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

[charlie]

Thanks Brad. Sounds Good.

On Fri, Feb 19, 2010 at 5:58 AM, Brad Chapman <chapmanb at 50mail.com> wrote:

> Li;
>
> > 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
>
> For Emboss commandline options that take two different inputs, like
> needle, I don't know of a way to pass them in via standard input.
> My approach would be to write to a temporary file for the input
> sequences. A fully worked example is here:
>
> http://gist.github.com/308708
>
> and pasted below.
>
> For your own debugging purposes,you should avoid redirecting stderr to
> the subprocess PIPE. Emboss will write out error messages about what
> is wrong with the commandline, and they get ignored silently.
>
> Hope this helps,
> Brad
>
>
> import os
> import subprocess
> import tempfile
>
> from Bio import SeqIO
> from Bio.Emboss.Applications import NeedleCommandline
>
> # read in file from somewhere
> in_file = os.path.join("Tests", "NeuralNetwork", "enolase.fasta")
> in_handle = open(in_file)
> gen = SeqIO.parse(in_handle, "fasta")
> a = gen.next()
> a.id = "1"
> b = gen.next()
> b.id = "2"
>
> # create temporary file
> (_, tmp_file) = tempfile.mkstemp()
> tmp_handle = open(tmp_file, "w")
> SeqIO.write([a, b], tmp_handle, 'fasta')
> tmp_handle.close()
>
> # run needle
> cline = NeedleCommandline( gapopen=10, gapextend=.5, outfile='stdout',
>        asequence='%s:%s' % (tmp_file, a.id),
>        bsequence='%s:%s' % (tmp_file, b.id))
> child = subprocess.Popen(str(cline), shell=True, stdout=subprocess.PIPE,)
> child.wait()
> os.remove(tmp_file)
> print child.returncode
>
> print child.stdout.read()
>