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#! /usr/bin/env python
##############################################################################
## DendroPy Phylogenetic Computing Library.
##
## Copyright 2010-2015 Jeet Sukumaran and Mark T. Holder.
## All rights reserved.
##
## See "LICENSE.rst" for terms and conditions of usage.
##
## If you use this work or any portion thereof in published work,
## please cite it as:
##
## Sukumaran, J. and M. T. Holder. 2010. DendroPy: a Python library
## for phylogenetic computing. Bioinformatics 26: 1569-1571.
##
##############################################################################
"""
Wrapper around calls to MUSCLE
"""
import dendropy
import subprocess
from dendropy.utility import processio
def muscle_align(char_matrix, muscle_args=None, muscle_path='muscle'):
cmd = [muscle_path]
if muscle_args:
cmd = cmd + muscle_args
p = subprocess.Popen(cmd,
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
stdout, stderr = processio.communicate(p, char_matrix.as_string("fasta"))
if p.returncode:
raise Exception(stderr)
d = char_matrix.__class__.get_from_string(stdout,
"fasta",
taxon_namespace=char_matrix.taxon_namespace)
return d
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