = replace_gene_by_genome_in_newick(gene_tree);
- append_string_to_file_full_path(gene_tree_reformatted + "\n", all_gene_tree_file);
+ if (!hasPolytomies(gene_tree)) {
+ gene_tree_reformatted = replace_gene_by_genome_in_newick(gene_tree);
+ append_string_to_file_full_path(gene_tree_reformatted + "\n", all_gene_tree_file);
+ } else if (ALLOW_POLYTOMIES) {
+ gene_tree_reformatted = replace_gene_by_genome_in_newick(gene_tree);
+ append_string_to_file_full_path(gene_tree_reformatted + "\n", all_gene_tree_file);
+ }
}
-
- String date = new SimpleDateFormat("dd-MM-yyyy HH:mm:ss").format(new Date());
- append_string_to_file_full_path(date + "\npantools astral_pro\nRuntime after alignments:\n", WORKING_DIRECTORY + "/log/used_commands");
- print_runtime(false, true);
graphDb.shutdown();
- // Run ASTRAL-pro (https://github.com/chaoszhang/ASTER at commit 2c1c469)
- String[] args = new String[] {pantools_path + "addons/ASTER/astral-pro", "-o", species_tree_file, all_gene_tree_file};
+ // Run ASTRAL-pro (https://github.com/chaoszhang/ASTER)
+ String[] args = new String[] {pantools_path + "ASTER/astral-pro", "-o", species_tree_file, all_gene_tree_file};
System.out.println("\rRunning ASTRAL-PRO for all alignments. (Database is unlocked and can be used by other functions.)");
if (LOG) {
System.out.println("ASTRAL-PRO command: " + Arrays.toString(args));
@@ -2629,48 +2672,70 @@ public class Phylogeny {
System.out.println("ASTRAL-pro could not be run and output file was not created.");
System.exit(1);
}
-
+
System.out.println("\nOutput can be found in:\n"
+ " all homology group trees: " + all_gene_tree_file + "\n"
- + " ASTRAL-PRO consensus tree: " + species_tree_file + "\n");
+ + " ASTRAL-PRO consensus tree: " + species_tree_file + "\n"
+ + "\nNB: Please bear in mind that ASTRAL-PRO is not accurate for trees that contain polytomies. We are still working on this.\n");
}
-
+
/**
* Replaces all gene labels in a gene tree by its genome number (Written by Dirk-Jan)
- * @param gene_tree
- * @return
+ * @param gene_tree newick format tree
+ * @return tree in which genome number only is left
*/
- public String replace_gene_by_genome_in_newick(String gene_tree) {
+ private String replace_gene_by_genome_in_newick(String gene_tree) {
String gene_tree_reformatted = gene_tree;
String genome;
-
+
for (int genome_number = total_genomes; genome_number > 0; genome_number--) {
genome = Integer.toString(genome_number);
String regex = genome + "_.*?:";
gene_tree_reformatted = gene_tree_reformatted.replaceAll(regex, genome + ":");
}
-
+
return gene_tree_reformatted;
}
/**
- *
+ * Checks of a gene tree has polytomies
+ * @param gene_tree newick format tree
+ * @return boolean whether tree has polytomies
+ */
+ private boolean hasPolytomies(String gene_tree) {
+ boolean output = false;
+ String[] splitTree = gene_tree.split(",");
+ for (int i = 1; i < splitTree.length - 1; i++) { //first and last part always contain brackets
+ String part = splitTree[i];
+ if (!part.contains("(") && !part.contains(")")) { //if any other part contains no bracket at all, it has at least one polytomy
+ output = true;
+ break;
+ }
+ }
+
+ return output;
+ }
+
+ /**
+ *
*/
public class retrieve_snps_NJ_core_snp_tree implements Runnable {
HashMap<String, Long> total_shared_snps_map;
HashMap<String, String> gene_info_map;
StringBuilder sites_per_group_builder;
-
- public retrieve_snps_NJ_core_snp_tree(HashMap<String, Long> total_shared_snps_map, HashMap<String, String> gene_info_map,
- StringBuilder sites_per_group_builder) {
-
- this.total_shared_snps_map = total_shared_snps_map;
- this.gene_info_map = gene_info_map;
- this.sites_per_group_builder = sites_per_group_builder;
-
- }
-
+ String msaMethod;
+
+ public retrieve_snps_NJ_core_snp_tree(HashMap<String, Long> total_shared_snps_map, HashMap<String, String> gene_info_map,
+ StringBuilder sites_per_group_builder, String msaMethod) {
+
+ this.total_shared_snps_map = total_shared_snps_map;
+ this.gene_info_map = gene_info_map;
+ this.sites_per_group_builder = sites_per_group_builder;
+ this.msaMethod = msaMethod;
+ }
+
public void run() {
+ String path = WORKING_DIRECTORY + "/alignments/msa_" + msaMethod + "/grouping_v" + grouping_version + "/";
while (!string_queue.isEmpty()) {
String sco_group;
try {
@@ -2686,38 +2751,38 @@ public class Phylogeny {
}
HashMap<String, Integer> shared_snps_map = new HashMap<>();//= create_shared_snps_map(true);
System.out.print("\r Reading alignments: " + string_queue.size() + " ");
- String alignment = WORKING_DIRECTORY + "/alignments/grouping_v" + grouping_version + "/groups/" + sco_group + "/output/" + nuc_or_prot + "_trimmed.afa";
- String genome_order_file = WORKING_DIRECTORY + "/alignments/grouping_v" + grouping_version + "/groups/" + sco_group + "/input/genome_order.info";
- int[] var_inf_sites = count_var_inf_sites_in_msa(shared_snps_map, null, null, alignment, sco_group,
- nuc_or_prot2, genome_order_file); // variable, informative, conserved sites
-
- append_sites_per_group(sites_per_group_builder, var_inf_sites, gene_info_map, sco_group);
+ String alignment = path + sco_group + "/output/" + nuc_or_prot + "_trimmed.afa";
+ String genome_order_file = path + sco_group + "/input/genome_order.info";
+ int[] var_inf_sites = count_var_inf_sites_in_msa(shared_snps_map, null, null, alignment, sco_group,
+ nuc_or_prot2, genome_order_file); // variable, informative, conserved sites
+
+ append_sites_per_group(sites_per_group_builder, var_inf_sites, gene_info_map, sco_group); // synchronized function
atomic_counter1.addAndGet(var_inf_sites[0]);
atomic_counter2.addAndGet(var_inf_sites[1]);
- increase_total_shared_snp_map(shared_snps_map, total_shared_snps_map, genome_order_file, "");
- increase_total_shared_snp_map(shared_snps_map, total_shared_snps_map, genome_order_file, "#inf");
- }
+ increase_total_shared_snp_map(shared_snps_map, total_shared_snps_map, genome_order_file, ""); // synchronized function
+ increase_total_shared_snp_map(shared_snps_map, total_shared_snps_map, genome_order_file, "#inf"); // synchronized function
+ }
}
}
-
+
/**
- *
+ *
* @param shared_snps_map
* @param total_shared_snps_map
- * @param genome_order_file
+ * @param genome_order_file
* @param informative
*/
- public static synchronized void increase_total_shared_snp_map(HashMap<String, Integer> shared_snps_map, HashMap<String, Long> total_shared_snps_map,
- String genome_order_file, String informative) {
-
+ public static synchronized void increase_total_shared_snp_map(HashMap<String, Integer> shared_snps_map, HashMap<String, Long> total_shared_snps_map,
+ String genome_order_file, String informative) {
+
ArrayList<String> protein_id_list = get_full_protein_identifiers(genome_order_file, false);
ArrayList<Integer> genome_order_list = read_genome_order_file(genome_order_file, false);
- for (int i=0; i < protein_id_list.size(); i++) {
+ for (int i=0; i < protein_id_list.size(); i++) {
int genome_nr1 = genome_order_list.get(i);
if (skip_array[genome_nr1-1]) {
continue;
}
- for (int j=0; j < protein_id_list.size(); j++) {
+ for (int j=0; j < protein_id_list.size(); j++) {
int genome_nr2 = genome_order_list.get(j);
if (skip_array[genome_nr2-1]) {
continue;
@@ -2735,86 +2800,107 @@ public class Phylogeny {
}
}
}
-
+
/**
* Synchronized function. Only 1 thread can access the map and append the stringbuilder
* @param sites_per_group_builder
* @param var_inf_sites
* @param gene_info_map
- * @param sco_group
+ * @param sco_group
*/
- public static synchronized void append_sites_per_group(StringBuilder sites_per_group_builder, int[] var_inf_sites,
- HashMap<String, String> gene_info_map, String sco_group) {
-
+ public static synchronized void append_sites_per_group(StringBuilder sites_per_group_builder, int[] var_inf_sites,
+ HashMap<String, String> gene_info_map, String sco_group) {
+
String info = gene_info_map.get(sco_group);
- sites_per_group_builder.append(info).append(var_inf_sites[0]).append(";").append(var_inf_sites[1]).append("\n");
+ sites_per_group_builder.append(info).append(var_inf_sites[0]).append(";").append(var_inf_sites[1]).append("\n");
}
-
+
/**
- *
- * @param sco_node_list
+ *
+ * @param sco_string_list
* @param group_info_map
+ * @param msaMethod
*/
- public void prepare_NJ_core_snp_tree_results(ArrayList<Node> sco_node_list, HashMap<String, String> group_info_map) {
+ public void prepareNJCorePhylogenyResults(ArrayList<String> sco_string_list, HashMap<String, String> group_info_map, String msaMethod) {
String output_path = WORKING_DIRECTORY + "core_snp_tree/";
HashMap<String, Long> total_shared_snps_map = new LinkedHashMap<>();
- StringBuilder sites_per_group_builder = new StringBuilder("#Homology group node id;names;gene sizes;(max) trimmed start;(max) trimmed end;"
+ StringBuilder sites_per_group_builder = new StringBuilder("#Homology group node id;gene names;gene sizes;(max) trimmed start;(max) trimmed end;"
+ "variable positions;informative positions\n");
string_queue = new LinkedBlockingQueue<>();
- atomic_counter1 = new AtomicLong(0); // variable sites
+ atomic_counter1 = new AtomicLong(0); // variable sites
atomic_counter2 = new AtomicLong(0); // informative sites
- for (Node hm_node : sco_node_list) {
- string_queue.add(hm_node.getId() +"");
- }
-
+ for (String group_id : sco_string_list) {
+ string_queue.add(group_id);
+ }
+
try {
ExecutorService es = Executors.newFixedThreadPool(THREADS);
for(int i = 1; i <= THREADS; i++) {
- es.execute(new retrieve_snps_NJ_core_snp_tree(total_shared_snps_map, group_info_map, sites_per_group_builder));
+ es.execute(new retrieve_snps_NJ_core_snp_tree(total_shared_snps_map, group_info_map, sites_per_group_builder, msaMethod));
}
es.shutdown();
es.awaitTermination(10, TimeUnit.DAYS);
} catch (InterruptedException e) {
-
+
}
write_SB_to_file_full_path(sites_per_group_builder, output_path + "sites_per_group.csv");
- System.out.println("\rTotal variable/informative positions: " + atomic_counter1.get() + "/" + atomic_counter2.get() + " ");
+
+ System.out.println("\rTotal variable sites : " + atomic_counter1.get() + "\n" +
+ "\rTotal informative sites: " + atomic_counter2.get());
if (atomic_counter1.get() == 0) {
- System.out.println("Unable to create a phylogeny as the " + adj_total_genomes + " genomes do not have any variation in the "
- + sco_node_list.size() + " homology groups\n");
+ System.out.println("Unable to create a phylogeny as the " + adj_total_genomes + " genomes do not have any variation in the "
+ + sco_string_list.size() + " homology groups\n");
return;
}
+ if (atomic_counter2.get() == 0) {
+ System.out.println("No parsimony informative sites were found in the homology groups\n");
+ }
+
String nuc_or_prot = "nuc";
if (Mode.startsWith("PROTEIN")) {
nuc_or_prot = "prot";
}
-
+
create_shared_sites_from_total_shared_map(total_shared_snps_map, output_path, atomic_counter1.get(), nuc_or_prot, "");
create_shared_sites_from_total_shared_map(total_shared_snps_map, output_path, atomic_counter2.get(), nuc_or_prot, "#inf");
- create_core_snp_nj_tree_rscript("variable", nuc_or_prot);
- System.out.println("\nOutput written to:\n "
+ create_core_snp_nj_tree_rscript(nuc_or_prot);
+ System.out.print("\nOutput written to:\n "
+ + output_path + "core_snp_NJ_tree.R\n "
+ output_path + "sites_per_group.csv\n "
- + output_path + "core_snp_tree_variable_sites.R\n "
+ output_path + "shared_variable_" + nuc_or_prot + "_positions.csv\n");
-
+
if (atomic_counter2.get() > 0) {
- create_core_snp_nj_tree_rscript("informative", nuc_or_prot);
- System.out.println(" " + output_path + "core_snp_tree_informative_sites.R\n "
- + output_path + "shared_informative_" + nuc_or_prot + "_positions.csv\n ");
- }
- }
-
- /**
- * Calculate the distance from the shared and total VARIABLE and INFORMATIVE sites
+ System.out.println(" " + output_path + "shared_informative_" + nuc_or_prot + "_positions.csv\n");
+ } else {
+ System.out.println("");
+ }
+ }
+
+ /**
+ * Calculate the distance from the shared and total VARIABLE and INFORMATIVE sites
+ *
+ * Creates
+ * - informative_nuc_distance.csv
+ * - informative_prot_distance.csv
+ *
+ * - variable_nuc_distance.csv
+ * - variable_prot_distance.csv
+ *
+ * - shared_informative_nuc_positions.csv
+ * - shared_informative_prot_positions.csv
+ *
+ * - shared_variable_nuc_positions.csv
+ * - shared_variable_prot_positions.csv
+ *
* @param shared_snps_map
* @param output_path
* @param total_sites
* @param nuc_or_prot
- * @param informative
+ * @param informative
*/
- public static void create_shared_sites_from_total_shared_map(HashMap<String, Long> shared_snps_map, String output_path, long total_sites,
- String nuc_or_prot, String informative) {
-
+ public static void create_shared_sites_from_total_shared_map(HashMap<String, Long> shared_snps_map, String output_path, long total_sites,
+ String nuc_or_prot, String informative) {
+
if (total_sites == 0) { // variable or parsimony informative
return;
}
@@ -2827,9 +2913,12 @@ public class Phylogeny {
continue;
}
String phenotype = get_phenotype_for_genome(i, true);
- header.append(i).append(phenotype).append(",");
all_genes.append(i).append(phenotype).append(",");
gene_count_all.append(i).append(phenotype).append(",");
+ header.append(i).append(phenotype);
+ if (i != total_genomes) {
+ header.append(",");
+ }
for (int j = 1; j <= total_genomes; j++) {
if (skip_array[j-1]) {
continue;
@@ -2847,11 +2936,15 @@ public class Phylogeny {
if (distance_str.equals("0.0000000000") && shared != total_sites) { // these are not actually zero
distance_str = "0.0000000001";
}
- all_genes.append(distance_str).append(",");
- gene_count_all.append(shared).append(",");
+ all_genes.append(distance_str);
+ gene_count_all.append(shared);
+ if (j != total_genomes) {
+ all_genes.append(",");
+ gene_count_all.append(",");
+ }
}
all_genes.append("\n");
- gene_count_all.append("\n");
+ gene_count_all.append("\n");
}
String header_str = header.toString();
header_str += "\n";
@@ -2862,94 +2955,100 @@ public class Phylogeny {
write_string_to_file_full_path(header_str + count2, output_path + "shared_informative_" + nuc_or_prot + "_positions.csv");
} else {
write_string_to_file_full_path(header_str + all_str, output_path + "variable_" + nuc_or_prot + "_distance.csv");
- write_string_to_file_full_path(header_str + count2, output_path + "shared_variable_" + nuc_or_prot + "_positions.csv");
+ write_string_to_file_full_path(header_str + count2, output_path + "shared_variable_" + nuc_or_prot + "_positions.csv");
}
}
-
+
/**
* Core SNP NJ tree
- * @param inf_or_var informative or variable sites as input
* @param nuc_or_prot 'nuc' or 'prot' string
*/
- public static void create_core_snp_nj_tree_rscript(String inf_or_var, String nuc_or_prot) {
- String R_LIB = check_r_libraries_environment();
+ public static void create_core_snp_nj_tree_rscript(String nuc_or_prot) {
+ String R_LIB = check_r_libraries_environment();
StringBuilder rscript = new StringBuilder();
String input_path = WD_full_path + "core_snp_tree/";
rscript.append("#! /usr/bin/env RScript\n")
+ .append("\n")
+ .append("# Select a distance based on variable or parsimony informative sites\n")
+ .append("# ").append(input_path).append("informative_").append(nuc_or_prot).append("_distance.csv\n")
+ .append("# ").append(input_path).append("variable_").append(nuc_or_prot).append("_distance.csv\n")
+ .append("\n")
.append("#Assuming the R libraries were installed via Conda, the next line can be ignored. If not, use it to manually install the required package\n")
.append("#install.packages(\"ape\", \"").append(R_LIB).append("\", \"https://cran.us.r-project.org\")\n")
.append("library(ape)\n")
- .append("input = read.csv(\"").append(input_path).append(inf_or_var).append("_").append(nuc_or_prot).append("_distance.csv\", sep=\",\",header = TRUE)\n")
- .append("input[").append((adj_total_genomes + 2)).append("] <- NULL\n")
+ .append("\n")
+ .append("input = read.csv(\"").append(input_path).append("informative_").append(nuc_or_prot).append("_distance.csv\", sep=\",\", header = TRUE)\n")
.append("df2 = subset(input, select = -c(Genomes))\n")
- .append("df.dist2 =as.matrix(df2, labels=TRUE)\n")
+ .append("df.dist2 = as.matrix(df2, labels=TRUE)\n")
.append("colnames(df.dist2) <- rownames(df.dist2) <- input[['Genomes']]\n")
.append("NJ_tree <- nj(df.dist2)\n")
+ .append("\n")
.append("pdf(NULL)\n")
.append("plot(NJ_tree, main = \"Neighbor Joining\")\n")
- .append("write.tree(NJ_tree, tree.names = TRUE, file=\"").append(input_path).append(inf_or_var).append("_core_snp.tree\")\n")
- .append("cat(\"\\nSpecies tree written to: ").append(input_path).append(inf_or_var).append("_core_snp.tree\\n\\n\")");
- write_SB_to_file_full_path(rscript, input_path + "core_snp_tree_" + inf_or_var + "_sites.R");
+ .append("write.tree(NJ_tree, tree.names = TRUE, file=\"").append(input_path).append("_core_snp_NJ.tree\")\n")
+ .append("cat(\"\\nSpecies tree written to: ").append(input_path).append("_core_snp_NJ.tree\\n\\n\")");
+ write_SB_to_file_full_path(rscript, input_path + "core_snp_NJ_tree.R");
}
-
+
/**
* Mode options nothing (0), protein, nucleotide, MJ, NJ
- * @return
+ * @return
*/
- public String check_mode_for_snp_tree() {
+ public String checkModeCorePhylogeny() {
String alignment_phylogeny_mode = "";
- if (Mode.equals("0")) { // no --mode was provided
- if (PROTEOME) {
- System.out.println("\rNo --mode selected. Preparing Maximum Likelihood phylogeny for protein sequences");
- alignment_phylogeny_mode = "ML,protein";
- } else { // pangenome
- System.out.println("\rNo --mode selected. Preparing Maximum Likelihood phylogeny for nucleotide sequences");
- alignment_phylogeny_mode = "ML,nucleotide";
- }
- } else if (Mode.contains("NJ")) {
- if (Mode.contains("PROTEIN") || PROTEOME) {
- System.out.println("\rPreparing Neighbor joining phylogeny for protein sequences");
- alignment_phylogeny_mode = "NJ,protein";
- } else {
- System.out.println("\rPreparing Neighbor joining phylogeny for nucleotide sequences");
- alignment_phylogeny_mode = "NJ,nucleotide";
- }
- } else if (Mode.contains("ML") || Mode.contains("PROTEIN") || Mode.contains("NUCLEOTIDE")) {
+ if (Mode.equals("0")) { // no --clustering-method was provided
+ if (PROTEOME) {
+ System.out.println("\rNo --clustering-method selected. Preparing Maximum Likelihood phylogeny for protein sequences");
+ alignment_phylogeny_mode = "ML,protein";
+ } else { // pangenome
+ System.out.println("\rNo --clustering-method selected. Preparing Maximum Likelihood phylogeny for nucleotide sequences");
+ alignment_phylogeny_mode = "ML,nucleotide";
+ }
+ } else if (CLUSTERING_METHOD.equals("NJ")) {
+ if (Mode.contains("PROTEIN") || PROTEOME) {
+ System.out.println("\rPreparing Neighbor joining phylogeny for protein sequences");
+ alignment_phylogeny_mode = "NJ,protein";
+ } else {
+ System.out.println("\rPreparing Neighbor joining phylogeny for nucleotide sequences");
+ alignment_phylogeny_mode = "NJ,nucleotide";
+ }
+ } else if (CLUSTERING_METHOD.equals("ML") || Mode.contains("PROTEIN") || Mode.contains("NUCLEOTIDE")) {
if (Mode.contains("PROTEIN") || PROTEOME) {
System.out.println("\rPreparing Maximum likelihood phylogeny for protein sequences");
alignment_phylogeny_mode = "ML,protein";
- } else {
+ } else {
System.out.println("\rPreparing Maximum likelihood phylogeny for nucleotide sequences");
alignment_phylogeny_mode = "ML,nucleotide";
}
} else {
- System.out.println("\rThe provided --mode argument is not recognized");
- System.exit(1);
+ System.out.println("\rThe provided --clustering-method argument is not recognized");
+ System.exit(1);
}
-
+
if (alignment_phylogeny_mode.contains("nucleotide")) {
- Mode = "BOTH"; // the initial alignment is done with both the protein and nucleotide sequences.
+ Mode = "BOTH"; // the initial alignment is done with both the protein and nucleotide sequences.
//After the first alignment round, Mode is set to NUCLEOTIDE
} else {
Mode = "PROTEIN";
}
return alignment_phylogeny_mode;
}
-
+
/**
- * @param single_copy_input_file
- * @return
+ * @param single_copy_input_file file location to single-copy homology group identifiers
+ * @param sco_node_list list with 'homology_group' node identifiers
+ * @return
*/
- public static HashMap<String, String> gather_info_for_core_snp_tree_log(String single_copy_input_file) {
+ public static HashMap<String, String> gatherInfoCorePhylogenyLog(String single_copy_input_file,
+ ArrayList<Node> sco_node_list) {
check_if_graphDb_is_available();
SELECTED_HMGROUPS = single_copy_input_file; // SCOs need to be read again because the database was closed
- HashMap<String, String> info_map = new HashMap<>();
+ HashMap<String, String> info_map = new HashMap<>();
try (Transaction tx = graphDb.beginTx()) { // start database transaction
- ArrayList<Node> sco_node_list = retrieve_hmgroups(true); // read the groups from single_copy_orthologs.csv
int counter = 0;
for (Node hm_node : sco_node_list) {
String group_id = hm_node.getId() +"";
- counter ++;
+ counter++;
if (counter % 100 == 0 || counter == sco_node_list.size()) {
System.out.print("\r Retrieving gene information: " + counter + "/" + sco_node_list.size() + " groups");
}
@@ -2984,18 +3083,17 @@ public class Phylogeny {
}
tx.success(); // transaction successful, commit changes
}
- System.out.print("\r ");
- graphDb.shutdown();
+ System.out.print("\r "); // spaces are intentional
return info_map;
}
-
+
/**
- *
+ *
* @param sco_group
- * @return
+ * @return
*/
public static String read_trimmed_info(long sco_group) {
- String input = WORKING_DIRECTORY + "alignments/grouping_v" + grouping_version + "/groups/" + sco_group + "/input/trimmed.info";
+ String input = WORKING_DIRECTORY + "alignments/msa_per_group/grouping_v" + grouping_version + "/" + sco_group + "/input/trimmed.info";
String start_stop = "";
try (BufferedReader in = new BufferedReader(new FileReader(input))) {
while (in.ready()) {
@@ -3017,11 +3115,11 @@ public class Phylogeny {
}
return start_stop;
}
-
+
/**
- *
+ *
* @param genome
- * @return
+ * @return
*/
public static String get_phenotype_with_underscore(int genome) {
String add = "";
@@ -3035,3 +3133,4 @@ public class Phylogeny {
return add;
}
}
+
diff --git a/src/pangenome/ProteomeLayer.java b/src/main/java/nl/wur/bif/pantools/pangenome/ProteomeLayer.java
similarity index 95%
rename from src/pangenome/ProteomeLayer.java
rename to src/main/java/nl/wur/bif/pantools/pangenome/ProteomeLayer.java
index 46de4cc4d52a726a20a90a841dd154f5e70184bd..7907571c2e190e956ed447e1b4b884a6705cadd7 100755
--- a/src/pangenome/ProteomeLayer.java
+++ b/src/main/java/nl/wur/bif/pantools/pangenome/ProteomeLayer.java
@@ -3,9 +3,9 @@
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
-package pangenome;
+package nl.wur.bif.pantools.pangenome;
-import alignment.LocalSequenceAlignment;
+import nl.wur.bif.pantools.alignment.LocalSequenceAlignment;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
@@ -16,7 +16,7 @@ import java.io.PrintWriter;
import java.util.LinkedList;
import java.util.ListIterator;
import java.util.Queue;
-import static pantools.Pantools.delete_file_in_DB;
+import static nl.wur.bif.pantools.pantools.Pantools.delete_file_in_DB;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Arrays;
@@ -39,77 +39,76 @@ import org.neo4j.graphdb.NotFoundException;
import org.neo4j.graphdb.Relationship;
import org.neo4j.graphdb.ResourceIterator;
import org.neo4j.graphdb.Transaction;
-import static pangenome.GenomeLayer.getFolderSize;
-import static pantools.Pantools.GRAPH_DATABASE_PATH;
-import static pantools.Pantools.RelTypes;
-import static pantools.Pantools.MAX_TRANSACTION_SIZE;
-import static pantools.Pantools.WORKING_DIRECTORY;
-import static pantools.Pantools.MIN_NORMALIZED_SIMILARITY;
-import static pantools.Pantools.INTERSECTION_RATE;
-import static pantools.Pantools.CONTRAST;
-import static pantools.Pantools.GAP_EXT;
-import static pantools.Pantools.GAP_OPEN;
-import static pantools.Pantools.MCL_INFLATION;
-import static pantools.Pantools.OUTPUT_PATH;
-import static pantools.Pantools.PATH_TO_THE_PROTEOMES_FILE;
-import static pantools.Pantools.THREADS;
-import static pantools.Pantools.create_panproteome_database;
-import static pantools.Pantools.executeCommand_for;
-import static pantools.Pantools.heapSize;
-import static pantools.Pantools.homology_group_label;
-import static pantools.Pantools.mRNA_label;
-import static pantools.Pantools.gene_label;
-import static pantools.Pantools.pangenome_label;
-import static pantools.Pantools.total_genomes;
-import static pantools.Pantools.skip_list;
+import static nl.wur.bif.pantools.pangenome.GenomeLayer.getFolderSize;
+import static nl.wur.bif.pantools.pantools.Pantools.GRAPH_DATABASE_PATH;
+import static nl.wur.bif.pantools.pantools.Pantools.RelTypes;
+import static nl.wur.bif.pantools.pantools.Pantools.MAX_TRANSACTION_SIZE;
+import static nl.wur.bif.pantools.pantools.Pantools.WORKING_DIRECTORY;
+import static nl.wur.bif.pantools.pantools.Pantools.MIN_NORMALIZED_SIMILARITY;
+import static nl.wur.bif.pantools.pantools.Pantools.INTERSECTION_RATE;
+import static nl.wur.bif.pantools.pantools.Pantools.CONTRAST;
+import static nl.wur.bif.pantools.pantools.Pantools.GAP_EXT;
+import static nl.wur.bif.pantools.pantools.Pantools.GAP_OPEN;
+import static nl.wur.bif.pantools.pantools.Pantools.MCL_INFLATION;
+import static nl.wur.bif.pantools.pantools.Pantools.OUTPUT_PATH;
+import static nl.wur.bif.pantools.pantools.Pantools.PATH_TO_THE_PROTEOMES_FILE;
+import static nl.wur.bif.pantools.pantools.Pantools.THREADS;
+import static nl.wur.bif.pantools.pantools.Pantools.create_panproteome_database;
+import static nl.wur.bif.pantools.pantools.Pantools.executeCommand_for;
+import static nl.wur.bif.pantools.pantools.Pantools.heapSize;
+import static nl.wur.bif.pantools.pantools.Pantools.homology_group_label;
+import static nl.wur.bif.pantools.pantools.Pantools.mRNA_label;
+import static nl.wur.bif.pantools.pantools.Pantools.gene_label;
+import static nl.wur.bif.pantools.pantools.Pantools.pangenome_label;
+import static nl.wur.bif.pantools.pantools.Pantools.total_genomes;
+import static nl.wur.bif.pantools.pantools.Pantools.skip_list;
import org.neo4j.graphdb.Label;
-import static pangenome.Classification.determine_frequency_list_int;
-import static pangenome.Classification.genome_overview;
-import static pangenome.Classification.get_annotation_identifiers;
-import static pangenome.Classification.get_percentage_str;
-import static pangenome.Classification.split_seq_in_parts_of_60bp;
-import static pangenome.Classification.try_incr_AL_hashmap;
-import static pangenome.Classification.try_incr_SB_hashmap;
-import static pangenome.Classification.try_incr_hashmap;
-import static pantools.Pantools.INPUT_FILE;
-import static pantools.Pantools.adj_total_genomes;
-import static pantools.Pantools.annotation_label;
-import static pantools.Pantools.graphDb;
-import static pantools.Pantools.check_if_graphDb_is_available;
+import static nl.wur.bif.pantools.pangenome.Classification.determine_frequency_list_int;
+import static nl.wur.bif.pantools.pangenome.Classification.genome_overview;
+import static nl.wur.bif.pantools.pangenome.Classification.get_annotation_identifiers;
+import static nl.wur.bif.pantools.pangenome.Classification.get_percentage_str;
+import static nl.wur.bif.pantools.pangenome.Classification.split_seq_in_parts_of_80bp;
+import static nl.wur.bif.pantools.pangenome.Classification.try_incr_AL_hashmap;
+import static nl.wur.bif.pantools.pangenome.Classification.try_incr_SB_hashmap;
+import static nl.wur.bif.pantools.pangenome.Classification.try_incr_hashmap;
+import static nl.wur.bif.pantools.pantools.Pantools.INPUT_FILE;
+import static nl.wur.bif.pantools.pantools.Pantools.adj_total_genomes;
+import static nl.wur.bif.pantools.pantools.Pantools.annotation_label;
+import static nl.wur.bif.pantools.pantools.Pantools.graphDb;
+import static nl.wur.bif.pantools.pantools.Pantools.check_if_graphDb_is_available;
-import static pantools.Pantools.create_directory_in_DB;
-import static pantools.Pantools.write_SB_to_file_in_DB;
-import static pantools.Pantools.write_string_to_file_in_DB;
-import static pantools.Pantools.check_if_file_exists;
+import static nl.wur.bif.pantools.pantools.Pantools.create_directory_in_DB;
+import static nl.wur.bif.pantools.pantools.Pantools.write_SB_to_file_in_DB;
+import static nl.wur.bif.pantools.pantools.Pantools.write_string_to_file_in_DB;
+import static nl.wur.bif.pantools.pantools.Pantools.check_if_file_exists;
-import static pantools.Pantools.copy_file;
-import static pangenome.create_skip_arrays.create_skip_arrays;
-import static pantools.Pantools.CDS_label;
-import static pantools.Pantools.FAST;
-import static pantools.Pantools.grouping_version;
+import static nl.wur.bif.pantools.pantools.Pantools.copy_file;
+import static nl.wur.bif.pantools.pangenome.create_skip_arrays.create_skip_arrays;
+import static nl.wur.bif.pantools.pantools.Pantools.CDS_label;
+import static nl.wur.bif.pantools.pantools.Pantools.FAST;
+import static nl.wur.bif.pantools.pantools.Pantools.grouping_version;
-import static pantools.Pantools.count_nodes;
-import static pantools.Pantools.NODE_VALUE;
-import static pantools.Pantools.PROTEOME;
-import static pantools.Pantools.longest_transcripts;
-import static pantools.Pantools.WD_full_path;
-import static pantools.Pantools.check_current_grouping_version;
-import static pantools.Pantools.check_grouping_version;
-import static pantools.Pantools.inactive_homology_group_label;
-import static pantools.Pantools.target_genome;
-import static pantools.Pantools.annotation_identifiers;
-import static pantools.Pantools.check_if_panproteome;
-import static pantools.Pantools.Mode;
-import static pantools.Pantools.append_string_to_file_full_path;
-import static pantools.Pantools.check_if_program_exists_stdout;
-import static pantools.Pantools.delete_file_full_path;
-import static pantools.Pantools.print_runtime;
-import static pantools.Pantools.remove_first_position_array;
-import static pantools.Pantools.report_number_of_threads;
-import static pantools.Pantools.VERSION;
-import static pantools.Pantools.exon_label;
-import static pantools.Pantools.intron_label;
-import static pantools.Pantools.skip_array;
+import static nl.wur.bif.pantools.pantools.Pantools.count_nodes;
+import static nl.wur.bif.pantools.pantools.Pantools.NODE_VALUE;
+import static nl.wur.bif.pantools.pantools.Pantools.PROTEOME;
+import static nl.wur.bif.pantools.pantools.Pantools.longest_transcripts;
+import static nl.wur.bif.pantools.pantools.Pantools.WD_full_path;
+import static nl.wur.bif.pantools.pantools.Pantools.check_current_grouping_version;
+import static nl.wur.bif.pantools.pantools.Pantools.inactive_homology_group_label;
+import static nl.wur.bif.pantools.pantools.Pantools.target_genome;
+import static nl.wur.bif.pantools.pantools.Pantools.annotation_identifiers;
+import static nl.wur.bif.pantools.pantools.Pantools.check_if_panproteome;
+import static nl.wur.bif.pantools.pantools.Pantools.Mode;
+import static nl.wur.bif.pantools.pantools.Pantools.append_string_to_file_full_path;
+import static nl.wur.bif.pantools.pantools.Pantools.check_if_program_exists_stdout;
+import static nl.wur.bif.pantools.pantools.Pantools.delete_file_full_path;
+import static nl.wur.bif.pantools.pantools.Pantools.print_runtime;
+import static nl.wur.bif.pantools.pantools.Pantools.remove_first_position_array;
+import static nl.wur.bif.pantools.pantools.Pantools.report_number_of_threads;
+import static nl.wur.bif.pantools.pantools.Pantools.VERSION;
+import static nl.wur.bif.pantools.pantools.Pantools.exon_label;
+import static nl.wur.bif.pantools.pantools.Pantools.intron_label;
+import static nl.wur.bif.pantools.pantools.Pantools.skip_array;
/**
* Implements all the functionalities related to the proteome layer of the pangenome.
@@ -851,7 +850,7 @@ public class ProteomeLayer {
/**
* Given a homology group complete all the pairwise similarities between its members and
* writes the weighted edges of the graph in SIMILARITY_GRAPH_FILE_NAME to be used by MCL clustering algorithm.
- * @param homology_group_node The homology group
+ * @param component The homology group
* @param pangenome_path The path to the current graph database
*/
private void write_similaity_matrix(LinkedList<Node> component, String pangenome_path) {
@@ -1364,7 +1363,7 @@ public class ProteomeLayer {
update_skip_array_based_on_anno_ids();
tx.success(); // transaction successful, commit changes
} catch (NotFoundException nfe) {
- System.out.println("Unable to start the pangenome database\n");
+ System.out.println("Unable to start the database\n");
System.exit(1);
}
@@ -1735,7 +1734,7 @@ public class ProteomeLayer {
tx.success(); // transaction successful, commit changes
} catch (NotFoundException nfe) {
System.out.println("Unable to start the database\n");
- return;
+ System.exit(1);
}
if (!FAST) { // do not remove 'is_similar' relations. Leaving these does not influence the next grouping
@@ -1748,7 +1747,7 @@ public class ProteomeLayer {
ArrayList<Node> hm_nodes_list;
remove_component_from_mrna_nodes(pangenome_node); // removes 'component' property. These are a remainder from the previous group run
try (Transaction tx = graphDb.beginTx()) { // start database transaction
- grouping_version = check_grouping_version();
+ grouping_version = check_highest_grouping_version();
if (grouping_version == 0) {
grouping_version ++;
}
@@ -1827,8 +1826,8 @@ public class ProteomeLayer {
}
System.out.println("Newest highest grouping is " + grouping_version);
put_grouping_version(false);
- }
- pangenome_node.removeProperty("grouping_v" + original_grouping_version);
+ }
+ pangenome_node.removeProperty("grouping_v" + original_grouping_version + "_skipped_genomes");
break;
}
}
@@ -2062,8 +2061,8 @@ public class ProteomeLayer {
check_if_panproteome(pangenome_node); // sets PROTEOME boolean that controls functions, retrieves 'K_size' & 'total_genomes' variables
tx.success(); // transaction successful, commit changes
} catch (NotFoundException nfe) {
- System.out.println("Unable to start the pangenome database\n");
- return;
+ System.out.println("Unable to start the database\n");
+ System.exit(1);
}
if (VERSION == null) {
System.out.println("No grouping version selected via --version\n");
@@ -2731,8 +2730,8 @@ public class ProteomeLayer {
/**
* Sets 'longest_transcript' property to mRNA, exon, intron and CDS nodes.
*
- * @param count_nodes
- * @param original_number_of_proteins
+ * @param count_nodes count the total number of longest transcripts
+ * @param original_number_of_proteins number of protein
* @return number of proteins, only counting the longest transcripts
*/
public int find_longest_transcript_per_gene(boolean count_nodes, int original_number_of_proteins) {
@@ -2753,17 +2752,17 @@ public class ProteomeLayer {
}
boolean file_exists = check_if_file_exists(WORKING_DIRECTORY + "proteins/longest_transcripts/proteins_" + anno_id + ".fasta");
if (file_exists && !count_nodes) {
- continue;
+ continue; // longest transcripts are already set and counting is not required
}
try (Transaction tx = graphDb.beginTx()) { // start database transaction, commit changes after every genome
String[] anno_id_array = anno_id.split("_");
duplicate_id_builder.append("#Genome ").append(anno_id_array[0]).append("\n");
ResourceIterator<Node> gene_nodes = graphDb.findNodes(gene_label, "annotation_id", anno_id);
- int gene_counter = 0, prot_per_genome = 0, prot_per_genome2 = 0;
+ int gene_counter = 0; // prot_per_genome = 0, prot_per_genome2 = 0;
StringBuilder longest_proteins = new StringBuilder();
while (gene_nodes.hasNext()) {
gene_counter ++;
- if (gene_counter % 100 == 0 || gene_counter == 1) {
+ if (gene_counter % 1000 == 0 || gene_counter == 1) {
System.out.print("\rFinding longest transcript per gene: Genome " + anno_id_array[0] + ", " + gene_counter + " ");
}
Node gene_node = gene_nodes.next();
@@ -2778,7 +2777,7 @@ public class ProteomeLayer {
}
if (first) {
first = false;
- prot_per_genome ++;
+ //prot_per_genome ++;
}
String protein = (String) mrna_node.getProperty("protein_sequence");
if (protein.length() > longest_transcript_length) {
@@ -2826,10 +2825,10 @@ public class ProteomeLayer {
}
protein_counter ++;
- prot_per_genome2 ++;
+ //prot_per_genome2 ++;
String protein_id = (String) longest_transcript_node.getProperty("protein_ID");
String protein_sequence = get_protein_sequence(longest_transcript_node);
- protein_sequence = split_seq_in_parts_of_60bp(protein_sequence);
+ protein_sequence = split_seq_in_parts_of_80bp(protein_sequence);
longest_proteins.append(">").append(protein_id).append("\n").append(protein_sequence).append("\n");
}
}
@@ -2864,7 +2863,19 @@ public class ProteomeLayer {
}
}
}
-
+
+ /**
+ * @return the highest grouping version number
+ */
+ public static int check_highest_grouping_version() {
+ Node pangenome_node = graphDb.findNodes(pangenome_label).next();
+ int highest_grouping = 0;
+ if (pangenome_node.hasProperty("highest_grouping")) {
+ highest_grouping = (int) pangenome_node.getProperty("highest_grouping");
+ }
+ return highest_grouping;
+ }
+
/**
* Groups similar proteins into homology groups.
*/
@@ -2903,7 +2914,7 @@ public class ProteomeLayer {
remove_component_from_mrna_nodes(pangenome_node); // removes 'component' property that is only used for grouping the proteins. These are a remainder from previous runs
try (Transaction tx = graphDb.beginTx()) {
stop_if_hmgroups_exist(); // stop when there are active homology groups
- grouping_version = check_grouping_version();
+ grouping_version = check_highest_grouping_version();
grouping_version ++;
total_genomes = (int) pangenome_node.getProperty("num_genomes");
pangenome_node.removeProperty("last_grouping_successful");
diff --git a/src/pangenome/create_skip_arrays.java b/src/main/java/nl/wur/bif/pantools/pangenome/create_skip_arrays.java
similarity index 94%
rename from src/pangenome/create_skip_arrays.java
rename to src/main/java/nl/wur/bif/pantools/pangenome/create_skip_arrays.java
index 6ac78b3d5e33155d6c0f42353703ffde125e4387..edd618e10d65303c20073c6064d4e685be3ce82d 100644
--- a/src/pangenome/create_skip_arrays.java
+++ b/src/main/java/nl/wur/bif/pantools/pangenome/create_skip_arrays.java
@@ -3,20 +3,20 @@
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
-package pangenome;
-import static pantools.Pantools.skip_list;
-import static pantools.Pantools.skip_seq_list;
-import static pantools.Pantools.skip_array;
-import static pantools.Pantools.skip_seq_array;
-import static pantools.Pantools.total_genomes;
-import static pantools.Pantools.skip_genomes;
-import static pantools.Pantools.target_genome;
-import static pantools.Pantools.adj_total_genomes;
-import static pantools.Pantools.genome_label;
-import static pantools.Pantools.gene_label;
-import static pantools.Pantools.annotation_label;
+package nl.wur.bif.pantools.pangenome;
+import static nl.wur.bif.pantools.pantools.Pantools.skip_list;
+import static nl.wur.bif.pantools.pantools.Pantools.skip_seq_list;
+import static nl.wur.bif.pantools.pantools.Pantools.skip_array;
+import static nl.wur.bif.pantools.pantools.Pantools.skip_seq_array;
+import static nl.wur.bif.pantools.pantools.Pantools.total_genomes;
+import static nl.wur.bif.pantools.pantools.Pantools.skip_genomes;
+import static nl.wur.bif.pantools.pantools.Pantools.target_genome;
+import static nl.wur.bif.pantools.pantools.Pantools.adj_total_genomes;
+import static nl.wur.bif.pantools.pantools.Pantools.genome_label;
+import static nl.wur.bif.pantools.pantools.Pantools.gene_label;
+import static nl.wur.bif.pantools.pantools.Pantools.annotation_label;
import java.util.ArrayList;
-import static pantools.Pantools.graphDb;
+import static nl.wur.bif.pantools.pantools.Pantools.graphDb;
import org.neo4j.graphdb.Node;
import org.neo4j.graphdb.ResourceIterator;
@@ -30,7 +30,7 @@ import org.neo4j.graphdb.ResourceIterable;
import java.util.List;
import java.util.HashSet;
import java.util.HashMap;
-import static pantools.Pantools.PROTEOME;
+import static nl.wur.bif.pantools.pantools.Pantools.PROTEOME;
/**
*
@@ -197,14 +197,14 @@ public class create_skip_arrays {
skip_genomes_based_on_gene_number(line.split("="));
} else if (line.startsWith("#SEQUENCE_MINIMUM_NUMBER_GENES =") && !line.equals("#SEQUENCE_MINIMUM_NUMBER_GENES =")) {
skip_sequences_based_on_gene_number(line.split("="));
- } else if (line.startsWith("#GENOMES_WITH_MCSCANX_ID")) {
+ } else if (line.startsWith("#GENOMES_WITH_MCSCANX_ID =" ) && !line.equals("#GENOMES_WITH_MCSCANX_ID =")) {
skip_genomes_based_on_having_mcscanx_id();
} else if (line.startsWith("#FIRST_X_SEQUENCES =") && !line.equals("#FIRST_X_SEQUENCES =")) {
- System.out.println("working on this :") ;
+ System.out.println("working on this 1:") ;
//skip_genomes_based_on_seq_nr();
System.exit(1);
- } else if (line.startsWith("#LARGEST_X_SEQUENCES =") && !line.equals("LARGEST_X_SEQUENCES =")) {
- System.out.println("working on this :") ;
+ } else if (line.startsWith("#LARGEST_X_SEQUENCES =") && !line.equals("#LARGEST_X_SEQUENCES =")) {
+ System.out.println("working on this 2:") ;
System.exit(1);
} else if (line.startsWith("#SELECT_SEQUENCE_IDENTIFIER =") && !line.equals("#SELECT_SEQUENCE_IDENTIFIER =")) {
select_genomes_sequences_based_on_identifiers(line);
diff --git a/src/pantools/Pantools.java b/src/main/java/nl/wur/bif/pantools/pantools/Pantools.java
similarity index 89%
rename from src/pantools/Pantools.java
rename to src/main/java/nl/wur/bif/pantools/pantools/Pantools.java
index 441b34394cf2458317764bdbb7550833587f4e9f..97da3f604423b6c4990b0696a5baef3e2ef2da58 100644
--- a/src/pantools/Pantools.java
+++ b/src/main/java/nl/wur/bif/pantools/pantools/Pantools.java
@@ -4,14 +4,16 @@
* and open the template in the editor.
*/
-package pantools;
+package nl.wur.bif.pantools.pantools;
-import index.IndexDatabase;
-import index.IndexPointer;
-import index.IndexScanner;
+import nl.wur.bif.pantools.index.IndexDatabase;
+import nl.wur.bif.pantools.index.IndexPointer;
+import nl.wur.bif.pantools.index.IndexScanner;
import java.io.BufferedInputStream;
import java.io.BufferedReader;
import java.io.BufferedWriter;
+
+import nl.wur.bif.pantools.utils.Utils;
import org.apache.commons.io.FileUtils;
import java.io.File;
import java.io.FileInputStream;
@@ -46,23 +48,24 @@ import org.neo4j.graphdb.factory.GraphDatabaseSettings;
import org.neo4j.graphdb.ResourceIterator;
import java.util.ArrayList;
import java.util.NoSuchElementException;
-import pangenome.AnnotationLayer;
-import pangenome.ProteomeLayer;
-import pangenome.GenomeLayer;
-import static pangenome.GenomeLayer.append_fwd;
-import static pangenome.GenomeLayer.append_rev;
-import static pangenome.GenomeLayer.get_outgoing_edge;
-import static pangenome.GenomeLayer.locate;
-import sequence.SequenceDatabase;
-import sequence.SequenceScanner;
-
-import pangenome.Classification;
-import pangenome.FunctionalAnnotations;
+import nl.wur.bif.pantools.pangenome.AnnotationLayer;
+import nl.wur.bif.pantools.pangenome.ProteomeLayer;
+import nl.wur.bif.pantools.pangenome.GenomeLayer;
+import nl.wur.bif.pantools.pangenome.MultipleSequenceAlignment;
+import static nl.wur.bif.pantools.pangenome.GenomeLayer.append_fwd;
+import static nl.wur.bif.pantools.pangenome.GenomeLayer.append_rev;
+import static nl.wur.bif.pantools.pangenome.GenomeLayer.get_outgoing_edge;
+import static nl.wur.bif.pantools.pangenome.GenomeLayer.locate;
+import nl.wur.bif.pantools.sequence.SequenceDatabase;
+import nl.wur.bif.pantools.sequence.SequenceScanner;
+
+import nl.wur.bif.pantools.pangenome.Classification;
+import nl.wur.bif.pantools.pangenome.FunctionalAnnotations;
import org.apache.commons.lang3.StringUtils;
import org.neo4j.graphdb.NotFoundException;
import static org.neo4j.graphdb.factory.GraphDatabaseSettings.keep_logical_logs;
-import pangenome.Phylogeny;
-import pangenome.ExecCommand;
+import nl.wur.bif.pantools.pangenome.Phylogeny;
+import nl.wur.bif.pantools.pangenome.ExecCommand;
/**
* Implements the main function and some shared variables and methods.
@@ -92,7 +95,6 @@ public class Pantools {
public static String RAW_ABUNDANCE_FILE = "";
public static String PATH_TO_THE_FIRST_SRA;
public static String PATH_TO_THE_SECOND_SRA;
- public static String FEATURE = "gene";
public static String SELECTED_FUNCTION = "none";
public static boolean CONNECT_ANNOTATIONS = false;
@@ -145,7 +147,7 @@ public class Pantools {
public static Label annotation_label = Label.label("annotation");
public static Label homology_group_label = Label.label("homology_group");
- public static Label variation_label = Label.label("variation"); // this label is not used?!
+// public static Label variation_label = Label.label("variation"); // this label is not used?!
public static Label feature_label = Label.label("feature");
// all annotation features that come from a gff have the feature label: gene, coding_gene, mRNA, tRNA, rRNA, CDS, exon, intron
public static Label gene_label = Label.label("gene");
@@ -165,13 +167,13 @@ public class Pantools {
public static Label pfam_label = Label.label("pfam");
public static Label tigrfam_label = Label.label("tigrfam");
public static Label inactive_homology_group_label = Label.label("inactive_homology_group");
- public static Label low_complexity_label = Label.label("low_complexity");
+// public static Label low_complexity_label = Label.label("low_complexity");
public static Label busco_label = Label.label("busco");
public static Label phobius_label = Label.label("phobius"); // always on top of 'mRNA' node
public static Label COG_label = Label.label("COG"); // always on top of 'mRNA' node
public static Label signalp_label = Label.label("signalp"); // always on top of 'mRNA' node
public static Label repeat_label = Label.label("repeat");
- public static Label synteny_label = Label.label("synteny");
+// public static Label synteny_label = Label.label("synteny");
public static String PATH_TO_THE_PANGENOME_DATABASE;
public static int total_genomes = 0; // number of genomes in pangenome
@@ -203,13 +205,18 @@ public class Pantools {
public static boolean compare_sequences = false;
public static boolean compare_genomes = false;
public static String SELECTED_LABEL;
- public static String NODE_PROPERTY;
+// public static String NODE_PROPERTY;
public static String NODE_VALUE;
public static String SELECTED_HMGROUPS;
public static String INPUT_FILE;
public static int grouping_version = -1;
public static String VERSION;
public static boolean FAST;
+ public static String CLUSTERING_METHOD = "ML";
+ public static boolean ALLOW_POLYTOMIES = false;
+ public static boolean VARIANTS = false;
+ public static boolean TRIMMING = true;
+ public static String msaMethod = "per_group";
public static int BLOSUM = 62;
public static HashMap<String, Integer> phenotype_threshold_map;
@@ -256,7 +263,7 @@ public class Pantools {
public static int num_degenerates;
public static long num_edges;
public static long num_bases;
- public static Node db_node;
+// public static Node db_node;
private static String[] label_strings;
public static Map<String,Label> labels;
@@ -266,7 +273,7 @@ public class Pantools {
public static Classification classification;
public static Phylogeny phylogeny;
public static FunctionalAnnotations functionalAnnotations;
- private static final String PANTOOLS_VERSION = "3.2";
+ private static String PANTOOLS_VERSION;
/**
* The main function of PanTools.
@@ -278,6 +285,7 @@ public class Pantools {
double y;
File theDir;
startTime = System.currentTimeMillis();
+ PANTOOLS_VERSION = Utils.getVersionInformation();
if (args.length < 1) {
print_help_message("global");
System.exit(1);
@@ -304,14 +312,14 @@ public class Pantools {
annLayer = new AnnotationLayer();
proLayer = new ProteomeLayer();
labels = new HashMap<>();
-
+
label_strings = new String[]{"pangenome", "genome", "sequence", "nucleotide", "degenerate", "annotation", "variation", "gene", "coding_gene",
"mRNA", "tRNA", "rRNA", "CDS", "exon", "intron", "feature", "broken_protein", "homology_group", "low_complexity"};
for (i = 0; i < label_strings.length; ++i) {
labels.put(label_strings[i], Label.label(label_strings[i]));
}
System.out.println("\n------------------------------- PanTools " + PANTOOLS_VERSION + " ------------------------------");
- pantools_path = Pantools.class.getProtectionDomain().getCodeSource().getLocation().getPath().replace("dist/pantools.jar", ""); // retrieve location of jar
+ find_pantools_path();
StringBuilder command = new StringBuilder();
int loop_counter = 0; // to prevent an endless loop
Path currentRelativePath = Paths.get("");
@@ -514,16 +522,6 @@ public class Pantools {
}
System.out.println("GAP_EXT = " + GAP_EXT);
break;
- case "--feature-type": case "-ft":
- if (labels.containsKey(args[i + 1])) {
- FEATURE = args[i + 1];
- i += 2;
- } else {
- System.out.println(args[i + 1] + " is not a unknown feature.");
- System.exit(1);
- }
- System.out.println("FEATURE = " + FEATURE);
- break;
case "--first-sra": case "-1":
PATH_TO_THE_FIRST_SRA = args[i + 1];
i += 2;
@@ -738,10 +736,10 @@ public class Pantools {
}
i += 2;
break;
- case "--property": case "-property":
- NODE_PROPERTY = args[i + 1];
- i += 2;
- break;
+// case "--property": case "-property":
+// NODE_PROPERTY = args[i + 1];
+// i += 2;
+// break;
case "--value": case "-value":
NODE_VALUE = args[i + 1];
i += 2;
@@ -749,6 +747,7 @@ public class Pantools {
case "--label":
SELECTED_LABEL = args[i + 1];
i += 2;
+ System.out.println("LABEL = " + SELECTED_LABEL);
break;
case "--node":
NODE_ID = args[i + 1];
@@ -770,6 +769,40 @@ public class Pantools {
System.out.println("MODE = " + Mode);
i += 2;
break;
+ case "--clustering-method":
+ CLUSTERING_METHOD = args[i + 1];
+ if (!(CLUSTERING_METHOD.equals("NJ") || CLUSTERING_METHOD.equals("ML"))) {
+ System.out.println("\n'--clustering-method' must be either NJ or ML");
+ System.exit(1);
+ }
+ i += 2;
+ break;
+ case "--allow-polytomies":
+ ALLOW_POLYTOMIES = true;
+ i += 1;
+ break;
+ case "--variants":
+ VARIANTS = true;
+ i += 1;
+ break;
+ case "--no-trimming":
+ TRIMMING = false; //used for MSA, will align sequences only once
+ i += 1;
+ break;
+ case "--method":
+ msaMethod = args[i + 1];
+ if (!(
+ msaMethod.equals("per_group") ||
+ msaMethod.equals("multiple_groups") ||
+ msaMethod.equals("regions") ||
+ msaMethod.equals("functions")
+ )) {
+ System.out.println("Invalid --method: " + msaMethod);
+ System.out.println("Please use either 'per_group', 'multiple_groups', 'regions' or 'functions'");
+ System.exit(1);
+ }
+ i += 2;
+ break;
case "--core-threshold": case "-ct":
core_threshold = Integer.parseInt(args[i + 1]);
if (core_threshold < 0 || core_threshold > 100) {
@@ -846,13 +879,15 @@ public class Pantools {
BLOSUM = Integer.parseInt(args[i + 1]);
} catch (NumberFormatException nfe) {
System.out.println("The value included with --blosum is not a number");
+ System.exit(1);
}
i += 2;
break;
case "--help": case "-h":
print_help_message(args[0]);
- System.exit(1);
+ System.exit(0);
break;
+
}
if (loop_counter > 50) {
@@ -900,15 +935,14 @@ public class Pantools {
case "locate_genes":
classification.locate_genes();
break;
- case "msa_of_group": case "msa_of_groups":
- if (Mode.contains("NO-TRIMMING")) {
- classification.msa_of_group_no_trimming();
- } else {
- classification.msa_of_group(true, false, false);
- }
- break;
- case "msa_of_multiple_groups":
- classification.msa_of_multiple_groups();
+ case "msa":
+ MultipleSequenceAlignment msa = new MultipleSequenceAlignment(
+ msaMethod,
+ VARIANTS,
+ true,
+ true
+ );
+ msa.alignSequences(true, true);
break;
case "metrics":
classification.metrics();
@@ -919,9 +953,6 @@ public class Pantools {
case "core_unique_thresholds":
classification.core_unique_thresholds();
break;
- case "msa_of_regions":
- classification.msa_of_regions();
- break;
case "order_matrix":
classification.order_matrix(true);
break;
@@ -939,7 +970,7 @@ public class Pantools {
break;
//Phylogeny related functions
- case "core_snp_tree": case "core_snp_phylogeny":
+ case "core_snp_tree": case "core_snp_phylogeny": case "core_phylogeny":
phylogeny.core_snp_tree();
break;
case "rename_phylogeny":
@@ -981,8 +1012,8 @@ public class Pantools {
case "compare_go":
functionalAnnotations.compare_go();
break;
- case "add_antismash_results": case "add_gene_clusters":
- functionalAnnotations.add_antismash_results();
+ case "add_antismash":
+ functionalAnnotations.add_antismash();
break;
case "add_functional_annotations": case "add_functions":
functionalAnnotations.add_functional_annotations();
@@ -1023,7 +1054,7 @@ public class Pantools {
proLayer.remove_grouping();
break;
case "rf": case "retrieve_features":
- annLayer.retrieve_feature();
+ annLayer.retrieve_features();
break;
case "rr": case "retrieve_regions":
seqLayer.retrieve_regions();
@@ -1064,7 +1095,7 @@ public class Pantools {
public static void print_pantools_version() {
System.out.println("PanTools version " + PANTOOLS_VERSION + "\n"
- + "Neo4j community edition 3.5.3\n"
+ + "Neo4j community edition 3.5.30\n"
+ "JDK 1.8, You are using Java " + System.getProperty("java.version") +"\n");
}
@@ -1416,15 +1447,16 @@ public class Pantools {
"\n" +
" Construction of a pangenome\n" +
" build_pangenome : Build a pangenome out of a set of genomes.\n" +
- " add_genomes : Add new genomes to an available pangenome.\n" +
+ " add_genomes : Add new genomes to a pangenome.\n" +
"\n" +
" Construction of a panproteome.\n" +
" build_panproteome : Build a panproteome out of a set of proteins.\n" +
"\n" +
" Adding annotation features to the genomes\n" +
" add_annotations : Add annotations to a pangenome.\n" +
- " add_functions : Add functional annotations to existing genomes.\n" +
- " add_phenotype : Add phenotypes to the pangenomes.\n" +
+ " add_functions : Add functional annotations to a pangenome.\n" +
+ " add_antismash : Add antiSMASH gene clusters to a pangenome.\n" +
+ " add_phenotype : Add phenotype information to a pangenome.\n" +
" busco_protein : Identify BUSCO genes in the pangenome.\n" +
"\n" +
" Removing data from a pangenome or panproteome\n" +
@@ -1439,10 +1471,9 @@ public class Pantools {
" move_grouping : Inactivate the current homology grouping.\n" +
" change_grouping : Activate one of inactive homology groupings.\n" +
"\n" +
- " Retrieving features/regions/genomes\n" +
- " retrieve_features : Retrieve the sequence of annotated features from the pangenome.\n" +
- " retrieve_regions : Retrieve the sequence of some genomic regios from the pangenome.\n" +
- " retrieve_genomes : Retrieve the full sequence of some genomes.\n" +
+ " Retrieving genomic regions, complete genomes or annotated features, \n" +
+ " retrieve_features : Retrieve sequences of annotated (GFF) features from the pangenome.\n" +
+ " retrieve_regions : Retrieve the full genome sequence or genomic regions from the pangenome.\n" +
"\n" +
" Read mappping\n" +
" map : Map single or paired-end short reads to all or a sebset of the constituent genomes.\n" +
@@ -1467,10 +1498,8 @@ public class Pantools {
" function_overview : Create an overview table for each functional annotation type in the pangenome.\n" +
" go_enrichment : Identify over or underrepresented GO terms in a set of genes.\n" +
"\n" +
- " Alignment functions\n" +
- " msa_of_group : Align the protein and nucleotide sequences of homology groups.\n" +
- " msa_of_multiple_groups : Use sequences from multiple homology groups for a single alignment.\n" +
- " msa_of_regions : Align a selection of genomic regions.\n" +
+ " Alignment functions\n" +
+ " msa : Align multiple protein and/or nucleotide sequences.\n" +
"\n" +
" Find genes\n" +
" find_genes_by_name : Find genes matching a gene name.\n" +
@@ -1479,7 +1508,7 @@ public class Pantools {
"\n" +
" Phylogeny\n" +
" Phylogenetic methods\n" +
- " core_snp_tree : Create a SNP tree from single-copy genes.\n" +
+ " core_phylogeny : Create a SNP tree from single-copy genes.\n" +
" consensus_tree : Create a consensus tree from gene trees.\n" +
" ani : Create an ANI distance tree.\n" +
" mlsa_find_genes : Step 1/3 of MLSA. Search and filter suitable genes for the MLSA.\n" +
@@ -1522,7 +1551,7 @@ public class Pantools {
"\n" +
" --database-path or -dp: Path to the pangenome database.\n" +
"\n" +
- " --genomes-file or -gf : A text file containing paths to FASTA files of genomes; each in a seperated line.\n" +
+ " --genomes-file or -gf : A text file containing paths to FASTA files of genomes; each in a separated line.\n" +
"\n" +
"Optional arguments:\n" +
"\n" +
@@ -1542,7 +1571,7 @@ public class Pantools {
"\n" +
" --database-path or -dp : Path to the pangenome database.\n" +
"\n" +
- " --proteomes-file or -pf: A text file containing paths to FASTA files of proteomes; each in a seperated line.\n" +
+ " --proteomes-file or -pf: A text file containing paths to FASTA files of proteomes; each in a separated line.\n" +
"\n" +
"Example --proteomes-file input file:\n" +
"/always/genome1.fasta\n" +
@@ -1558,7 +1587,7 @@ public class Pantools {
" --database-path or -dp: Path to the pangenome database.\n" +
"\n" +
" --genomes-file or -gf : A text file containing paths to FASTA files of the new genomes to be added to the pangeome, " +
- "each on a seperate line.\n" +
+ "each on a separate line.\n" +
"\n" +
"Example --genomes-file input file:\n" +
"/always/genome4.fasta\n" +
@@ -1598,7 +1627,7 @@ public class Pantools {
"\n" +
" --reference: or -ref : Only include a selection of genomes.\n" +
"\n" +
- " --annotations-file or -af : A text file with the identifiers of annotations to be included, each on a seperate line.\n" +
+ " --annotations-file or -af : A text file with the identifiers of annotations to be included, each on a separate line.\n" +
" The most recent annotation is selected for genomes without an identifier.\n" +
"\n" +
"Optional arguments that influence the clustering sensivity:\n" +
@@ -1616,28 +1645,30 @@ public class Pantools {
" --contrast or -ct : The contrast factor (default value: 8, valid range: (0..10)).\n");
break;
case "rf": case "retrieve_features":
- System.out.println("retrieve_features or rf : To retrieve the sequence of annotated features from the pangenome.\n" +
+ System.out.println("retrieve_features : Retrieve sequences of annotated (GFF) features from the pangenome.\n" +
"\n" +
"Required arguments:\n" +
"\n" +
" --database-path or -dp : Path to the pangenome database.\n" +
"\n" +
- " --genome-numbers or -gn: A text file containing genome_numbers for which the features will be retrieved.\n" +
- "\n" +
- " --feature-type or -ft : The feature name; for example gene, mRNA, exon, tRNA, etc. (default value: gene).\n" +
+ " --label : The GFF feature name; for example gene, mRNA, exon, tRNA, etc. \n" +
"\n" +
- "Optional argument:\n" +
+ "Requires one of the following arguments:\n" +
+ "\n" +
+ " --genome-numbers or -gn: A text file containing genome_numbers for which the features will be retrieved.\n" +
+ "\n" +
+ " --skip or -sk : Exclude a selection of genomes.\n" +
"\n" +
- " --output-path or -op : Path to the output files (default value: Database path determined by -dp).\n");
+ " --reference: or -ref : Only include a selection of genomes.\n");
break;
case "rr": case "retrieve_regions":
- System.out.println("retrieve_regions or rr : To retrieve the sequence of some genomic regios from the pangenome.\n" +
+ System.out.println("retrieve_regions or rr : Retrieve the full genome sequence or genomic regions from the pangenome.\n" +
"Required arguments:\n" +
"\n" +
" --database-path or -dp: Path to the pangenome database.\n" +
"\n" +
" --regions-file or -rf : A text file containing records with genome_number, sequence_number, " +
- "begin and end positions seperated by one space for each region.\n" +
+ "begin and end positions separated by one space for each region.\n" +
" Place a minus symbol behind a region to extract the reverse complement sequence.\n" +
"\n" +
"Optional argument:\n" +
@@ -1645,23 +1676,21 @@ public class Pantools {
" --output-path or -op : Path to the output files (default value: Database path determined by -dp).\n" +
"\n" +
"Example --regions-file input file:\n" +
+ "1\n" +
+ "1 1\n" +
"1 1 1 10000\n" +
- "195 1 477722 478426\n" +
- "71 10 17346 18056 -\n" +
- "138 47 159593 160300 -\n");
+ "1 1 1000 1500 -\n" +
+ "2\n" +
+ "138 47 159593 160300 -\n" +
+ "195 1 477722 478426\n");
break;
case "rg": case "retrieve_genomes":
System.out.println("retrieve_genomes or rg : To retrieve the full sequence of some genomes.\n" +
- "\n" +
- "Required arguments:\n" +
- "\n" +
- " --database-path or -dp : Path to the pangenome database.\n" +
- "\n" +
- " --genome-numbers or -gn: A text file containing genome numbers to be retrieved in each line.\n" +
- "\n" +
- "Optional argument:\n" +
- "\n" +
- " --output-path or -op : Path to the output files (default value: Database path determined by -dp).\n");
+ "\n" +
+ "As of PanTools version 3.3, this functionality is integrated into 'retrieve_regions'.\n" +
+ "\n" +
+ "Check the manual on how to run:\n\n" +
+ " pantools retrieve_regions --help\n");
break;
case "m": case "map":
System.out.println("map or m : To map single or paired-end short reads to all or a sebset of the constituent genomes.\n" +
@@ -1843,7 +1872,7 @@ public class Pantools {
"\n" +
" --database-path or -dp : Path to the database.\n" +
"\n" +
- " --homology-groups or -hm : A text file with homology group node identifiers, seperated by a comma.\n" +
+ " --homology-groups or -hm : A text file with homology group node identifiers, separated by a comma.\n" +
"\n" +
"Optional arguments:\n" +
"\n" +
@@ -1851,7 +1880,7 @@ public class Pantools {
" Option 1, name of function identifier from GO, PFAM, InterPro or TIGRAM (example GO:1990620).\n" +
" Option 2, 'signal_peptide' or 'transmembrane' for Phobius and SignalP annotations.\n" +
"\n" +
- " --name : One or multiple gene names, seperated by a comma.\n" +
+ " --name : One or multiple gene names, separated by a comma.\n" +
"\n" +
" --skip or -sk : Exclude a selection of genomes.\n" +
"\n" +
@@ -1919,7 +1948,7 @@ public class Pantools {
"\n" +
" --database-path or -dp : Path to the database.\n" +
"\n" +
- " --homology-groups -hm : A text file with homology group node identifiers, seperated by a comma.\n" +
+ " --homology-groups -hm : A text file with homology group node identifiers, separated by a comma.\n" +
"\n" +
"Optional arguments:\n" +
"\n" +
@@ -1939,58 +1968,61 @@ public class Pantools {
"\n" +
" --mode ignore-copies : Duplicated and co-localized genes no longer break up clusters.\n");
break;
- case "msa_of_group": case "msa_of_groups":
- System.out.println("msa_of_group : Multiple sequence alignments of one or multiple homology groups.\n" +
- "\n" +
- "Required software: MAFFT, FastTree.\n" +
- "Required arguments:\n" +
- "\n" +
- " --database-path or -dp : Path to the database.\n" +
- "\n" +
- "Optional arguments:\n" +
- "\n" +
- " --homology-groups or -hm : Text file with homology group node identifiers (default is all groups).\n" +
- "\n" +
- " --phenotype or -ph : A phenotype name, used to identify phenotype specific SNPs/substitutions.\n" +
- "\n" +
- " --phenotype-threshold or -pt: Threshold for phenotype specific SNPs. "
- + "Default is 100% of the sequences with the phenotype present in an homology group.\n" +
- "\n" +
- " --skip or -sk : Exclude a selection of genomes. " +
- "The alignment is still made with all sequences in the homology group and this only effects the SNPs/substitutions counting.\n" +
- "\n" +
- " --reference or -ref : Only include a selection of genomes. " +
- "The alignment is still made with all sequences in the homology group and this only effects the SNPs/substitutions counting.\n" +
- "\n" +
- " --threads or -tn : The number of parallel working threads for MAFFT (default is 1).\n" +
- "\n" +
- " --mode nucleotide or protein: Choose to only align nucleotide or protein sequences (default is both).\n" +
- "\n" +
- " --mode no-trimming : Align the sequences only once.\n");
- break;
- case "msa_of_multiple_groups":
- System.out.println("msa_of_multiple_groups : Use sequences from multiple homology groups for a single alignment\n" +
- "\n" +
- "Required software: MAFFT, FastTree\n" +
- "Required arguments:\n" +
- "\n" +
- " --database-path or -dp : Path to the database.\n" +
- "\n" +
- " --homology-groups or -hm : Text file with homology group node identifiers.\n" +
- "\n" +
- "Optional arguments:\n" +
- "\n" +
- " --phenotype or -ph : A phenotype name, used to identify phenotype specific SNPs/substitutions.\n" +
- "\n" +
- " --skip or -sk : Exclude a selection of genomes.\n" +
- "\n" +
- " --reference or -ref : Only include a selection of genomes.\n" +
- "\n" +
- " --phenotype-threshold or -pt: Threshold for phenotype specific SNPs. Default is 100% of the sequences with the phenotype.\n" +
- "\n" +
- " --mode nucleotide or protein: Choose to only align nucleotide or protein sequences (default is both).\n" +
- "\n" +
- " --threads or -tn : The number of parallel working threads for MAFFT (default is 1).\n");
+ case "msa":
+ System.out.println("msa : Create multiple sequence alignments.\n" +
+ "\n" +
+ "Required software: MAFFT, FastTree.\n" +
+ "\n" +
+ "Required arguments:\n" +
+ "\n" +
+ " --database-path or -dp : Path to the database.\n" +
+ "\n" +
+ "Optional arguments:\n" +
+ "\n" +
+ " --method : Method for aligning sequences. Can be either:\n" +
+ " per_group : Align sequences per homology group (default)\n" +
+ " multiple_groups : Align sequences of multiple homology groups\n" +
+ " regions : Align sequences per region\n" +
+ " functions : Align sequences per functional annotation\n" +
+ "\n" +
+ " --homology-groups or -hm : Text file with homology group node identifiers.\n" +
+ " Can be used for '--method per_group' and '--method multiple_groups'.\n" +
+ " Default is all active homology groups.\n" +
+ "\n" +
+ " --blosum : BLOSUM matrix number to use for alignment and calculating informative positions\n" +
+ " Default is 62, but 45 and 80 are possible as well.\n" +
+ "\n" +
+ " --phenotype or -ph : A phenotype name, used to identify phenotype specific SNPs/substitutions.\n" +
+ "\n" +
+ " --phenotype-threshold or -pt: Threshold for phenotype specific SNPs.\n" +
+ " Default is 100% of the sequences with the phenotype present in an homology group.\n" +
+ "\n" +
+ " --skip or -sk : Exclude a selection of genomes for the alignment.\n" +
+ " Does not affect '--method regions'.\n" +
+ "\n" +
+ " --reference or -ref : Only include a selection of genomes for the alignment.\n" +
+ " Does not affect '--method regions'.\n" +
+ "\n" +
+ " --threads or -tn : The number of parallel working threads (default is 1).\n" +
+ "\n" +
+ " --mode nucleotide or protein: Choose to only align nucleotide or protein sequences (default is both if applicable).\n" +
+ "\n" +
+ " --no-trimming : Align the sequences only once (and thus don't perform trimming).\n" +
+ "\n" +
+ " --name : One or multiple function identifiers (GO, InterPro, PFAM, TIGRFAM), separated by a comma.\n" +
+ " ONLY used with '--method functions'.\n" +
+ "\n" +
+ " --regions-file or -rf : A text file containing genome locations.\n" +
+ " ONLY used with '--method regions'.\n" +
+ " Each line should contain: a genome number, sequence number, begin and end positions separated by one space.\n" +
+ " Place a minus symbol behind a region to extract the reverse complement sequence." +
+ "\n" +
+ "\n" +
+ "Example --regions-file input file:\n" +
+ "1 1 1 10000\n" +
+ "195 1 477722 478426\n" +
+ "71 10 17346 18056 -\n" +
+ "138 47 159593 160300 -\n");
break;
case "move_grouping":
System.out.println("move_grouping : Inactivate the currently active homology grouping\n" +
@@ -2012,30 +2044,6 @@ public class Pantools {
"\n" +
" --reference or -ref : Only include a selection of genomes. This automatically lowers the threshold for core genes.\n");
break;
- case "msa_of_regions":
- System.out.println("msa_of_regions : Align a selection of genomic regions\n" +
- "\n" +
- "Required software: MAFFT, FastTree\n" +
- "Required arguments:\n" +
- "\n" +
- "--regions-file or -rf : A text file containing genome locations with on each line:" +
- " a genome number, sequence number, begin and end positions separated by one space.\n" +
- " Place a minus symbol behind a region to extract the reverse complement sequence." +
- "\n" +
- "Optional arguments:\n" +
- "\n" +
- " --phenotype or -ph : A phenotype name, used to identify phenotype specific SNPs/substitutions.\n" +
- "\n" +
- " --phenotype-threshold or -pt : Threshold for phenotype specific SNPs. Default is 100% of the sequences with the phenoptype.\n" +
- "\n" +
- " --threads or -tn : The number of parallel working threads for MAFFT (default is 1).\n" +
- "\n" +
- "Example --regions-file input file:\n" +
- "1 1 1 10000\n" +
- "195 1 477722 478426\n" +
- "71 10 17346 18056 -\n" +
- "138 47 159593 160300 -\n");
- break;
case "order_matrix":
System.out.println("order matrix : Order the values of a matrix file created by PanTools\n" +
"\n" +
@@ -2096,7 +2104,7 @@ public class Pantools {
"\n" +
" --longest-transcript or -lt: Only search against the longest protein-coding transcript of genes.\n" +
"\n" +
- " --annotations-file or -af : A text file with the identifiers of annotations to be included, each on a seperate line.\n" +
+ " --annotations-file or -af : A text file with the identifiers of annotations to be included, each on a separate line.\n" +
" The most recent annotation is selected for genomes without an identifier.\n");
break;
case "find_genes_in_region": case "find_genes_in_regions":
@@ -2128,12 +2136,12 @@ public class Pantools {
"\n" +
"Requires either one of the following arguments:\n" +
"\n" +
- " --node : One or multiple identifiers of function nodes (GO, InterPro, PFAM, TIGRFAM), seperated by a comma.\n" +
+ " --node : One or multiple identifiers of function nodes (GO, InterPro, PFAM, TIGRFAM), separated by a comma.\n" +
"\n" +
- " --name : One or multiple function identifiers (GO, InterPro, PFAM, TIGRFAM), seperated by a comma.\n");
+ " --name : One or multiple function identifiers (GO, InterPro, PFAM, TIGRFAM), separated by a comma.\n");
break;
- case "core_snp_tree":
- System.out.println("core_snp_tree : Create a SNP tree from single-copy genes\n" +
+ case "core_snp_tree": case "core_phylogeny":
+ System.out.println("core_phylogeny : Infer a core phylogeny on SNPs or amino acid substitutions from single-copy groups\n" +
"\n" +
"Required software: MAFFT, IQ-tree (Only required for Maximum-Likelihood).\n" +
"Required arguments:\n" +
@@ -2142,7 +2150,7 @@ public class Pantools {
"\n" +
"Optional arguments:\n" +
"\n" +
- " --mode ML or NJ : Neighbour joining or Maximum likelihood (default).\n" +
+ " --clustering-method ML or NJ: Neighbour joining or Maximum likelihood (default).\n" +
"\n" +
" --mode nucleotide or protein: Infer the tree on informative positions in nucleotide or protein alignments.\n" +
"\n" +
@@ -2161,7 +2169,7 @@ public class Pantools {
"\n" +
" --database-path or -dp : Path to the database.\n" +
"\n" +
- " --input-file or -if : A phylogenetic tree in newick format.\n" +
+ " --input-file or -if : A phylogenetic tree in newick or nexus format.\n" +
"\n" +
"Optional arguments:\n" +
"\n" +
@@ -2221,7 +2229,7 @@ public class Pantools {
"\n" +
" --database-path or -dp: Path to the database.\n" +
"\n" +
- " --name : One or multiple gene names, seperated by a comma.\n" +
+ " --name : One or multiple gene names, separated by a comma.\n" +
"\n" +
"Optional arguments:\n" +
"\n" +
@@ -2239,7 +2247,7 @@ public class Pantools {
"\n" +
" --database-path or -dp: Path to the database.\n" +
"\n" +
- " --name : One or multiple names of genes to be included in the concatenated sequence, seperated by a comma.\n" +
+ " --name : One or multiple names of genes to be included in the concatenated sequence, separated by a comma.\n" +
"\n" +
"Optional arguments:\n" +
"\n" +
@@ -2264,9 +2272,14 @@ public class Pantools {
" --threads or tn : Number of threads (default is 1).\n");
break;
case "consensus_tree":
- System.out.println("Build a consensus tree for all genomes in the pangenome (or proteomes in panproteome) using ASTRAL-Pro\n"
- + "(https://github.com/chaoszhang/ASTER at commit 2c1c469 is used for this, but NOT needed as required software "
- + "since it is already installed)\n"
+ System.out.println("\nBuilding phylogeny using user-specified groups\n"
+ + "Using ASTRAL-PRO (https://github.com/chaoszhang/ASTER at commit 2c1c469) for this.\n"
+ + "Please cite the original authors:\n"
+ + "Chao Zhang, Celine Scornavacca, Erin K Molloy, Siavash Mirarab, ASTRAL-Pro: Quartet-Based Species-\n"
+ + "Tree Inference despite Paralogy, Molecular Biology and Evolution, Volume 37, Issue 11, November 2020, \n"
+ + "Pages 3292–3307, https://doi.org/10.1093/molbev/msaa139\n\n"
+ + "Please make sure the following file is executable: " + pantools_path + "ASTER/astral-pro\n"
+ + "One can compile this file by running: `cd " + pantools_path + "ASTER && g++ -std=gnu++11 -march=native -Ofast -pthread astral.cpp -o astral && g++ -std=gnu++11 -march=native -Ofast -pthread astral-pro.cpp -o astral-pro`\n"
+ "\n"
+ "Required software: MAFFT FastTree (ASTRAL-Pro).\n"
+ "\n"
@@ -2278,16 +2291,19 @@ public class Pantools {
+ "\n"
+ "Optional arguments:\n"
+ "\n"
- // skip currently does not work for the consensus tree
- //+ " --skip or -sk : Exclude a selection of genomes. "
- //+ "The alignment is still made with all sequences in the homology group and this only effects the SNPs/substitutions counting.\n"
- //+ "\n"
- //+ " --reference or -ref : Only include a selection of genomes. "
- //+ "The alignment is still made with all sequences in the homology group and this only effects the SNPs/substitutions counting.\n"
- //+ "\n"
- + " --threads or -tn : The number of parallel working threads for MAFFT (default is 1).\n");
- // + "\n"
- // + " --mode nucleotide or --mode protein : Choose to only align nucleotide or protein sequences (default is both).\n");
+ + " --skip or -sk : Exclude a selection of genomes. "
+ + "The alignment is still made with all sequences in the homology group and this only effects the SNPs/substitutions counting.\n"
+ + "\n"
+ + " --reference or -ref : Only include a selection of genomes. "
+ + "The alignment is still made with all sequences in the homology group and this only effects the SNPs/substitutions counting.\n"
+ + "\n"
+ + " --threads or -tn : The number of parallel working threads for MAFFT (default is 1).\n"
+ + "\n"
+ + " --no-trimming : Whether or not to perform trimming.\n"
+ + "\n"
+ + " --allow-polytomies : Allow polytomies in data for ASTRAL-PRO (not advised)\n"
+ + "\n"
+ + " --mode nucleotide or --mode protein : Choose to use aligned nucleotide or protein sequences (default is protein).\n");
break;
case "show_go":
System.out.println("show_go : For a given GO term, show the child terms, all parent terms higher in the hierarchy, and connected mRNA nodes\n" +
@@ -2298,9 +2314,9 @@ public class Pantools {
"\n" +
"Requires either one of the following arguments:\n" +
"\n" +
- " --node : One or multiple identifiers of GO nodes, seperated by a comma.\n" +
+ " --node : One or multiple identifiers of GO nodes, separated by a comma.\n" +
"\n" +
- " --name : One or multiple GO term identifiers, seperated by a comma.\n");
+ " --name : One or multiple GO term identifiers, separated by a comma.\n");
break;
case "compare_go":
System.out.println("compare_go : For two given GO terms, move up in the GO hierarchy to see if they are related.\n" +
@@ -2311,22 +2327,23 @@ public class Pantools {
"\n" +
"Requires either one of the following arguments:\n" +
"\n" +
- " --node : Two node identifiers of 'GO' nodes, seperated by a comma.\n" +
+ " --node : Two node identifiers of 'GO' nodes, separated by a comma.\n" +
"\n" +
- " --name : Two GO identifiers, seperated by a comma.\n");
+ " --name : Two GO identifiers, separated by a comma.\n");
break;
- case "add_antismash_results": case "add_gene_clusters":
- System.out.println("add_antismash_results : Include antiSMASH output to the pangenome.\n" +
+ case "add_antismash":
+ System.out.println("add_antismash : Include antiSMASH gene clusters into the pangenome.\n" +
+ "PanTools' antiSMASH parser is currently compatible with output from antiSMASH version(s): 6.0.0\n" +
"\n" +
"Required arguments:\n" +
"\n" +
" --database-path or -dp : Path to the pangenome database.\n" +
"\n" +
- " --input-file or -if : A text file with on each line a genome number and the full path to the corresponding antiSMASH output file,"
+ " --input-file or -if : A text file with on each line a genome number and the full path to the corresponding antiSMASH output .json file,"
+ " separated by a space.\n" +
"\n" +
"Optional argument:\n" +
- " --annotations-file or -af : A text file with the identifiers of annotations to be included, each on a seperate line.\n" +
+ " --annotations-file or -af : A text file with the identifiers of annotations to be included, each on a separate line.\n" +
" The most recent annotation is selected for genomes without an identifier.\n");
break;
case "add_functional_annotations": case "add_functions":
@@ -2344,7 +2361,7 @@ public class Pantools {
"\n" +
" --mode shared-functions : Find shared functions between similar sequences and put these on the 'is_similar' relationships.\n" +
"\n" +
- " --annotations-file or -af: A text file with the identifiers of annotations to be included, each on a seperate line.\n" +
+ " --annotations-file or -af: A text file with the identifiers of annotations to be included, each on a separate line.\n" +
" The most recent annotation is selected for genomes without an identifier.\n");
break;
case "functional_annotation_overview": case "function_overview":
@@ -2360,7 +2377,7 @@ public class Pantools {
"\n" +
" --reference or -ref : Only include a selection of genomes.\n" +
"\n" +
- " --annotations-file or -af: A text file with the identifiers of annotations to be included, each on a seperate line.\n" +
+ " --annotations-file or -af: A text file with the identifiers of annotations to be included, each on a separate line.\n" +
" The most recent annotation is selected for genomes without an identifier.\n");
break;
case "functional_classification": case "function_classification":
@@ -2397,9 +2414,9 @@ public class Pantools {
"\n" +
"Requires either one of the following arguments:\n" +
"\n" +
- " --homology-groups or -hm: A text file with homology group node identifiers, seperated by a comma.\n" +
+ " --homology-groups or -hm: A text file with homology group node identifiers, separated by a comma.\n" +
"\n" +
- " --node : mRNA node identifiers, seperated by a comma on the command line.\n" +
+ " --node : mRNA node identifiers, separated by a comma on the command line.\n" +
"\n" +
"Optional arguments:\n" +
"\n" +
@@ -2449,7 +2466,7 @@ public class Pantools {
"\n" +
" --reference or -ref : Only include a selection of genomes.\n" +
"\n" +
- " --annotations-file or -af: A text file with the identifiers of annotations to be removed, each on a seperate line.\n");
+ " --annotations-file or -af: A text file with the identifiers of annotations to be removed, each on a separate line.\n");
break;
default:
System.out.println("The provided subcommand '" + help + "' was not recognized, no manual available!\n");
@@ -2460,6 +2477,29 @@ public class Pantools {
"\n-----------------------------------------------------------------------\n");
}
+ /**
+ * Determine the location of PanTools' GIT repository.
+ */
+ public static void find_pantools_path() {
+ String full_path = Pantools.class.getProtectionDomain().getCodeSource().getLocation().getPath();
+ String[] path_array;
+ if (full_path.contains("/target/")) { // .jar location when compiled with Maven
+ path_array = full_path.split("/target/");
+ } else if (full_path.contains("/dist/")) { // .jar location when compiled with Ant
+ path_array = full_path.split("/dist/");
+ } else {
+ //path_array = new String[0];
+ System.out.println("No .jar file found in " + full_path + "/dist/ or " + full_path + "target/");
+ return;
+ }
+
+ if (!path_array[0].endsWith("/pantools")) {
+ System.out.println("PanTools' .jar file must be located inside the pantools/dist/ or pantools/target/ directories.");
+ System.exit(1);
+ }
+ pantools_path = path_array[0] + "/";
+ }
+
/**
* Estimates and prints the peak memory used during the execution of the program.
*/
@@ -2478,9 +2518,9 @@ public class Pantools {
/**
* Prints the number of threads to screen and returns number as string
- * @param print
+ * @param print print to terminal
* @param multiple_allowed - if the function is able to use more threads
- * @return
+ * @return number of threads as string
*/
public static String report_number_of_threads(boolean print, boolean multiple_allowed) {
if (THREADS == 1 && print && multiple_allowed) {
@@ -2488,16 +2528,15 @@ public class Pantools {
} else if (THREADS > 1 && !multiple_allowed && print) {
System.out.println("Multiple threads are selected but this function is only able to use 1. Using 1 thread");
}
- String threads_str = String.valueOf(THREADS);
- return threads_str;
+ return String.valueOf(THREADS);
}
/**
*
- * @param print
- * @param append_log
+ * @param print print to terminal
+ * @param append append output to file
*/
- public static void print_runtime(boolean print, boolean append_log) {
+ public static void print_runtime(boolean print, boolean append) {
long runtime_seconds = (System.currentTimeMillis() - startTime) / 1000;
String runtime_str;
String mins = " minutes", seconds = " seconds";
@@ -2532,7 +2571,7 @@ public class Pantools {
if (print) {
System.out.println(runtime_str);
}
- if (append_log) {
+ if (append) {
append_string_to_file_full_path(runtime_str +"\n\n", WORKING_DIRECTORY + "/log/used_commands");
}
}
@@ -2818,6 +2857,9 @@ public class Pantools {
* @return
*/
public static boolean check_if_file_exists(String path) {
+ if (LOG) {
+ System.out.println("Checking existence of: " + path);
+ }
File file = new File(path);
boolean exists = file.exists();
if (exists) { // if the file exists, check if anything is in there
@@ -2852,63 +2894,71 @@ public class Pantools {
return correct_label;
}
-
/**
- * Almost all of the arrays placed in nodes have a zero at the beginning. I don't know why?!
- *
- * @param old_copy_number_array
- * @return
+ * Almost all arrays holding counts for genome numbers placed in nodes have a zero at the beginning. I don't know why?!
+ * @param original_array array
+ * @return new array where the first value is removed.
*/
- public static int[] remove_first_position_array(int[] old_copy_number_array) {
- int[] new_copy_number_array = new int[old_copy_number_array.length-1];
- int counter = 0;
- for (int cn : old_copy_number_array) {
- if (counter > 0) {
- new_copy_number_array[counter-1] = cn;
- }
- counter++;
+ public static int[] remove_first_position_array(int[] original_array) {
+ int[] new_array = new int[original_array.length-1];
+ for (int i=1; i < original_array.length; i++) { // skip the first position in the original array;
+ new_array[i-1] = original_array[1];
}
- return new_copy_number_array;
+ return new_array;
}
- public static long[] remove_first_position_array(long[] old_copy_number_array) {
- long[] new_copy_number_array = new long[old_copy_number_array.length-1];
- int counter = 0;
- for (long cn : old_copy_number_array) {
- if (counter > 0) {
- new_copy_number_array[counter-1] = cn;
- }
- counter++;
+ /**
+ * Almost all arrays holding counts for genome numbers placed in nodes have a zero at the beginning. I don't know why?!
+ * @param original_array array
+ * @return new array where the first value is removed.
+ */
+ public static long[] remove_first_position_array(long[] original_array) {
+ long[] new_array = new long[original_array.length-1];
+ for (int i=1; i < original_array.length; i++) { // skip the first position in the original array;
+ new_array[i-1] = original_array[1];
}
- return new_copy_number_array;
+ return new_array;
}
/**
- * Write a StringBuilder to a file
- * @param output_builder
- * @param output_file
+ * Write a StringBuilder to a file. File is written inside database directory
+ * @param output_builder Stringbuilder
+ * @param output_file (path to) file name
*/
public static void write_SB_to_file_in_DB(StringBuilder output_builder, String output_file) {
try (BufferedWriter out = new BufferedWriter(new FileWriter(WORKING_DIRECTORY + output_file))) {
out.write(output_builder.toString());
- out.close();
} catch (IOException ioe) {
System.out.println(ioe.getMessage());
System.out.println("\nUnable to create: " + WORKING_DIRECTORY + output_file + "\n");
System.exit(1);
}
}
-
+
/**
- * Write a StringBuilder to an already existing file
- * @param output_builder
- * @param output_file
+ * Write a string to a file. File is written inside database directory
+ * @param output_str string
+ * @param output_file (path to) file name
+ */
+ public static void write_string_to_file_in_DB(String output_str, String output_file) {
+ try (BufferedWriter out = new BufferedWriter(new FileWriter(WORKING_DIRECTORY + output_file))) {
+ out.write(output_str);
+ } catch (IOException ioe) {
+ System.out.println(ioe.getMessage());
+ System.out.println("\nUnable to create: " + WORKING_DIRECTORY + output_file + "\n");
+ System.exit(1);
+ }
+ }
+
+ /**
+ * Write a StringBuilder to an already existing file. File is written inside database directory
+ * @param output_builder Stringbuilder
+ * @param output_file (path to) file name
*/
public static void append_SB_to_file_in_DB(StringBuilder output_builder, String output_file) {
String output_str = output_builder.toString();
try (FileWriter fw = new FileWriter(WORKING_DIRECTORY + output_file, true)) { // true allows to append the original instead of overwriting
fw.write(output_str);
- fw.close();
} catch(IOException ioe) {
System.out.println(ioe.getMessage());
System.out.println("\nUnable to create: " + WORKING_DIRECTORY + output_file + "\n");
@@ -2917,9 +2967,9 @@ public class Pantools {
}
/**
- * Write one file to an already existing file. input is added to output
- * @param input_file
- * @param output_file
+ * Append the content of one file to another (existing) file.
+ * @param input_file input comes from this file
+ * @param output_file output is written to this file
*/
public static void append_file_to_other_file(String input_file, String output_file) {
try (FileWriter fw = new FileWriter(output_file, true)) { //the true will append the new data
@@ -2938,13 +2988,27 @@ public class Pantools {
/**
* Write a StringBuilder to a file
- * @param output_builder
- * @param output_file
+ * @param output_builder stringbuilder
+ * @param output_file (path to) file name
*/
public static void write_SB_to_file_full_path(StringBuilder output_builder, String output_file) {
try (BufferedWriter out = new BufferedWriter(new FileWriter(output_file))) {
out.write(output_builder.toString());
- out.close();
+ } catch (IOException ioe) {
+ System.out.println(ioe.getMessage());
+ System.out.println("\nUnable to create: " + output_file + "\n");
+ System.exit(1);
+ }
+ }
+
+ /**
+ * Write a String to a file
+ * @param output_str string
+ * @param output_file (path to) file name
+ */
+ public static void write_string_to_file_full_path(String output_str, String output_file) {
+ try (BufferedWriter out = new BufferedWriter(new FileWriter(output_file))) {
+ out.write(output_str);
} catch (IOException ioe) {
System.out.println(ioe.getMessage());
System.out.println("\nUnable to create: " + output_file + "\n");
@@ -2954,13 +3018,12 @@ public class Pantools {
/**
* Write a String to an already existing file
- * @param output_str
- * @param output_file
+ * @param output_str string
+ * @param output_file (path to) file name
*/
public static void append_string_to_file_full_path(String output_str, String output_file) {
try (BufferedWriter out = new BufferedWriter(new FileWriter(output_file, true))) {
out.write(output_str);
- out.close();
} catch (IOException ioe) {
System.out.println(ioe.getMessage());
System.out.println("\nUnable to create: " + output_file + "\n");
@@ -2970,14 +3033,13 @@ public class Pantools {
/**
* Write a StringBuilder to an already existing file
- * @param output_builder
- * @param output_file
+ * @param output_builder stringbuilder
+ * @param output_file (path to) file name
*/
public static void append_SB_to_file_full_path(StringBuilder output_builder, String output_file) {
String output_str = output_builder.toString();
try (FileWriter fw = new FileWriter(output_file, true)) { //the true will append the new data
fw.write(output_str);
- fw.close();
} catch(IOException ioe) {
System.out.println(ioe.getMessage());
System.out.println("\nUnable to create: " + output_file + "\n");
@@ -2985,32 +3047,7 @@ public class Pantools {
}
}
- /**
- *
- * @param output_str
- * @param output_file
- */
- public static void write_string_to_file_in_DB(String output_str, String output_file) {
- try (BufferedWriter out = new BufferedWriter(new FileWriter(WORKING_DIRECTORY + output_file))) {
- out.write(output_str);
- out.close();
- } catch (IOException ioe) {
- System.out.println(ioe.getMessage());
- System.out.println("\nUnable to create: " + WORKING_DIRECTORY + output_file + "\n");
- System.exit(1);
- }
- }
- public static void write_string_to_file_full_path(String output_str, String output_file) {
- try (BufferedWriter out = new BufferedWriter(new FileWriter(output_file))) {
- out.write(output_str);
- out.close();
- } catch (IOException ioe) {
- System.out.println(ioe.getMessage());
- System.out.println("\nUnable to create: " + output_file + "\n");
- System.exit(1);
- }
- }
public static void copy_file(String string1, String string2) { // original and new position
File file1 = new File(string1);
@@ -3344,8 +3381,8 @@ public class Pantools {
/**
* Check if a program's location can be found using the linux command 'which PROGRAM_NAME'
- * @param command_str
- * @return
+ * @param command_str string to be executed
+ * @return output of command
*/
public static String find_program_location(String command_str) {
write_log = true;
@@ -3369,22 +3406,9 @@ public class Pantools {
write_log = false;
return line;
}
-
- /**
- *
- * @return
- */
- public static int check_grouping_version() {
- Node pangenome_node = graphDb.findNodes(pangenome_label).next();
- int highest_grouping = 0;
- if (pangenome_node.hasProperty("highest_grouping")) {
- highest_grouping = (int) pangenome_node.getProperty("highest_grouping");
- }
- return highest_grouping;
- }
/**
- *
+ * Check which grouping version is currently active. If no grouping is active, set 'grouping_version' to -1
*/
public static void check_current_grouping_version() {
try {
@@ -3399,9 +3423,10 @@ public class Pantools {
}
/**
- * Sets the 'K_SIZE', and 'total_genomes' variables
- * @param pangenome_node
- * @param function_name
+ * Check if database is pangenome or panproteome.
+ * Sets the 'K_SIZE' and 'total_genomes' variables
+ * @param pangenome_node the 'pangenome' node
+ * @param function_name the function that was initialized by the user
*/
public static void stop_if_panproteome(Node pangenome_node, String function_name) {
if (pangenome_node.hasProperty("k_mer_size")) {
@@ -3415,7 +3440,7 @@ public class Pantools {
/**
* Sets the 'K_SIZE', 'PROTEOME' and 'total_genomes' variables
- * @param pangenome_node
+ * @param pangenome_node the 'pangenome' node
*/
public static void check_if_panproteome(Node pangenome_node) {
if (pangenome_node.hasProperty("k_mer_size")) { // The "k_mer_size" property is only present in pangenomes
diff --git a/src/sequence/SequenceDatabase.java b/src/main/java/nl/wur/bif/pantools/sequence/SequenceDatabase.java
similarity index 98%
rename from src/sequence/SequenceDatabase.java
rename to src/main/java/nl/wur/bif/pantools/sequence/SequenceDatabase.java
index 7ccf385b544ae55401f9d2579bc873e88a8fee90..0d33057fcf418455095b6a6203791c4008dc2d8b 100755
--- a/src/sequence/SequenceDatabase.java
+++ b/src/main/java/nl/wur/bif/pantools/sequence/SequenceDatabase.java
@@ -3,7 +3,7 @@
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
-package sequence;
+package nl.wur.bif.pantools.sequence;
import java.util.*;
import java.io.BufferedReader;
@@ -21,13 +21,13 @@ import java.nio.file.Paths;
import org.neo4j.graphdb.GraphDatabaseService;
import org.neo4j.graphdb.Node;
import org.neo4j.graphdb.Transaction;
-import static pantools.Pantools.binary;
-import static pantools.Pantools.genome_label;
-import static pantools.Pantools.open_file;
-import static pantools.Pantools.is_fasta;
-import static pantools.Pantools.is_fastq;
-import static pantools.Pantools.pangenome_label;
-import static pantools.Pantools.sequence_label;
+import static nl.wur.bif.pantools.pantools.Pantools.binary;
+import static nl.wur.bif.pantools.pantools.Pantools.genome_label;
+import static nl.wur.bif.pantools.pantools.Pantools.open_file;
+import static nl.wur.bif.pantools.pantools.Pantools.is_fasta;
+import static nl.wur.bif.pantools.pantools.Pantools.is_fastq;
+import static nl.wur.bif.pantools.pantools.Pantools.pangenome_label;
+import static nl.wur.bif.pantools.pantools.Pantools.sequence_label;
/**
* Implements the class for a 4-bit compressed sequence database.
@@ -435,8 +435,7 @@ public class SequenceDatabase {
/**
* Adds new genomes to the genome database.
- *
- * @param path Path to the genome database
+ *
* @param genome_paths_file A text file containing path to the genomes
*/
public void add_genomes(String genome_paths_file) {
diff --git a/src/sequence/SequenceScanner.java b/src/main/java/nl/wur/bif/pantools/sequence/SequenceScanner.java
similarity index 98%
rename from src/sequence/SequenceScanner.java
rename to src/main/java/nl/wur/bif/pantools/sequence/SequenceScanner.java
index 108bb87324a4f9c20756a9d2af5d0e69ef6a58ec..c9cfbb5ca2f07b1067cbf063003c9894f5934b68 100755
--- a/src/sequence/SequenceScanner.java
+++ b/src/main/java/nl/wur/bif/pantools/sequence/SequenceScanner.java
@@ -3,14 +3,14 @@
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
-package sequence;
+package nl.wur.bif.pantools.sequence;
-import index.IndexScanner;
-import index.kmer;
-import static pangenome.Classification.get_percentage_str;
-import static pantools.Pantools.DEBUG;
-import static pantools.Pantools.complement;
-import static pantools.Pantools.sym;
+import nl.wur.bif.pantools.index.IndexScanner;
+import nl.wur.bif.pantools.index.kmer;
+import static nl.wur.bif.pantools.pangenome.Classification.get_percentage_str;
+import static nl.wur.bif.pantools.pantools.Pantools.DEBUG;
+import static nl.wur.bif.pantools.pantools.Pantools.complement;
+import static nl.wur.bif.pantools.pantools.Pantools.sym;
/**
* Implements the class for scanning a 4-bit compressed sequence database.
diff --git a/src/main/java/nl/wur/bif/pantools/utils/Utils.java b/src/main/java/nl/wur/bif/pantools/utils/Utils.java
new file mode 100644
index 0000000000000000000000000000000000000000..bb799104b774a1450c34e6a1940c0250454c3bdc
--- /dev/null
+++ b/src/main/java/nl/wur/bif/pantools/utils/Utils.java
@@ -0,0 +1,47 @@
+package nl.wur.bif.pantools.utils;
+
+import java.io.IOException;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.Properties;
+
+/**
+ * A bunch of random utilities.
+ */
+public class Utils {
+ private static final Path GIT_PROPERTIES_PATH = Paths.get("/git.properties");
+
+ public static Properties readPropertiesFile(Path path) throws IOException {
+ // TODO: this method should also allow for loading from properties files outside jars
+ final Properties properties = new Properties();
+ properties.load(Utils.class.getResourceAsStream(path.toString()));
+ return properties;
+ }
+
+ /**
+ * Return build version of PanTools and abbreviated commit ID, also indicating if the current state of the code base
+ * is dirty (containing changed files not staged). Build version is the latest tag.
+ *
+ * Will throw an {{@link IllegalArgumentException}} in case the git.properties file is found, but does not contain
+ * a needed item.
+ * @return string containing the PanTools version and abbreviated commit ID, with a comma in in-between.
+ */
+ public static String getVersionInformation() {
+ try {
+ // Try to read from git.properties, which will be included in a Maven-generated jar
+ final Properties properties = readPropertiesFile(GIT_PROPERTIES_PATH);
+ final String buildVersion = properties.getProperty("git.build.version");
+ final String abbreviatedCommitId = properties.getProperty("git.commit.id.abbrev");
+
+ return String.format("version %s, abbrev. commit ID %s", buildVersion, abbreviatedCommitId);
+ } catch (IOException e) {
+ // TODO: if exception is thrown because of missing file or something else
+ // Caused (most likely) by missing git.properties file, return unknown version
+ // TODO: use JGit to extract information from local repository
+ } catch (NullPointerException ignored) {
+ throw new IllegalArgumentException("missing build version or abbreviated commit ID in " + GIT_PROPERTIES_PATH);
+ }
+
+ return "development version";
+ }
+}
\ No newline at end of file
diff --git a/test/alignment/BoundedLocalSequenceAlignmentTest.java b/test/alignment/BoundedLocalSequenceAlignmentTest.java
deleted file mode 100755
index 218ab37e678fcd00c57020efb60f8d279bc98a8b..0000000000000000000000000000000000000000
--- a/test/alignment/BoundedLocalSequenceAlignmentTest.java
+++ /dev/null
@@ -1,53 +0,0 @@
-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
-package alignment;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.BeforeClass;
-import org.junit.Test;
-import static pantools.Pantools.GAP_EXT;
-import static pantools.Pantools.GAP_OPEN;
-
-/**
- *
- * @author sheik005
- */
-public class BoundedLocalSequenceAlignmentTest {
-
- public BoundedLocalSequenceAlignmentTest() {
- }
-
- @BeforeClass
- public static void setUpClass() {
- }
-
- @AfterClass
- public static void tearDownClass() {
- }
-
- @Before
- public void setUp() {
- }
-
- @After
- public void tearDown() {
- }
-
- /**
- * Test of initialize_NUCC_matrix method, of class LocalSequenceAlignment.
- */
- @Test
- public void test() {
- int i, j, m, n, bound = 2;
- BoundedLocalSequenceAlignment instance = new BoundedLocalSequenceAlignment(GAP_OPEN, GAP_EXT, 1000, bound, 0, 'N');
- String seq1, seq2;
- seq1 = "AGGCAAATTAAGAGAACAA";
- seq2 = "AGTAGCAAATTAAGAGAACAAAA";
- instance.align(seq1, seq2);
- }
-}
diff --git a/test/alignment/LocalSequenceAlignmentTest.java b/test/alignment/LocalSequenceAlignmentTest.java
deleted file mode 100644
index 79d8ec0b9bcf6e08b464ccba15a91a8ea684ff6f..0000000000000000000000000000000000000000
--- a/test/alignment/LocalSequenceAlignmentTest.java
+++ /dev/null
@@ -1,57 +0,0 @@
-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
-package alignment;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.BeforeClass;
-import org.junit.Test;
-import static org.junit.Assert.*;
-import static pantools.Pantools.GAP_EXT;
-import static pantools.Pantools.GAP_OPEN;
-
-/**
- *
- * @author sheik005
- */
-public class LocalSequenceAlignmentTest {
-
- public LocalSequenceAlignmentTest() {
- }
-
- @BeforeClass
- public static void setUpClass() {
- }
-
- @AfterClass
- public static void tearDownClass() {
- }
-
- @Before
- public void setUp() {
- }
-
- @After
- public void tearDown() {
- }
-
- @Test
- public void test(){
- int i, j, m, n;
- LocalSequenceAlignment instance = new LocalSequenceAlignment(GAP_OPEN, GAP_EXT, 1000, 0, 'N');
- String seq1, seq2;
- seq2 = "TTTAGAGGCGAGATGGTAGTACAGGAAATTTAAGAGGACAAATCTTTTTCTCTTT";
- seq1 = "AGGCAAATTAAGAGAACAA";
- instance.align(seq1, seq2);
- System.out.println(instance.get_cigar());
- System.out.println(instance.get_alignment());
- System.out.println(instance.get_offset());
- System.out.println(instance.get_identity());
- System.out.println(instance.get_similarity());
- }
-
-}
diff --git a/test/pangenome/AnnotationLayerTest.java b/test/pangenome/AnnotationLayerTest.java
deleted file mode 100755
index 6a4b1d3845c94ca3807815b9ca22af1861e2e8e6..0000000000000000000000000000000000000000
--- a/test/pangenome/AnnotationLayerTest.java
+++ /dev/null
@@ -1,103 +0,0 @@
-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
-package pangenome;
-
-import java.io.BufferedReader;
-import java.io.FileReader;
-import java.io.IOException;
-import java.util.HashMap;
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.BeforeClass;
-import org.junit.Test;
-import org.neo4j.graphdb.Label;
-import static org.neo4j.graphdb.Label.label;
-import static pantools.Pantools.print_peak_memory;
-import static pantools.Pantools.startTime;
-import static pantools.Pantools.WORKING_DIRECTORY;
-import static pantools.Pantools.PATH_TO_THE_ANNOTATIONS_FILE;
-import static pantools.Pantools.PATH_TO_THE_GENOME_NUMBERS_FILE;
-import static pantools.Pantools.labels;
-
-/**
- *
- * @author sheik005
- */
-public class AnnotationLayerTest {
- private static String test_directory;
-
- public AnnotationLayerTest() {
- test_directory = System.getProperty("user.home") + "/pantools/example/";
- }
-
- @BeforeClass
- public static void setUpClass() {
- }
-
- @AfterClass
- public static void tearDownClass() {
- }
-
- @Before
- public void setUp() {
- }
-
- @After
- public void tearDown() {
- }
-
- /**
- * Test of retrieve_genes method, of class AnnotationLayer.
- */
- @Test
- public void testRetrieve_genes() {
- System.out.println("retrieve_features");
- labels = new HashMap<String,Label>();
- String[] label_strings = new String[]{
- "pangenome", "genome","sequence","nucleotide","degenerate",
- "annotation","variation","gene","coding_gene", "mRNA",
- "tRNA", "rRNA", "CDS", "exon", "intron", "feature",
- "broken_protein", "homology_group", "low_complexity"};
- for (int i = 0; i < label_strings.length; ++i)
- labels.put(label_strings[i], label(label_strings[i]));
- AnnotationLayer instance = new AnnotationLayer();
-
- PATH_TO_THE_ANNOTATIONS_FILE = test_directory + "sample_annotations_path.txt";
- PATH_TO_THE_GENOME_NUMBERS_FILE = test_directory + "sample_genome_numbers.txt";
- WORKING_DIRECTORY = System.getProperty("user.home") + "/test/";
- instance.add_annotations();
- instance.retrieve_feature();
- if(are_the_same("genes.1.fasta", test_directory + "sample_genes.1.fasta") &&
- are_the_same("genes.2.fasta", test_directory + "sample_genes.2.fasta"))
- System.out.println("Genes extracted properly.");
- else
- System.out.println("Test failed.");
- System.out.println("Total time : " + (System.currentTimeMillis() - startTime) / 1000 + "." + (System.currentTimeMillis() - startTime) % 1000 + " seconds");
- print_peak_memory();
- System.out.println("-----------------------------------------------------------------------");
- }
-
- public boolean are_the_same(String file_name1, String file_name2) {
- BufferedReader in1, in2;
- try {
- System.out.println("Comparing " + file_name1 + " and " + file_name2 + "...");
- in1 = new BufferedReader(new FileReader(file_name1));
- in2 = new BufferedReader(new FileReader(file_name2));
- do
- if( !in1.readLine().toUpperCase().trim().equals(in2.readLine().toUpperCase().trim()) )
- return false;
- while (in1.ready() && in2.ready()) ;
- in1.close();
- in2.close();
- } catch (IOException e) {
- System.out.println(e.getMessage());
- return false;
- }
- return true;
- }
-
-}
diff --git a/test/pangenome/GenomeLayerTest.java b/test/pangenome/GenomeLayerTest.java
deleted file mode 100755
index 42ff650bb7e6b3d884e1c535cac76a7e116d1844..0000000000000000000000000000000000000000
--- a/test/pangenome/GenomeLayerTest.java
+++ /dev/null
@@ -1,170 +0,0 @@
-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
-package pangenome;
-
-import java.io.BufferedReader;
-import java.io.FileReader;
-import java.io.IOException;
-import java.util.HashMap;
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.BeforeClass;
-import org.junit.Test;
-import org.junit.FixMethodOrder;
-import org.junit.runners.MethodSorters;
-import org.neo4j.graphdb.Label;
-import static org.neo4j.graphdb.Label.label;
-import static pantools.Pantools.print_peak_memory;
-import static pantools.Pantools.startTime;
-import static pantools.Pantools.K_SIZE;
-import static pantools.Pantools.PATH_TO_THE_GENOMES_FILE;
-import static pantools.Pantools.PATH_TO_THE_GENOME_NUMBERS_FILE;
-import static pantools.Pantools.WORKING_DIRECTORY;
-import static pantools.Pantools.PATH_TO_THE_REGIONS_FILE;
-import static pantools.Pantools.labels;
-
-@FixMethodOrder(MethodSorters.NAME_ASCENDING)
-public class GenomeLayerTest {
- private static String test_directory;
-
- public GenomeLayerTest() {
- test_directory = System.getProperty("user.home") + "/pantools/example/";
- K_SIZE = -1;
- }
-
- @BeforeClass
- public static void setUpClass() {
- }
-
- @AfterClass
- public static void tearDownClass() {
- }
-
- @Before
- public void setUp() {
- }
-
- @After
- public void tearDown() {
- }
-
- /**
- * Test of build method, of class GenomeLayer.
- */
- @Test
- public void test1_Build() {
- System.out.println("Testing build:");
- labels = new HashMap<String,Label>();
- String[] label_strings = new String[]{
- "pangenome", "genome","sequence","nucleotide","degenerate",
- "annotation","variation","gene","coding_gene", "mRNA",
- "tRNA", "rRNA", "CDS", "exon", "intron", "feature",
- "broken_protein", "homology_group", "low_complexity"};
- for (int i = 0; i < label_strings.length; ++i)
- labels.put(label_strings[i], label(label_strings[i]));
- GenomeLayer instance = new GenomeLayer();
- K_SIZE = 11;
- PATH_TO_THE_GENOMES_FILE = test_directory + "sample_genomes_path.txt";
- WORKING_DIRECTORY = System.getProperty("user.home") + "/test/";
- instance.initialize_pangenome();
- System.out.println("Total time : " + (System.currentTimeMillis() - startTime) / 1000 + "." + (System.currentTimeMillis() - startTime) % 1000 + " seconds");
- print_peak_memory();
- System.out.println("-----------------------------------------------------------------------");
- }
-
- /**
- * Test of add method, of class GenomeLayer.
- */
- @Test
- public void test2_Add() {
- System.out.println("Testing add:");
- GenomeLayer instance = new GenomeLayer();
- K_SIZE = 11;
- PATH_TO_THE_GENOMES_FILE = test_directory + "sample_genomes_path_1.txt";
- WORKING_DIRECTORY = System.getProperty("user.home") + "/cumulative_test";
- instance.initialize_pangenome();
- PATH_TO_THE_GENOMES_FILE = test_directory + "sample_genomes_path_2.txt";
- instance.add_genomes();
- System.out.println("Total time : " + (System.currentTimeMillis() - startTime) / 1000 + "." + (System.currentTimeMillis() - startTime) % 1000 + " seconds");
- print_peak_memory();
- System.out.println("-----------------------------------------------------------------------");
- }
-
-
- /**
- * Test of retrieve_regions method, of class GenomeLayer.
- */
- @Test
- public void test4_Retrieve_regions() {
- System.out.println("Testing retrieve_regions:");
- GenomeLayer instance = new GenomeLayer();
- PATH_TO_THE_REGIONS_FILE = test_directory + "sample_genomic_regions.txt";
- WORKING_DIRECTORY = System.getProperty("user.home") + "/test/";
- instance.retrieve_regions();
- String[] fields = PATH_TO_THE_REGIONS_FILE.split("\\/");
- if( are_the_same(WORKING_DIRECTORY + "/" + fields[fields.length - 1] + ".fasta", test_directory + "sample_genomic_regions.fasta") )
- System.out.println("Regions extracted properly.");
- else
- System.out.println("Test failed.");
- System.out.println("Total time : " + (System.currentTimeMillis() - startTime) / 1000 + "." + (System.currentTimeMillis() - startTime) % 1000 + " seconds");
- print_peak_memory();
- System.out.println("-----------------------------------------------------------------------");
- }
-
- /**
- * Test of reconstruct_genomes method, of class GenomeLayer.
- */
- @Test
- public void test5_Reconstruct_genomes() {
- System.out.println("reconstruct_genomes");
- GenomeLayer instance = new GenomeLayer();
- PATH_TO_THE_GENOME_NUMBERS_FILE = test_directory + "sample_genome_numbers.txt";
- WORKING_DIRECTORY = System.getProperty("user.home") + "/test/";
- instance.retrieve_genomes();
- String genome_file;
- try {
- PATH_TO_THE_GENOMES_FILE = test_directory + "sample_genomes_path.txt";
- BufferedReader in = new BufferedReader(new FileReader(PATH_TO_THE_GENOMES_FILE));
- for (int i = 1 ; in.ready() ; ++i) {
- genome_file = in.readLine().trim();
- if (genome_file.equals("")) {
- continue;
- }
- if( are_the_same(WORKING_DIRECTORY + "Genome_" + i + ".fasta", genome_file) )
- System.out.println("Genome " + i +" extracted properly.");
- else
- System.out.println("Genome " + i +" extraction failed.");
- }
- in.close();
- } catch (IOException e) {
- System.out.println(e.getMessage());
- System.exit(1);
- }
- System.out.println("Total time : " + (System.currentTimeMillis() - startTime) / 1000 + "." + (System.currentTimeMillis() - startTime) % 1000 + " seconds");
- print_peak_memory();
- System.out.println("-----------------------------------------------------------------------");
- }
-
- public boolean are_the_same(String file_name1, String file_name2) {
- BufferedReader in1, in2;
- try {
- in1 = new BufferedReader(new FileReader(file_name1));
- in2 = new BufferedReader(new FileReader(file_name2));
- System.out.println("Comparing " + file_name1 + " and " + file_name2 + "...");
- do
- if( !in1.readLine().toUpperCase().trim().equals(in2.readLine().toUpperCase().trim()) )
- return false;
- while (in1.ready() && in2.ready()) ;
- in1.close();
- in2.close();
- } catch (IOException e) {
- System.out.println(e.getMessage());
- return false;
- }
- return true;
- }
-}
diff --git a/test/pangenome/ProteomeLayerTest.java b/test/pangenome/ProteomeLayerTest.java
deleted file mode 100755
index b44427e2c8c75b4d8acb5e6772f27a0f1b111745..0000000000000000000000000000000000000000
--- a/test/pangenome/ProteomeLayerTest.java
+++ /dev/null
@@ -1,69 +0,0 @@
-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
-package pangenome;
-
-import java.util.HashMap;
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.BeforeClass;
-import org.junit.Test;
-import org.neo4j.graphdb.Label;
-import static org.neo4j.graphdb.Label.label;
-import static pantools.Pantools.print_peak_memory;
-import static pantools.Pantools.startTime;
-import static pantools.Pantools.WORKING_DIRECTORY;
-import static pantools.Pantools.labels;
-
-/**
- *
- * @author sheik005
- */
-public class ProteomeLayerTest {
-
- public ProteomeLayerTest() {
- }
-
- @BeforeClass
- public static void setUpClass() {
- }
-
- @AfterClass
- public static void tearDownClass() {
- }
-
- @Before
- public void setUp() {
- }
-
- @After
- public void tearDown() {
- }
-
- /**
- * Test of group method, of class ProteomeLayer.
- */
- @Test
- public void testGroup() {
- System.out.println("group");
- labels = new HashMap<String,Label>();
- String[] label_strings = new String[]{
- "pangenome", "genome","sequence","nucleotide","degenerate",
- "annotation","variation","gene","coding_gene", "mRNA",
- "tRNA", "rRNA", "CDS", "exon", "intron", "feature",
- "broken_protein", "homology_group", "low_complexity"};
- for (int i = 0; i < label_strings.length; ++i)
- labels.put(label_strings[i], label(label_strings[i]));
- WORKING_DIRECTORY = System.getProperty("user.home") + "/test";
- String[] args = new String[]{"", WORKING_DIRECTORY, "-d", "8"};
- ProteomeLayer instance = new ProteomeLayer();
- instance.group();
- System.out.println("Total time : " + (System.currentTimeMillis() - startTime) / 1000 + "." + (System.currentTimeMillis() - startTime) % 1000 + " seconds");
- print_peak_memory();
- System.out.println("-----------------------------------------------------------------------");
- }
-
-}
diff --git a/test_code/alignment/BoundedLocalSequenceAlignmentTest.java b/test_code/alignment/BoundedLocalSequenceAlignmentTest.java
deleted file mode 100755
index 218ab37e678fcd00c57020efb60f8d279bc98a8b..0000000000000000000000000000000000000000
--- a/test_code/alignment/BoundedLocalSequenceAlignmentTest.java
+++ /dev/null
@@ -1,53 +0,0 @@
-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
-package alignment;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.BeforeClass;
-import org.junit.Test;
-import static pantools.Pantools.GAP_EXT;
-import static pantools.Pantools.GAP_OPEN;
-
-/**
- *
- * @author sheik005
- */
-public class BoundedLocalSequenceAlignmentTest {
-
- public BoundedLocalSequenceAlignmentTest() {
- }
-
- @BeforeClass
- public static void setUpClass() {
- }
-
- @AfterClass
- public static void tearDownClass() {
- }
-
- @Before
- public void setUp() {
- }
-
- @After
- public void tearDown() {
- }
-
- /**
- * Test of initialize_NUCC_matrix method, of class LocalSequenceAlignment.
- */
- @Test
- public void test() {
- int i, j, m, n, bound = 2;
- BoundedLocalSequenceAlignment instance = new BoundedLocalSequenceAlignment(GAP_OPEN, GAP_EXT, 1000, bound, 0, 'N');
- String seq1, seq2;
- seq1 = "AGGCAAATTAAGAGAACAA";
- seq2 = "AGTAGCAAATTAAGAGAACAAAA";
- instance.align(seq1, seq2);
- }
-}
diff --git a/test_code/alignment/LocalSequenceAlignmentTest.java b/test_code/alignment/LocalSequenceAlignmentTest.java
deleted file mode 100644
index 79d8ec0b9bcf6e08b464ccba15a91a8ea684ff6f..0000000000000000000000000000000000000000
--- a/test_code/alignment/LocalSequenceAlignmentTest.java
+++ /dev/null
@@ -1,57 +0,0 @@
-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
-package alignment;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.BeforeClass;
-import org.junit.Test;
-import static org.junit.Assert.*;
-import static pantools.Pantools.GAP_EXT;
-import static pantools.Pantools.GAP_OPEN;
-
-/**
- *
- * @author sheik005
- */
-public class LocalSequenceAlignmentTest {
-
- public LocalSequenceAlignmentTest() {
- }
-
- @BeforeClass
- public static void setUpClass() {
- }
-
- @AfterClass
- public static void tearDownClass() {
- }
-
- @Before
- public void setUp() {
- }
-
- @After
- public void tearDown() {
- }
-
- @Test
- public void test(){
- int i, j, m, n;
- LocalSequenceAlignment instance = new LocalSequenceAlignment(GAP_OPEN, GAP_EXT, 1000, 0, 'N');
- String seq1, seq2;
- seq2 = "TTTAGAGGCGAGATGGTAGTACAGGAAATTTAAGAGGACAAATCTTTTTCTCTTT";
- seq1 = "AGGCAAATTAAGAGAACAA";
- instance.align(seq1, seq2);
- System.out.println(instance.get_cigar());
- System.out.println(instance.get_alignment());
- System.out.println(instance.get_offset());
- System.out.println(instance.get_identity());
- System.out.println(instance.get_similarity());
- }
-
-}
diff --git a/test_code/pangenome/AnnotationLayerTest.java b/test_code/pangenome/AnnotationLayerTest.java
deleted file mode 100755
index 6a4b1d3845c94ca3807815b9ca22af1861e2e8e6..0000000000000000000000000000000000000000
--- a/test_code/pangenome/AnnotationLayerTest.java
+++ /dev/null
@@ -1,103 +0,0 @@
-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
-package pangenome;
-
-import java.io.BufferedReader;
-import java.io.FileReader;
-import java.io.IOException;
-import java.util.HashMap;
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.BeforeClass;
-import org.junit.Test;
-import org.neo4j.graphdb.Label;
-import static org.neo4j.graphdb.Label.label;
-import static pantools.Pantools.print_peak_memory;
-import static pantools.Pantools.startTime;
-import static pantools.Pantools.WORKING_DIRECTORY;
-import static pantools.Pantools.PATH_TO_THE_ANNOTATIONS_FILE;
-import static pantools.Pantools.PATH_TO_THE_GENOME_NUMBERS_FILE;
-import static pantools.Pantools.labels;
-
-/**
- *
- * @author sheik005
- */
-public class AnnotationLayerTest {
- private static String test_directory;
-
- public AnnotationLayerTest() {
- test_directory = System.getProperty("user.home") + "/pantools/example/";
- }
-
- @BeforeClass
- public static void setUpClass() {
- }
-
- @AfterClass
- public static void tearDownClass() {
- }
-
- @Before
- public void setUp() {
- }
-
- @After
- public void tearDown() {
- }
-
- /**
- * Test of retrieve_genes method, of class AnnotationLayer.
- */
- @Test
- public void testRetrieve_genes() {
- System.out.println("retrieve_features");
- labels = new HashMap<String,Label>();
- String[] label_strings = new String[]{
- "pangenome", "genome","sequence","nucleotide","degenerate",
- "annotation","variation","gene","coding_gene", "mRNA",
- "tRNA", "rRNA", "CDS", "exon", "intron", "feature",
- "broken_protein", "homology_group", "low_complexity"};
- for (int i = 0; i < label_strings.length; ++i)
- labels.put(label_strings[i], label(label_strings[i]));
- AnnotationLayer instance = new AnnotationLayer();
-
- PATH_TO_THE_ANNOTATIONS_FILE = test_directory + "sample_annotations_path.txt";
- PATH_TO_THE_GENOME_NUMBERS_FILE = test_directory + "sample_genome_numbers.txt";
- WORKING_DIRECTORY = System.getProperty("user.home") + "/test/";
- instance.add_annotations();
- instance.retrieve_feature();
- if(are_the_same("genes.1.fasta", test_directory + "sample_genes.1.fasta") &&
- are_the_same("genes.2.fasta", test_directory + "sample_genes.2.fasta"))
- System.out.println("Genes extracted properly.");
- else
- System.out.println("Test failed.");
- System.out.println("Total time : " + (System.currentTimeMillis() - startTime) / 1000 + "." + (System.currentTimeMillis() - startTime) % 1000 + " seconds");
- print_peak_memory();
- System.out.println("-----------------------------------------------------------------------");
- }
-
- public boolean are_the_same(String file_name1, String file_name2) {
- BufferedReader in1, in2;
- try {
- System.out.println("Comparing " + file_name1 + " and " + file_name2 + "...");
- in1 = new BufferedReader(new FileReader(file_name1));
- in2 = new BufferedReader(new FileReader(file_name2));
- do
- if( !in1.readLine().toUpperCase().trim().equals(in2.readLine().toUpperCase().trim()) )
- return false;
- while (in1.ready() && in2.ready()) ;
- in1.close();
- in2.close();
- } catch (IOException e) {
- System.out.println(e.getMessage());
- return false;
- }
- return true;
- }
-
-}
diff --git a/test_code/pangenome/GenomeLayerTest.java b/test_code/pangenome/GenomeLayerTest.java
deleted file mode 100755
index 42ff650bb7e6b3d884e1c535cac76a7e116d1844..0000000000000000000000000000000000000000
--- a/test_code/pangenome/GenomeLayerTest.java
+++ /dev/null
@@ -1,170 +0,0 @@
-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
-package pangenome;
-
-import java.io.BufferedReader;
-import java.io.FileReader;
-import java.io.IOException;
-import java.util.HashMap;
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.BeforeClass;
-import org.junit.Test;
-import org.junit.FixMethodOrder;
-import org.junit.runners.MethodSorters;
-import org.neo4j.graphdb.Label;
-import static org.neo4j.graphdb.Label.label;
-import static pantools.Pantools.print_peak_memory;
-import static pantools.Pantools.startTime;
-import static pantools.Pantools.K_SIZE;
-import static pantools.Pantools.PATH_TO_THE_GENOMES_FILE;
-import static pantools.Pantools.PATH_TO_THE_GENOME_NUMBERS_FILE;
-import static pantools.Pantools.WORKING_DIRECTORY;
-import static pantools.Pantools.PATH_TO_THE_REGIONS_FILE;
-import static pantools.Pantools.labels;
-
-@FixMethodOrder(MethodSorters.NAME_ASCENDING)
-public class GenomeLayerTest {
- private static String test_directory;
-
- public GenomeLayerTest() {
- test_directory = System.getProperty("user.home") + "/pantools/example/";
- K_SIZE = -1;
- }
-
- @BeforeClass
- public static void setUpClass() {
- }
-
- @AfterClass
- public static void tearDownClass() {
- }
-
- @Before
- public void setUp() {
- }
-
- @After
- public void tearDown() {
- }
-
- /**
- * Test of build method, of class GenomeLayer.
- */
- @Test
- public void test1_Build() {
- System.out.println("Testing build:");
- labels = new HashMap<String,Label>();
- String[] label_strings = new String[]{
- "pangenome", "genome","sequence","nucleotide","degenerate",
- "annotation","variation","gene","coding_gene", "mRNA",
- "tRNA", "rRNA", "CDS", "exon", "intron", "feature",
- "broken_protein", "homology_group", "low_complexity"};
- for (int i = 0; i < label_strings.length; ++i)
- labels.put(label_strings[i], label(label_strings[i]));
- GenomeLayer instance = new GenomeLayer();
- K_SIZE = 11;
- PATH_TO_THE_GENOMES_FILE = test_directory + "sample_genomes_path.txt";
- WORKING_DIRECTORY = System.getProperty("user.home") + "/test/";
- instance.initialize_pangenome();
- System.out.println("Total time : " + (System.currentTimeMillis() - startTime) / 1000 + "." + (System.currentTimeMillis() - startTime) % 1000 + " seconds");
- print_peak_memory();
- System.out.println("-----------------------------------------------------------------------");
- }
-
- /**
- * Test of add method, of class GenomeLayer.
- */
- @Test
- public void test2_Add() {
- System.out.println("Testing add:");
- GenomeLayer instance = new GenomeLayer();
- K_SIZE = 11;
- PATH_TO_THE_GENOMES_FILE = test_directory + "sample_genomes_path_1.txt";
- WORKING_DIRECTORY = System.getProperty("user.home") + "/cumulative_test";
- instance.initialize_pangenome();
- PATH_TO_THE_GENOMES_FILE = test_directory + "sample_genomes_path_2.txt";
- instance.add_genomes();
- System.out.println("Total time : " + (System.currentTimeMillis() - startTime) / 1000 + "." + (System.currentTimeMillis() - startTime) % 1000 + " seconds");
- print_peak_memory();
- System.out.println("-----------------------------------------------------------------------");
- }
-
-
- /**
- * Test of retrieve_regions method, of class GenomeLayer.
- */
- @Test
- public void test4_Retrieve_regions() {
- System.out.println("Testing retrieve_regions:");
- GenomeLayer instance = new GenomeLayer();
- PATH_TO_THE_REGIONS_FILE = test_directory + "sample_genomic_regions.txt";
- WORKING_DIRECTORY = System.getProperty("user.home") + "/test/";
- instance.retrieve_regions();
- String[] fields = PATH_TO_THE_REGIONS_FILE.split("\\/");
- if( are_the_same(WORKING_DIRECTORY + "/" + fields[fields.length - 1] + ".fasta", test_directory + "sample_genomic_regions.fasta") )
- System.out.println("Regions extracted properly.");
- else
- System.out.println("Test failed.");
- System.out.println("Total time : " + (System.currentTimeMillis() - startTime) / 1000 + "." + (System.currentTimeMillis() - startTime) % 1000 + " seconds");
- print_peak_memory();
- System.out.println("-----------------------------------------------------------------------");
- }
-
- /**
- * Test of reconstruct_genomes method, of class GenomeLayer.
- */
- @Test
- public void test5_Reconstruct_genomes() {
- System.out.println("reconstruct_genomes");
- GenomeLayer instance = new GenomeLayer();
- PATH_TO_THE_GENOME_NUMBERS_FILE = test_directory + "sample_genome_numbers.txt";
- WORKING_DIRECTORY = System.getProperty("user.home") + "/test/";
- instance.retrieve_genomes();
- String genome_file;
- try {
- PATH_TO_THE_GENOMES_FILE = test_directory + "sample_genomes_path.txt";
- BufferedReader in = new BufferedReader(new FileReader(PATH_TO_THE_GENOMES_FILE));
- for (int i = 1 ; in.ready() ; ++i) {
- genome_file = in.readLine().trim();
- if (genome_file.equals("")) {
- continue;
- }
- if( are_the_same(WORKING_DIRECTORY + "Genome_" + i + ".fasta", genome_file) )
- System.out.println("Genome " + i +" extracted properly.");
- else
- System.out.println("Genome " + i +" extraction failed.");
- }
- in.close();
- } catch (IOException e) {
- System.out.println(e.getMessage());
- System.exit(1);
- }
- System.out.println("Total time : " + (System.currentTimeMillis() - startTime) / 1000 + "." + (System.currentTimeMillis() - startTime) % 1000 + " seconds");
- print_peak_memory();
- System.out.println("-----------------------------------------------------------------------");
- }
-
- public boolean are_the_same(String file_name1, String file_name2) {
- BufferedReader in1, in2;
- try {
- in1 = new BufferedReader(new FileReader(file_name1));
- in2 = new BufferedReader(new FileReader(file_name2));
- System.out.println("Comparing " + file_name1 + " and " + file_name2 + "...");
- do
- if( !in1.readLine().toUpperCase().trim().equals(in2.readLine().toUpperCase().trim()) )
- return false;
- while (in1.ready() && in2.ready()) ;
- in1.close();
- in2.close();
- } catch (IOException e) {
- System.out.println(e.getMessage());
- return false;
- }
- return true;
- }
-}
diff --git a/test_code/pangenome/ProteomeLayerTest.java b/test_code/pangenome/ProteomeLayerTest.java
deleted file mode 100755
index b44427e2c8c75b4d8acb5e6772f27a0f1b111745..0000000000000000000000000000000000000000
--- a/test_code/pangenome/ProteomeLayerTest.java
+++ /dev/null
@@ -1,69 +0,0 @@
-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
-package pangenome;
-
-import java.util.HashMap;
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.BeforeClass;
-import org.junit.Test;
-import org.neo4j.graphdb.Label;
-import static org.neo4j.graphdb.Label.label;
-import static pantools.Pantools.print_peak_memory;
-import static pantools.Pantools.startTime;
-import static pantools.Pantools.WORKING_DIRECTORY;
-import static pantools.Pantools.labels;
-
-/**
- *
- * @author sheik005
- */
-public class ProteomeLayerTest {
-
- public ProteomeLayerTest() {
- }
-
- @BeforeClass
- public static void setUpClass() {
- }
-
- @AfterClass
- public static void tearDownClass() {
- }
-
- @Before
- public void setUp() {
- }
-
- @After
- public void tearDown() {
- }
-
- /**
- * Test of group method, of class ProteomeLayer.
- */
- @Test
- public void testGroup() {
- System.out.println("group");
- labels = new HashMap<String,Label>();
- String[] label_strings = new String[]{
- "pangenome", "genome","sequence","nucleotide","degenerate",
- "annotation","variation","gene","coding_gene", "mRNA",
- "tRNA", "rRNA", "CDS", "exon", "intron", "feature",
- "broken_protein", "homology_group", "low_complexity"};
- for (int i = 0; i < label_strings.length; ++i)
- labels.put(label_strings[i], label(label_strings[i]));
- WORKING_DIRECTORY = System.getProperty("user.home") + "/test";
- String[] args = new String[]{"", WORKING_DIRECTORY, "-d", "8"};
- ProteomeLayer instance = new ProteomeLayer();
- instance.group();
- System.out.println("Total time : " + (System.currentTimeMillis() - startTime) / 1000 + "." + (System.currentTimeMillis() - startTime) % 1000 + " seconds");
- print_peak_memory();
- System.out.println("-----------------------------------------------------------------------");
- }
-
-}