Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/SMART/Java/Python/getWigDistance.py @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 #! /usr/bin/env python
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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2 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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3 # Copyright INRA-URGI 2009-2010
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4 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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5 # This software is governed by the CeCILL license under French law and
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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6 # abiding by the rules of distribution of free software. You can use,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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7 # modify and/ or redistribute the software under the terms of the CeCILL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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8 # license as circulated by CEA, CNRS and INRIA at the following URL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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9 # "http://www.cecill.info".
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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10 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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11 # As a counterpart to the access to the source code and rights to copy,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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12 # modify and redistribute granted by the license, users are provided only
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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13 # with a limited warranty and the software's author, the holder of the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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14 # economic rights, and the successive licensors have only limited
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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15 # liability.
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16 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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17 # In this respect, the user's attention is drawn to the risks associated
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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18 # with loading, using, modifying and/or developing or reproducing the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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19 # software by the user in light of its specific status of free software,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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20 # that may mean that it is complicated to manipulate, and that also
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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21 # therefore means that it is reserved for developers and experienced
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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22 # professionals having in-depth computer knowledge. Users are therefore
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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23 # encouraged to load and test the software's suitability as regards their
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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24 # requirements in conditions enabling the security of their systems and/or
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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25 # data to be ensured and, more generally, to use and operate it in the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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26 # same conditions as regards security.
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27 #
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28 # The fact that you are presently reading this means that you have had
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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29 # knowledge of the CeCILL license and that you accept its terms.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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30 #
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31 """
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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32 Cluster the data into regions (defined by size and overlap with next region) and keep only highest peaks.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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33 """
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34
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35 from optparse import OptionParser
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36 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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37 from commons.core.parsing.WigParser import WigParser
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38 from SMART.Java.Python.misc.Progress import Progress
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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39 from SMART.Java.Python.misc.RPlotter import RPlotter
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40
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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41
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42 if __name__ == "__main__":
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43
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44 # parse command line
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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]"
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46
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47 parser = OptionParser(description = description)
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48 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in transcript format given by -f]")
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49 parser.add_option("-f", "--inputFormat", dest="inputFormat", action="store", type="string", help="format of the input file [compulsory] [format: transcript file format]")
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50 parser.add_option("-w", "--wig", dest="wig", action="store", type="string", help="wig file name [compulsory] [format: file in WIG format]")
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51 parser.add_option("-d", "--distance", dest="distance", action="store", default=1000, type="int", help="distance around position [compulsory] [format: int] [default: 1000]")
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52 parser.add_option("-s", "--strands", dest="strands", action="store_true", default=False, help="consider both strands separately [format: boolean] [default: False]")
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53 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in PNG format]")
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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]")
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55 parser.add_option("-l", "--log", dest="log", action="store_true", default=False, help="use log scale for y-axis [format: boolean] [default: False]")
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56 parser.add_option("-k", "--keep", dest="keep", action="store_true", default=False, help="keep temporary files [format: boolean] [default: False]")
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57 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
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58 (options, args) = parser.parse_args()
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59
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60 # create parsers and writers
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61 transcriptParser = TranscriptContainer(options.inputFileName, options.inputFormat, options.verbosity)
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62 wigParser = WigParser(options.wig)
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63 wigParser.setStrands(options.strands)
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64 wigParser.setDefaultValue(options.defaultValue)
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65
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66 # allocate data
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67 strands = (1, -1) if options.strands else (1, )
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68 values = {}
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69 for strand in strands:
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70 values[strand] = dict([(i, 0.0) for i in range(-options.distance, options.distance+1)])
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71
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72 # read transcripts
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73 progress = Progress(transcriptParser.getNbTranscripts(), "Parsing %s" % (options.inputFileName), options.verbosity)
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74 for transcript in transcriptParser.getIterator():
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75 transcript.removeExons()
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76 transcript.restrictStart(2)
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77 transcript.extendStart(options.distance)
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78 transcript.extendEnd(options.distance-1)
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79 theseValues = transcript.extractWigData(wigParser)
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80 if len(strands) == 1:
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81 theseValues = {1: theseValues}
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82 for strand in strands:
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83 if len(theseValues[strand]) < 2 * options.distance + 1:
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84 theseValues[strand] = [options.defaultValue] * (2 * options.distance + 1 - len(theseValues[strand])) + theseValues[strand]
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85 if len(theseValues[strand]) != 2 * options.distance + 1:
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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))
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87 for i in range(-options.distance, options.distance+1):
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88 values[strand][i] += theseValues[strand][i + options.distance]
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89 progress.inc()
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90 progress.done()
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91
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92 for strand in strands:
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93 for i in range(-options.distance, options.distance+1):
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94 values[strand][i] /= transcriptParser.getNbTranscripts() * strand
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95
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96 # draw plot
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97 plotter = RPlotter(options.outputFileName, options.verbosity, options.keep)
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98 plotter.setXLabel("Distance")
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99 plotter.setYLabel("WigValue")
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100 for strand in strands:
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101 plotter.addLine(values[strand])
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102 if options.log:
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103 plotter.setLog("y")
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104 plotter.plot()
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105