6
+ − 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 """Compare overlap of a transcript list and list of read, and get some info depending on the coverage"""
+ − 32
+ − 33 import os
+ − 34 from optparse import OptionParser
+ − 35 from commons.core.parsing.SequenceListParser import *
+ − 36 from commons.core.writer.Gff3Writer import *
+ − 37 from SMART.Java.Python.mySql.MySqlConnection import *
+ − 38 from SMART.Java.Python.structure.TranscriptListsComparator import *
+ − 39 from SMART.Java.Python.misc.RPlotter import *
+ − 40 from SMART.Java.Python.misc.Progress import *
+ − 41
+ − 42
+ − 43 if __name__ == "__main__":
+ − 44
+ − 45 # parse command line
+ − 46 description = "Get Info per Coverage v1.0.1: Get a list of information clustered by the density of the coverage on a genome. [Category: Personnal]"
+ − 47
+ − 48 parser = OptionParser(description = description)
+ − 49 parser.add_option("-i", "--input1", dest="inputFileName1", action="store", type="string", help="input file 1 [compulsory] [format: file in transcript format given by -f]")
+ − 50 parser.add_option("-f", "--format1", dest="format1", action="store", type="string", help="format of file 1 [compulsory] [format: transcript file format]")
+ − 51 parser.add_option("-j", "--input2", dest="inputFileName2", action="store", type="string", help="input file 2 [compulsory] [format: file in transcript format given by -g]")
+ − 52 parser.add_option("-g", "--format2", dest="format2", action="store", type="string", help="format of file 2 [compulsory] [format: transcript file format]")
+ − 53 parser.add_option("-o", "--output", dest="output", action="store", default=None, type="string", help="output file [compulsory] [format: output file in TXT format]")
+ − 54 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
+ − 55 parser.add_option("-l", "--log", dest="log", action="store", default=None, type="string", help="write a log file [format: bool] [default: false]")
+ − 56 (options, args) = parser.parse_args()
+ − 57
+ − 58 logHandle = None
+ − 59 if options.log != None:
+ − 60 logHandle = open(options.log, "w")
+ − 61
+ − 62 transcriptContainer1 = TranscriptContainer(options.inputFileName1, options.format1, options.verbosity)
+ − 63 transcriptContainer2 = TranscriptContainer(options.inputFileName2, options.format2, options.verbosity)
+ − 64
+ − 65 transcriptListComparator = TranscriptListsComparator(logHandle, options.verbosity)
+ − 66 transcriptListComparator.restrictToStart(transcriptListComparator.REFERENCE, 10)
+ − 67 transcriptListComparator.getColinearOnly(True)
+ − 68 transcriptListComparator.computeOddsPerTranscript(True)
+ − 69 transcriptListComparator.setInputTranscriptContainer(transcriptListComparator.QUERY, transcriptContainer1)
+ − 70 transcriptListComparator.setInputTranscriptContainer(transcriptListComparator.REFERENCE, transcriptContainer2)
+ − 71 transcriptListComparator.compareTranscriptList()
+ − 72 transcriptTables = transcriptListComparator.getOutputTables()
+ − 73
+ − 74 sizesWithIntrons = {}
+ − 75 sizesWithoutIntrons = {}
+ − 76 nbExons = {}
+ − 77 averageSizesWithIntrons = {}
+ − 78 averageSizesWithoutIntrons = {}
+ − 79 averageNbExons = {}
+ − 80 sumSizesWithIntrons = {}
+ − 81 sumSizesWithoutIntrons = {}
+ − 82 sumSizesNbExons = {}
+ − 83 coverages = transcriptListComparator.getOddsPerTranscript()
+ − 84
+ − 85 progress = Progress(transcriptContainer2.getNbTranscripts(), "Reading transcript file again", options.verbosity)
+ − 86 for transcript in transcriptContainer2.getIterator():
+ − 87 if transcript.name in coverages:
+ − 88 if transcript.getSizeWithIntrons() not in averageSizesWithIntrons:
+ − 89 averageSizesWithIntrons[transcript.getSizeWithIntrons()] = coverages[transcript.name]
+ − 90 else:
+ − 91 averageSizesWithIntrons[transcript.getSizeWithIntrons()] += coverages[transcript.name]
+ − 92 if transcript.getSizeWithIntrons() not in sumSizesWithIntrons:
+ − 93 sumSizesWithIntrons[transcript.getSizeWithIntrons()] = 1
+ − 94 else:
+ − 95 sumSizesWithIntrons[transcript.getSizeWithIntrons()] += 1
+ − 96 if transcript.getSize() not in averageSizesWithoutIntrons:
+ − 97 averageSizesWithoutIntrons[transcript.getSize()] = coverages[transcript.name]
+ − 98 else:
+ − 99 averageSizesWithoutIntrons[transcript.getSize()] += coverages[transcript.name]
+ − 100 if transcript.getSize() not in sumSizesWithoutIntrons:
+ − 101 sumSizesWithoutIntrons[transcript.getSize()] = 1
+ − 102 else:
+ − 103 sumSizesWithoutIntrons[transcript.getSize()] += 1
+ − 104 if transcript.getNbExons() not in averageNbExons:
+ − 105 averageNbExons[transcript.getNbExons()] = coverages[transcript.name]
+ − 106 else:
+ − 107 averageNbExons[transcript.getNbExons()] += coverages[transcript.name]
+ − 108 if transcript.getNbExons() not in sumSizesNbExons:
+ − 109 sumSizesNbExons[transcript.getNbExons()] = 1
+ − 110 else:
+ − 111 sumSizesNbExons[transcript.getNbExons()] += 1
+ − 112 sizesWithIntrons[transcript.name] = (transcript.getSizeWithIntrons(), coverages[transcript.name])
+ − 113 sizesWithoutIntrons[transcript.name] = (transcript.getSize(), coverages[transcript.name])
+ − 114 nbExons[transcript.name] = (transcript.getNbExons(), coverages[transcript.name])
+ − 115 progress.inc()
+ − 116 progress.done()
+ − 117
+ − 118 plotterSizeWithIntrons = RPlotter("%sWithIntrons.png" % (options.output), options.verbosity)
+ − 119 plotterSizeWithIntrons.setPoints(True)
+ − 120 plotterSizeWithIntrons.setMaximumX(10000)
+ − 121 plotterSizeWithIntrons.setMaximumY(1000)
+ − 122 plotterSizeWithIntrons.setLog("y")
+ − 123 plotterSizeWithIntrons.addLine(sizesWithIntrons)
+ − 124 plotterSizeWithIntrons.plot()
+ − 125
+ − 126 plotterSizeWithoutIntrons = RPlotter("%sWithoutIntrons.png" % (options.output), options.verbosity)
+ − 127 plotterSizeWithoutIntrons.setPoints(True)
+ − 128 plotterSizeWithoutIntrons.setMaximumX(10000)
+ − 129 plotterSizeWithoutIntrons.setMaximumY(1000)
+ − 130 plotterSizeWithoutIntrons.setLog("y")
+ − 131 plotterSizeWithoutIntrons.addLine(sizesWithoutIntrons)
+ − 132 plotterSizeWithoutIntrons.plot()
+ − 133
+ − 134 plotterNbExons = RPlotter("%sNbExons.png" % (options.output), options.verbosity)
+ − 135 plotterNbExons.setPoints(True)
+ − 136 plotterNbExons.addLine(nbExons)
+ − 137 plotterNbExons.plot()
+ − 138
+ − 139 for element in averageSizesWithIntrons:
+ − 140 averageSizesWithIntrons[element] = int(float(averageSizesWithIntrons[element]) / sumSizesWithIntrons[element])
+ − 141 plotterAverageSizeWithIntrons = RPlotter("%sAverageWithIntrons.png" % (options.output), options.verbosity)
+ − 142 plotterAverageSizeWithIntrons.setMaximumX(10000)
+ − 143 plotterAverageSizeWithIntrons.setMaximumY(1000)
+ − 144 plotterAverageSizeWithIntrons.setLog("y")
+ − 145 plotterAverageSizeWithIntrons.addLine(averageSizesWithIntrons)
+ − 146 plotterAverageSizeWithIntrons.plot()
+ − 147 print "min/avg/med/max sizes with introns: %d/%.2f/%.1f/%d" % Utils.getMinAvgMedMax(averageSizesWithIntrons)
+ − 148
+ − 149 for element in averageSizesWithoutIntrons:
+ − 150 averageSizesWithoutIntrons[element] = int(float(averageSizesWithoutIntrons[element]) / sumSizesWithoutIntrons[element])
+ − 151 plotterAverageSizeWithoutIntrons = RPlotter("%sAverageWithoutIntrons.png" % (options.output), options.verbosity)
+ − 152 plotterAverageSizeWithoutIntrons.setMaximumX(10000)
+ − 153 plotterAverageSizeWithoutIntrons.setMaximumY(1000)
+ − 154 plotterAverageSizeWithoutIntrons.setLog("y")
+ − 155 plotterAverageSizeWithoutIntrons.addLine(averageSizesWithoutIntrons)
+ − 156 plotterAverageSizeWithoutIntrons.plot()
+ − 157 print "min/avg/med/max sizes without introns: %d/%.2f/%.1f/%d" % Utils.getMinAvgMedMax(averageSizesWithoutIntrons)
+ − 158
+ − 159 for element in averageNbExons:
+ − 160 averageNbExons[element] = int(float(averageNbExons[element]) / sumSizesNbExons[element])
+ − 161 plotterAverageNbExons = RPlotter("%sAverageNbExons.png" % (options.output), options.verbosity)
+ − 162 plotterAverageNbExons.addLine(averageNbExons)
+ − 163 plotterAverageNbExons.plot()
+ − 164 print "min/avg/med/max # exons: %d/%.2f/%.1f/%d" % Utils.getMinAvgMedMax(averageNbExons)
+ − 165
+ − 166 if options.log:
+ − 167 logHandle.close()
