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# Copyright 2013 by Christian Brueffer. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Command line wrapper for the multiple sequence alignment program MSAProbs."""
from Bio.Application import _Argument, _Option, _Switch, AbstractCommandline
class MSAProbsCommandline(AbstractCommandline):
"""Command line wrapper for MSAProbs.
http://msaprobs.sourceforge.net
Notes
-----
Last checked against version: 0.9.7
References
----------
Yongchao Liu, Bertil Schmidt, Douglas L. Maskell: "MSAProbs: multiple
sequence alignment based on pair hidden Markov models and partition
function posterior probabilities". Bioinformatics, 2010, 26(16): 1958 -1964
Examples
--------
>>> from Bio.Align.Applications import MSAProbsCommandline
>>> in_file = "unaligned.fasta"
>>> out_file = "aligned.cla"
>>> cline = MSAProbsCommandline(infile=in_file, outfile=out_file, clustalw=True)
>>> print(cline)
msaprobs -o aligned.cla -clustalw unaligned.fasta
You would typically run the command line with cline() or via
the Python subprocess module, as described in the Biopython tutorial.
"""
def __init__(self, cmd="msaprobs", **kwargs):
"""Initialize the class."""
# order of parameters is the same as in msaprobs -help
self.parameters = [
_Option(
["-o", "--outfile", "outfile"],
"specify the output file name (STDOUT by default)",
filename=True,
equate=False,
),
_Option(
["-num_threads", "numthreads"],
"specify the number of threads used, and otherwise detect automatically",
checker_function=lambda x: isinstance(x, int),
),
_Switch(
["-clustalw", "clustalw"],
"use CLUSTALW output format instead of FASTA format",
),
_Option(
["-c", "consistency"],
"use 0 <= REPS <= 5 (default: 2) passes of consistency transformation",
checker_function=lambda x: isinstance(x, int) and 0 <= x <= 5,
),
_Option(
["-ir", "--iterative-refinement", "iterative_refinement"],
"use 0 <= REPS <= 1000 (default: 10) passes of iterative-refinement",
checker_function=lambda x: isinstance(x, int) and 0 <= x <= 1000,
),
_Switch(["-v", "verbose"], "report progress while aligning (default: off)"),
_Option(
["-annot", "annot"],
"write annotation for multiple alignment to FILENAME",
filename=True,
),
_Switch(
["-a", "--alignment-order", "alignment_order"],
"print sequences in alignment order rather than input order (default: off)",
),
_Option(["-version", "version"], "print out version of MSAPROBS"),
_Argument(["infile"], "Multiple sequence input file", filename=True),
]
AbstractCommandline.__init__(self, cmd, **kwargs)
if __name__ == "__main__":
from Bio._utils import run_doctest
run_doctest()
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