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| # 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 AbstractCommandline, _Option, _Switch, _Argument | |
| 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() | |