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# -*- coding: utf-8 -*-
# Copyright 2012 by Christian Brueffer. All rights reserved.
#
# 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 motif finding program XXmotif."""
from __future__ import print_function
import os
from Bio.Application import AbstractCommandline, _Option, _Switch, _Argument
class XXmotifCommandline(AbstractCommandline):
"""Command line wrapper for XXmotif.
http://xxmotif.genzentrum.lmu.de/
Example:
>>> from Bio.motifs.applications import XXmotifCommandline
>>> out_dir = "results"
>>> in_file = "sequences.fasta"
>>> xxmotif_cline = XXmotifCommandline(outdir=out_dir, seqfile=in_file, revcomp=True)
>>> print(xxmotif_cline)
XXmotif results sequences.fasta --revcomp
You would typically run the command line with xxmotif_cline() or via
the Python subprocess module, as described in the Biopython tutorial.
Citations:
Luehr S, Hartmann H, and Söding J. The XXmotif web server for eXhaustive,
weight matriX-based motif discovery in nucleotide sequences,
Nucleic Acids Res. 40: W104-W109 (2012).
Hartmann H, Guthoehrlein EW, Siebert M., Luehr S, and Söding J. P-value
based regulatory motif discovery using positional weight matrices
(to be published)
Last checked against version: 1.3
"""
def __init__(self, cmd="XXmotif", **kwargs):
# order of parameters is the same as in XXmotif --help
_valid_alphabet = set("ACGTNX")
self.parameters = \
[
_Argument(["outdir", "OUTDIR"],
"output directory for all results",
filename=True,
is_required=True,
# XXmotif currently does not accept spaces in the outdir name
checker_function=lambda x: " " not in x),
_Argument(["seqfile", "SEQFILE"],
"file name with sequences from positive set in FASTA format",
filename=True,
is_required=True,
# XXmotif currently only accepts a pure filename
checker_function=lambda x: os.path.split(x)[0] == ""),
# Options
_Option(["--negSet", "negSet", "NEGSET", "negset"],
"sequence set which has to be used as a reference set",
filename=True,
equate=False),
_Switch(["--zoops", "ZOOPS", "zoops"],
"use zero-or-one occurrence per sequence model (DEFAULT)"),
_Switch(["--mops", "MOPS", "mops"],
"use multiple occurrence per sequence model"),
_Switch(["--oops", "OOPS", "oops"],
"use one occurrence per sequence model"),
_Switch(["--revcomp", "REVCOMP", "revcomp"],
"search in reverse complement of sequences as well (DEFAULT: NO)"),
_Option(["--background-model-order", "background-model-order", "BACKGROUND-MODEL-ORDER",
"background_model_order"],
"order of background distribution (DEFAULT: 2, 8(--negset) )",
checker_function=lambda x: isinstance(x, int),
equate=False),
_Option(["--pseudo", "PSEUDO", "pseudo"],
"percentage of pseudocounts used (DEFAULT: 10)",
checker_function=lambda x: isinstance(x, int),
equate=False),
_Option(["-g", "--gaps", "GAPS", "gaps"],
"maximum number of gaps used for start seeds [0-3] (DEFAULT: 0)",
checker_function=lambda x: x in [0 - 3],
equate=False),
_Option(["--type", "TYPE", "type"],
"defines what kind of start seeds are used (DEFAULT: ALL)"
"possible types: ALL, FIVEMERS, PALINDROME, TANDEM, NOPALINDROME, NOTANDEM",
checker_function=lambda x: x in ["ALL", "all",
"FIVEMERS", "fivemers",
"PALINDROME", "palindrome",
"TANDEM", "tandem",
"NOPALINDROME", "nopalindrome",
"NOTANDEM", "notandem"],
equate=False),
_Option(["--merge-motif-threshold", "merge-motif-threshold", "MERGE-MOTIF-THRESHOLD",
"merge_motif_threshold"],
"defines the similarity threshold for merging motifs (DEFAULT: HIGH)"
"possible modes: LOW, MEDIUM, HIGH",
checker_function=lambda x: x in ["LOW", "low",
"MEDIUM", "medium",
"HIGH", "high"],
equate=False),
_Switch(["--no-pwm-length-optimization", "no-pwm-length-optimization", "NO-PWM-LENGTH-OPTIMIZATION",
"no_pwm_length_optimization"],
"do not optimize length during iterations (runtime advantages)"),
_Option(["--max-match-positions", "max-match-positions", "MAX-MATCH-POSITIONS",
"max_match_positions"],
"max number of positions per motif (DEFAULT: 17, higher values will lead to very long runtimes)",
checker_function=lambda x: isinstance(x, int),
equate=False),
_Switch(["--batch", "BATCH", "batch"],
"suppress progress bars (reduce output size for batch jobs)"),
_Option(["--maxPosSetSize", "maxPosSetSize", "MAXPOSSETSIZE", "maxpossetsize"],
"maximum number of sequences from the positive set used [DEFAULT: all]",
checker_function=lambda x: isinstance(x, int),
equate=False),
# does not make sense in biopython
# _Switch(["--help", "help", "HELP"],
# "print this help page"),
_Option(["--trackedMotif", "trackedMotif", "TRACKEDMOTIF", "trackedmotif"],
"inspect extensions and refinement of a given seed (DEFAULT: not used)",
checker_function=lambda x: any((c in _valid_alphabet) for c in x),
equate=False),
# Using conservation information
_Option(["--format", "FORMAT", "format"],
"defines what kind of format the input sequences have (DEFAULT: FASTA)",
checker_function=lambda x: x in ["FASTA", "fasta",
"MFASTA", "mfasta"],
equate=False),
_Option(["--maxMultipleSequences", "maxMultipleSequences", "MAXMULTIPLESEQUENCES",
"maxmultiplesequences"],
"maximum number of sequences used in an alignment [DEFAULT: all]",
checker_function=lambda x: isinstance(x, int),
equate=False),
# Using localization information
_Switch(["--localization", "LOCALIZATION", "localization"],
"use localization information to calculate combined P-values"
"(sequences should have all the same length)"),
_Option(["--downstream", "DOWNSTREAM", "downstream"],
"number of residues in positive set downstream of anchor point (DEFAULT: 0)",
checker_function=lambda x: isinstance(x, int),
equate=False),
# Start with self defined motif
_Option(["-m", "--startMotif", "startMotif", "STARTMOTIF", "startmotif"],
"Start motif (IUPAC characters)",
checker_function=lambda x: any((c in _valid_alphabet) for c in x),
equate=False),
_Option(["-p", "--profileFile", "profileFile", "PROFILEFILE", "profilefile"],
"profile file",
filename=True,
equate=False),
_Option(["--startRegion", "startRegion", "STARTREGION", "startregion"],
"expected start position for motif occurrences relative to anchor point (--localization)",
checker_function=lambda x: isinstance(x, int),
equate=False),
_Option(["--endRegion", "endRegion", "ENDREGION", "endregion"],
"expected end position for motif occurrences relative to anchor point (--localization)",
checker_function=lambda x: isinstance(x, int),
equate=False),
# XXmotif wrapper options
_Switch(["--XXmasker", "masker"],
"mask the input sequences for homology, repeats and low complexity regions"),
_Switch(["--XXmasker-pos", "maskerpos"],
"mask only the positive set for homology, repeats and low complexity regions"),
_Switch(["--no-graphics", "nographics"],
"run XXmotif without graphical output"),
]
AbstractCommandline.__init__(self, cmd, **kwargs)
if __name__ == "__main__":
from Bio._utils import run_doctest
run_doctest()
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