Commits · master · Lokhorst, Wouter / BiG-SCAPE · GitLab

Snippets Groups Projects

Oct 31, 2017
- Move html output folders into each networks output folder (i.e. networks_all,... · c7f60b2d
  Kautsar, Satria authored 7 years ago
  c7f60b2d
Oct 18, 2017
- implement domain color · d42b9109
  Kautsar, Satria authored 7 years ago
  
  d42b9109
Oct 17, 2017
- Finalized first version of html output · 404dd95a
  Kautsar, Satria authored 7 years ago
  
  404dd95a
Oct 16, 2017
- Minor change: silence info on whether a bgc is in a contig edge unless given the -v parameter · c9e6c580
  Jorge Navarro Muñoz authored 7 years ago
  
  c9e6c580
- Bugfix: forgot to output startA,startB values for totally unrelated BGC pairs · d99cf141
  Jorge Navarro Muñoz authored 7 years ago
  
  d99cf141
- template generation for html output · 38509b24
  Kautsar, Satria authored 7 years ago
  
  38509b24
Oct 11, 2017
- Small speedup for LCS + planning for BiG-SCAPE's visualization · 2aacd067
  Jorge Navarro Muñoz authored 7 years ago
  2aacd067
Oct 10, 2017
- New comparison mode and code cleanup · 0c717f82
  Jorge Navarro Muñoz authored 7 years ago
  0c717f82
- Bugfix: GCC calling crashed if there was only a single GCF · dba3b72c
  Jorge Navarro Muñoz authored 7 years ago
  
  dba3b72c
Sep 29, 2017
- Feature: also add Organism info in Network_Annotation · 7f56a8c8
  Jorge Navarro Muñoz authored 7 years ago
  
  7f56a8c8
Sep 28, 2017
- Feature: add taxonomy from original input file into Networks_Annotation · d20d142e
  Jorge Navarro Muñoz authored 7 years ago
  
  d20d142e
Sep 26, 2017
- Improvements and bugfixes · c428ec54
  Jorge Navarro Muñoz authored 7 years ago
  c428ec54
Sep 13, 2017
- LCS: make the code more Python3-compatible · 639cc4f4
  Jorge Navarro Muñoz authored 8 years ago
  
  639cc4f4
- Code cleanup, deleted old files, added (Annotated!) MIBiG reference bgcs (1.3) · 89b869a4
  Jorge Navarro Muñoz authored 8 years ago
  89b869a4
Sep 12, 2017
- change to js writing file to avoid bug in visualization · 49d294b9
  Emzo de los Santos authored 8 years ago
  
  49d294b9
- changed clans clustering based on the changes we discussed: · ace9893a
  Emzo de los Santos authored 8 years ago
  ace9893a
- Python 3 compatible code. With many thanks to Wouter Lokhorst · 00e1dc64
  Jorge Navarro Muñoz authored 8 years ago
  00e1dc64
- BiG-SCAPE: default location for anchor_domains file is same as BiG-SCAPE. Also, · 06c46d74
  Jorge Navarro Muñoz authored 8 years ago
  06c46d74
Sep 07, 2017
- Implement LCS mode. Use to try to cope with fragmented BGCs that may overlap · deba3829
  Jorge Navarro Muñoz authored 8 years ago
  deba3829
Aug 22, 2017
- added code for clustering families into clans · add0c3e0
  Emzo de los Santos authored 8 years ago
  
  add0c3e0
Aug 21, 2017
- Internal: BGC data is now passed using a new 'bgc_data' object instead of a tuple · 02fa4a8d
  Jorge Navarro Muñoz authored 8 years ago
  
  02fa4a8d
Aug 18, 2017
- Parameters: clarified help text of --no_classify parameter (thanks to Giang-Son Nguyen) · f5c1fc2c
  Jorge Navarro Muñoz authored 8 years ago
  
  f5c1fc2c
Aug 10, 2017
- fixed bug in json file generator for gene direction · 1ba0bb33
  Emzo de los Santos authored 8 years ago
  
  1ba0bb33
Aug 08, 2017
- Small improvement: Merged the functions that find and checked input gbks with · cbd1d531
  Jorge Navarro Muñoz authored 8 years ago
  cbd1d531
- Small improvements: Change list of anchor domains to a set for quick checking. · 5d705bdf
  Jorge Navarro Muñoz authored 8 years ago
  5d705bdf
Aug 04, 2017
- fixed bug: typo · 0cd182c1
  Emzo de los Santos authored 8 years ago
  
  0cd182c1
- modified js generating code to include what descriptor of Pfam clans... · 275a4bce
  Emzo de los Santos authored 8 years ago
  275a4bce
Aug 01, 2017
- Bugfix: preserve BGC order data for visualization files · 8525f7ff
  Jorge Navarro Muñoz authored 8 years ago
  
  8525f7ff
Jul 17, 2017
- Calculate distance: slight performance improvement. When checking every domain · 41bacff1
  Jorge Navarro Muñoz authored 8 years ago
  41bacff1
- --hybrids BugFix: fixed bad behaviour of classifier due to typo · 944c2510
  Jorge Navarro Muñoz authored 8 years ago
  944c2510
Jul 11, 2017
- Sorting logic bugfix: avoid adding certain BGCs more than once · 203e0fc1
  Jorge Navarro Muñoz authored 8 years ago
  203e0fc1
Jul 10, 2017
- Sorting logic: extended hybrids mode bugfix; Take 'banned classes' into account · de0ac5a2
  Jorge Navarro Muñoz authored 8 years ago
  
  de0ac5a2
Jul 07, 2017
- Sorting logic: Extend --hybrids mode to bin BGCs with mixed classes from Others · a55e3656
  Jorge Navarro Muñoz authored 8 years ago
  a55e3656
- Renamed DDS ('Domain Duplication Score') for DSS ('Domain Sequence Similarity') · 45ce1223
  Jorge Navarro Muñoz authored 8 years ago
  
  45ce1223
- Renamed 'metagenomic' mode for 'local' mode · 436ea2e6
  Jorge Navarro Muñoz authored 8 years ago
  
  436ea2e6
Jun 02, 2017
- BGC classification: also enable --banned_classes for --samples + --mix case · 34aeb739
  Jorge Navarro Muñoz authored 8 years ago
  
  34aeb739
- BGC classification: allow banned classes in --mix mode · 519f963e
  Jorge Navarro Muñoz authored 8 years ago
  
  519f963e
- BGC classification: fix blank spaces in 'product' qualifier in input files · 98316a03
  Jorge Navarro Muñoz authored 8 years ago
  
  98316a03
Jun 01, 2017
- Fixed small bug when reporting multi-product input files · c11b1e9d
  Jorge Navarro Muñoz authored 8 years ago
  
  c11b1e9d
May 31, 2017
- Bugfix: Pick one (and not both) Pfam domain in case they have the same score. · cdd77652
  Jorge Navarro Muñoz authored 8 years ago
  cdd77652