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+ − 1 #! /usr/bin/env python
+ − 2 #
+ − 3 # Copyright INRA-URGI 2009-2010
+ − 4 #
+ − 5 # This software is governed by the CeCILL license under French law and
+ − 6 # abiding by the rules of distribution of free software. You can use,
+ − 7 # modify and/ or redistribute the software under the terms of the CeCILL
+ − 8 # license as circulated by CEA, CNRS and INRIA at the following URL
+ − 9 # "http://www.cecill.info".
+ − 10 #
+ − 11 # As a counterpart to the access to the source code and rights to copy,
+ − 12 # modify and redistribute granted by the license, users are provided only
+ − 13 # with a limited warranty and the software's author, the holder of the
+ − 14 # economic rights, and the successive licensors have only limited
+ − 15 # liability.
+ − 16 #
+ − 17 # In this respect, the user's attention is drawn to the risks associated
+ − 18 # with loading, using, modifying and/or developing or reproducing the
+ − 19 # software by the user in light of its specific status of free software,
+ − 20 # that may mean that it is complicated to manipulate, and that also
+ − 21 # therefore means that it is reserved for developers and experienced
+ − 22 # professionals having in-depth computer knowledge. Users are therefore
+ − 23 # encouraged to load and test the software's suitability as regards their
+ − 24 # requirements in conditions enabling the security of their systems and/or
+ − 25 # data to be ensured and, more generally, to use and operate it in the
+ − 26 # same conditions as regards security.
+ − 27 #
+ − 28 # The fact that you are presently reading this means that you have had
+ − 29 # knowledge of the CeCILL license and that you accept its terms.
+ − 30 #
+ − 31 """
+ − 32 Cluster the data into regions (defined by size and overlap with next region) and keep only highest peaks.
+ − 33 """
+ − 34
+ − 35 from optparse import OptionParser
+ − 36 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
+ − 37 from commons.core.parsing.WigParser import WigParser
+ − 38 from SMART.Java.Python.misc.Progress import Progress
+ − 39 from SMART.Java.Python.misc.RPlotter import RPlotter
+ − 40
+ − 41
+ − 42 if __name__ == "__main__":
+ − 43
+ − 44 # parse command line
+ − 45 description = "Get WIG Data v1.0.2: Compute the average data around some genomic coordinates using WIG files (thus covering a large proportion of the genome). [Category: WIG Tools]"
+ − 46
+ − 47 parser = OptionParser(description = description)
+ − 48 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in transcript format given by -f]")
+ − 49 parser.add_option("-f", "--inputFormat", dest="inputFormat", action="store", type="string", help="format of the input file [compulsory] [format: transcript file format]")
+ − 50 parser.add_option("-w", "--wig", dest="wig", action="store", type="string", help="wig file name [compulsory] [format: file in WIG format]")
+ − 51 parser.add_option("-d", "--distance", dest="distance", action="store", default=1000, type="int", help="distance around position [compulsory] [format: int] [default: 1000]")
+ − 52 parser.add_option("-s", "--strands", dest="strands", action="store_true", default=False, help="consider both strands separately [format: boolean] [default: False]")
+ − 53 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in PNG format]")
+ − 54 parser.add_option("-a", "--default", dest="defaultValue", action="store", default=0.0, type="float", help="default value (when value is NA) [default: 0.0] [format: float]")
+ − 55 parser.add_option("-l", "--log", dest="log", action="store_true", default=False, help="use log scale for y-axis [format: boolean] [default: False]")
+ − 56 parser.add_option("-k", "--keep", dest="keep", action="store_true", default=False, help="keep temporary files [format: boolean] [default: False]")
+ − 57 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
+ − 58 (options, args) = parser.parse_args()
+ − 59
+ − 60 # create parsers and writers
+ − 61 transcriptParser = TranscriptContainer(options.inputFileName, options.inputFormat, options.verbosity)
+ − 62 wigParser = WigParser(options.wig)
+ − 63 wigParser.setStrands(options.strands)
+ − 64 wigParser.setDefaultValue(options.defaultValue)
+ − 65
+ − 66 # allocate data
+ − 67 strands = (1, -1) if options.strands else (1, )
+ − 68 values = {}
+ − 69 for strand in strands:
+ − 70 values[strand] = dict([(i, 0.0) for i in range(-options.distance, options.distance+1)])
+ − 71
+ − 72 # read transcripts
+ − 73 progress = Progress(transcriptParser.getNbTranscripts(), "Parsing %s" % (options.inputFileName), options.verbosity)
+ − 74 for transcript in transcriptParser.getIterator():
+ − 75 transcript.removeExons()
+ − 76 transcript.restrictStart(2)
+ − 77 transcript.extendStart(options.distance)
+ − 78 transcript.extendEnd(options.distance-1)
+ − 79 theseValues = transcript.extractWigData(wigParser)
+ − 80 if len(strands) == 1:
+ − 81 theseValues = {1: theseValues}
+ − 82 for strand in strands:
+ − 83 if len(theseValues[strand]) < 2 * options.distance + 1:
+ − 84 theseValues[strand] = [options.defaultValue] * (2 * options.distance + 1 - len(theseValues[strand])) + theseValues[strand]
+ − 85 if len(theseValues[strand]) != 2 * options.distance + 1:
+ − 86 raise Exception("Got something wrong with the size of the WIG data concerning %s: %d found instead of %d" % (transcript, len(theseValues[strand]), 2 * options.distance + 1))
+ − 87 for i in range(-options.distance, options.distance+1):
+ − 88 values[strand][i] += theseValues[strand][i + options.distance]
+ − 89 progress.inc()
+ − 90 progress.done()
+ − 91
+ − 92 for strand in strands:
+ − 93 for i in range(-options.distance, options.distance+1):
+ − 94 values[strand][i] /= transcriptParser.getNbTranscripts() * strand
+ − 95
+ − 96 # draw plot
+ − 97 plotter = RPlotter(options.outputFileName, options.verbosity, options.keep)
+ − 98 plotter.setXLabel("Distance")
+ − 99 plotter.setYLabel("WigValue")
+ − 100 for strand in strands:
+ − 101 plotter.addLine(values[strand])
+ − 102 if options.log:
+ − 103 plotter.setLog("y")
+ − 104 plotter.plot()
+ − 105
