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8e93363 Feb 8, 2012
executable file 31 lines (21 sloc) 778 Bytes
#!/usr/bin/env python
from subprocess import Popen,PIPE
import sys,re
def muscle(seqs,nohead=False):
if nohead:
label_seqs = list(enumerate(seqs))
label_seqs = zip(seqs[:-1:2],seqs[1::2])
mh = Popen(['muscle'],stdin=PIPE,stderr=PIPE,stdout=PIPE)
mh.stdin.write('\n'.join(['>%s\n%s' % (l,s) for l,s in label_seqs]))
alnstr = mh.communicate()[0]
csep = re.sub(r'>(.+?)\n',r',\1,',alnstr).replace('\n','')[1:]
if nohead:
seqli = csep.split(',')
return [seq for idx,seq in sorted(zip([int(i) for i in seqli[::2]],seqli[1::2]))]
return csep
#return ','.join(alnstr.strip().replace('\n','').split('>'))
if __name__ == '__main__':
seqs = sys.argv[1].split(',')
print muscle(seqs)
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