# -*- 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): u"""Command line wrapper for XXmotif. http://xxmotif.genzentrum.lmu.de/ Notes ----- Last checked against version: 1.3 References ---------- 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, Genome Res. 23: 181–194 (2013) Examples -------- >>> 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. """ def __init__(self, cmd="XXmotif", **kwargs): """Initialize the class.""" # 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()