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# -*- coding: utf-8 -*-
# Copyright 2011 by Andreas Wilm. All rights reserved.
# Based on ClustalW wrapper copyright 2009 by Cymon J. Cox.
#
# Wrapper for Clustal Omega by Andreas Wilm (2011). Used _Clustalw.py
# as template.
#
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Command line wrapper for the multiple alignment program Clustal Omega.
"""
from __future__ import print_function
from Bio.Application import _Option, _Switch, AbstractCommandline
class ClustalOmegaCommandline(AbstractCommandline):
"""Command line wrapper for clustal omega
http://www.clustal.org/omega
Example:
--------
>>> from Bio.Align.Applications import ClustalOmegaCommandline
>>> in_file = "unaligned.fasta"
>>> out_file = "aligned.fasta"
>>> clustalomega_cline = ClustalOmegaCommandline(infile=in_file, outfile=out_file, verbose=True, auto=True)
>>> print(clustalomega_cline)
clustalo -i unaligned.fasta -o aligned.fasta --auto -v
You would typically run the command line with clustalomega_cline() or via
the Python subprocess module, as described in the Biopython tutorial.
Citation:
---------
Sievers F, Wilm A, Dineen DG, Gibson TJ, Karplus K, Li W, Lopez R,
McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG (2011).
Fast, scalable generation of high-quality protein multiple
sequence alignments using Clustal Omega.
Molecular Systems Biology 7:539 doi:10.1038/msb.2011.75
Last checked against versions: 1.2.0
"""
def __init__(self, cmd="clustalo", **kwargs):
# order parameters in the same order as clustalo --help
self.parameters = \
[
# Sequence Input
_Option(["-i", "--in", "--infile", "infile"],
"Multiple sequence input file",
filename=True,
equate=False),
_Option(["--hmm-in", "HMM input", "hmm_input"],
"HMM input files",
filename=True,
equate=False),
_Switch(["--dealign", "dealign"],
"Dealign input sequences"),
_Option(["--profile1", "--p1", "profile1"],
"Pre-aligned multiple sequence file (aligned columns will be kept fix).",
filename=True,
equate=False),
_Option(["--profile2", "--p2", "profile2"],
"Pre-aligned multiple sequence file (aligned columns will be kept fix).",
filename=True,
equate=False),
_Option(["-t", "--seqtype", "seqtype"],
"{Protein, RNA, DNA} Force a sequence type (default: auto).",
equate=False,
checker_function=lambda x: x in ["protein", "rna", "dna",
"Protein", "RNA", "DNA",
"PROTEIN"]),
_Switch(["--is-profile", "isprofile"],
"disable check if profile, force profile (default no)"),
_Option(["--infmt", "infmt"],
"""Forced sequence input file format (default: auto)
Allowed values: a2m, fa[sta], clu[stal], msf, phy[lip], selex, st[ockholm], vie[nna]
""",
equate=False,
checker_function=lambda x: x in ["a2m", "fa", "fasta",
"clu", "clustal",
"msf",
"phy", "phylip",
"selex",
"st", "stockholm",
"vie", "vienna"]),
# Clustering
_Option(["--distmat-in", "distmat_in"],
"Pairwise distance matrix input file (skips distance computation).",
filename=True,
equate=False),
_Option(["--distmat-out", "distmat_out"],
"Pairwise distance matrix output file.",
filename=True,
equate=False),
_Option(["--guidetree-in", "guidetree_in"],
"Guide tree input file (skips distance computation and guide-tree clustering step).",
filename=True,
equate=False),
_Option(["--guidetree-out", "guidetree_out"],
"Guide tree output file.",
filename=True,
equate=False),
_Switch(["--full", "distmat_full"],
"Use full distance matrix for guide-tree calculation (slow; mBed is default)"),
_Switch(["--full-iter", "distmat_full_iter"],
"Use full distance matrix for guide-tree calculation during iteration (mBed is default)"),
_Option(["--cluster-size", "clustersize"],
"soft maximum of sequences in sub-clusters",
checker_function=lambda x: isinstance(x, int)),
_Option(["--clustering-out", "clusteringout"],
"Clustering output file",
filename=True),
_Switch(["--use-kimura", "usekimura"],
"use Kimura distance correction for aligned sequences (default no)"),
_Switch(["--percent-id", "percentid"],
"convert distances into percent identities (default no)"),
# Alignment Output
_Option(["-o", "--out", "--outfile", "outfile"],
"Multiple sequence alignment output file (default: stdout).",
filename=True,
equate=False),
_Option(["--outfmt", "outfmt"],
"MSA output file format:"
" a2m=fa[sta],clu[stal],msf,phy[lip],selex,st[ockholm],vie[nna]"
" (default: fasta).",
equate=False,
checker_function=lambda x: x in ["a2m", "fa", "fasta",
"clu", "clustal",
"msf",
"phy", "phylip",
"selex",
"st", "stockholm",
"vie", "vienna"]),
_Switch(["--residuenumber", "--resno", "residuenumber"],
"in Clustal format print residue numbers (default no)"),
_Option(["--wrap", "wrap"],
"number of residues before line-wrap in output",
checker_function=lambda x: isinstance(x, int)),
_Option(["--output-order", "outputorder"],
"MSA output order like in input/guide-tree",
checker_function=lambda x: x in ["input-order", "tree-order"]),
# Iteration
_Option(["--iterations", "--iter", "iterations"],
"Number of (combined guide-tree/HMM) iterations",
equate=False,
checker_function=lambda x: isinstance(x, int)),
_Option(["--max-guidetree-iterations", "max_guidetree_iterations"],
"Maximum number of guidetree iterations",
equate=False,
checker_function=lambda x: isinstance(x, int)),
_Option(["--max-hmm-iterations", "max_hmm_iterations"],
"Maximum number of HMM iterations",
equate=False,
checker_function=lambda x: isinstance(x, int)),
# Limits (will exit early, if exceeded):
_Option(["--maxnumseq", "maxnumseq"],
"Maximum allowed number of sequences",
equate=False,
checker_function=lambda x: isinstance(x, int)),
_Option(["--maxseqlen", "maxseqlen"],
"Maximum allowed sequence length",
equate=False,
checker_function=lambda x: isinstance(x, int)),
# Miscellaneous:
_Switch(["--auto", "auto"],
"Set options automatically (might overwrite some of your options)"),
_Option(["--threads", "threads"],
"Number of processors to use",
equate=False,
checker_function=lambda x: isinstance(x, int)),
_Option(["-l", "--log", "log"],
"Log all non-essential output to this file.",
filename=True,
equate=False),
_Switch(["-h", "--help", "help"],
"Print help and exit."),
_Switch(["-v", "--verbose", "verbose"],
"Verbose output"),
_Switch(["--version", "version"],
"Print version information and exit"),
_Switch(["--long-version", "long_version"],
"Print long version information and exit"),
_Switch(["--force", "force"],
"Force file overwriting."),
]
AbstractCommandline.__init__(self, cmd, **kwargs)
if __name__ == "__main__":
from Bio._utils import run_doctest
run_doctest()
|
