From 32d04dbedb62334f9ae410adb53334496c0965fc Mon Sep 17 00:00:00 2001
From: Tobias Schmidt <tobias.schmidt@unibas.ch>
Date: Wed, 3 Nov 2010 16:27:53 +0100
Subject: [PATCH] Revert "added nopgap flag to clustalw binding"
This reverts commit d1818e3bce3784307ddbe60c50155abd0bb8dc69.
---
modules/bindings/pymod/clustalw.py | 4 +---
1 file changed, 1 insertion(+), 3 deletions(-)
diff --git a/modules/bindings/pymod/clustalw.py b/modules/bindings/pymod/clustalw.py
index e737cea57..f61d4f24f 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, nopgap=False):
+def ClustalW(seq1, seq2=None, clustalw=None, keep_files=False):
clustalw_path=settings.Locate(('clustalw', 'clustalw2'),
explicit_file_name=clustalw)
@@ -32,8 +32,6 @@ def ClustalW(seq1, seq2=None, clustalw=None, keep_files=False, nopgap=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)
--
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