[Biopython] example request for using stdin and stdout with 'needle' in EMBOSS

charlie charlie.xia.fdu at gmail.com
Thu Feb 18 21:35:13 UTC 2010


Hi all,

Wonder if anyone can provide an example for using needle but take stdin as
input and stdout as output within biopython.
I did like this, but it doesn't work.

cline = NeedleCoomandline( gapopen=10, gapextend=.5, outfile='stdout',
asequence='stdin', bsequence='stdout')
child = subprocess.Popen( cline, shell=True, stdout=PIPE, stdin = PIPE,
stderr = PIPE )
SeqIO.write( a, child.stdin, 'fasta')
SeqIO.write( b, child.stdin, 'fasta')
child.stdin.close()
print child.returncode

returncode is None

THanks

Li



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