Spaces:
No application file
No application file
File size: 10,382 Bytes
b7731cd |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 |
# 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()
|