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Commit d1818e3b authored by Tobias Schmidt's avatar Tobias Schmidt
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added nopgap flag to clustalw binding

parent d711f981
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......@@ -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)
......
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