# Copyright 2012 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 motif finding program XXmotif.""" import os from Bio.Application import _Argument from Bio.Application import _Option from Bio.Application import _Switch from Bio.Application import AbstractCommandline class XXmotifCommandline(AbstractCommandline): """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()