needle_ex.py

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()