From d1818e3bce3784307ddbe60c50155abd0bb8dc69 Mon Sep 17 00:00:00 2001
From: Tobias Schmidt <tobias.schmidt@unibas.ch>
Date: Fri, 22 Oct 2010 13:13:42 +0200
Subject: [PATCH] added nopgap flag to clustalw binding
---
modules/bindings/pymod/clustalw.py | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/modules/bindings/pymod/clustalw.py b/modules/bindings/pymod/clustalw.py
index f61d4f24f..e737cea57 100644
--- a/modules/bindings/pymod/clustalw.py
+++ b/modules/bindings/pymod/clustalw.py
@@ -3,7 +3,7 @@ from ost import settings, io, seq, LogError
import os
import subprocess
-def ClustalW(seq1, seq2=None, clustalw=None, keep_files=False):
+def ClustalW(seq1, seq2=None, clustalw=None, keep_files=False, nopgap=False):
clustalw_path=settings.Locate(('clustalw', 'clustalw2'),
explicit_file_name=clustalw)
@@ -32,6 +32,8 @@ def ClustalW(seq1, seq2=None, clustalw=None, keep_files=False):
command='%s -infile="%s" -output=fasta -outfile="%s"' % (clustalw_path,
temp_dir.files[0],
out)
+ if nopgap:
+ command+=" -nopgap"
ps=subprocess.Popen(command, shell=True, stdout=subprocess.PIPE)
ps.stdout.readlines()
aln=io.LoadAlignment(out)
--
GitLab