From 76efefe7ea3cfd6cae8347a21379e2f1cdaf886e Mon Sep 17 00:00:00 2001
From: "Workum, Dirk-Jan van" <dirk-jan.vanworkum@wur.nl>
Date: Wed, 9 Mar 2022 12:59:25 +0000
Subject: [PATCH] small improvement to running fasttree
---
.../pangenome/MultipleSequenceAlignment.java | 25 +++++++++++++------
1 file changed, 18 insertions(+), 7 deletions(-)
diff --git a/src/main/java/nl/wur/bif/pantools/pangenome/MultipleSequenceAlignment.java b/src/main/java/nl/wur/bif/pantools/pangenome/MultipleSequenceAlignment.java
index 95c5984cd..e70796040 100644
--- a/src/main/java/nl/wur/bif/pantools/pangenome/MultipleSequenceAlignment.java
+++ b/src/main/java/nl/wur/bif/pantools/pangenome/MultipleSequenceAlignment.java
@@ -1585,7 +1585,7 @@ public class MultipleSequenceAlignment {
String output = outPath + "nuc" + dot + "newick";
if (!check_if_file_exists(output)) {
- Future<?> f = es.submit(new runFasttree(input, output));
+ Future<?> f = es.submit(new runFasttree(input, output, true));
futures.add(f);
}
}
@@ -1595,7 +1595,7 @@ public class MultipleSequenceAlignment {
String output = outPath + "prot" + dot + "newick";
if (!check_if_file_exists(output)) {
- Future<?> f = es.submit(new runFasttree(input, output));
+ Future<?> f = es.submit(new runFasttree(input, output, false));
futures.add(f);
}
}
@@ -2308,17 +2308,24 @@ public class MultipleSequenceAlignment {
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) {
+ 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 fasttreeCommand = "FastTree " +
- input +
- " 1> " +
- output;
+ String fasttree = "FastTree ";
+ if (isNucleotide) {
+ fasttree += "-nt ";
+ }
+ String fasttreeCommand = fasttree + input +
+ " 1> " + output +
+ " 2> " + log;
if (LOG) {
System.out.println(fasttreeCommand);
@@ -2326,6 +2333,10 @@ public class MultipleSequenceAlignment {
runCommand(fasttreeCommand); //run FastTree
+ if (!LOG) {
+ delete_file_full_path(log);
+ }
+
return "Starting alignment of " + input;
}
--
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