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1 #! /usr/bin/env python
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2 #
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3 # Copyright INRA-URGI 2009-2011
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4 #
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5 # This software is governed by the CeCILL license under French law and
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6 # abiding by the rules of distribution of free software. You can use,
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7 # modify and/ or redistribute the software under the terms of the CeCILL
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8 # license as circulated by CEA, CNRS and INRIA at the following URL
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9 # "http://www.cecill.info".
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10 #
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11 # As a counterpart to the access to the source code and rights to copy,
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12 # modify and redistribute granted by the license, users are provided only
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13 # with a limited warranty and the software's author, the holder of the
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14 # economic rights, and the successive licensors have only limited
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15 # liability.
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16 #
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17 # In this respect, the user's attention is drawn to the risks associated
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18 # with loading, using, modifying and/or developing or reproducing the
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19 # software by the user in light of its specific status of free software,
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20 # that may mean that it is complicated to manipulate, and that also
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21 # therefore means that it is reserved for developers and experienced
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22 # professionals having in-depth computer knowledge. Users are therefore
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23 # encouraged to load and test the software's suitability as regards their
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24 # requirements in conditions enabling the security of their systems and/or
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25 # data to be ensured and, more generally, to use and operate it in the
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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
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29 # knowledge of the CeCILL license and that you accept its terms.
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30 #
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31 import os, random
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32 from optparse import OptionParser, OptionGroup
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33 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
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34 from SMART.Java.Python.misc.Progress import Progress
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35 from commons.core.writer.Gff3Writer import Gff3Writer
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36
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37
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38 class CoverageComputer(object):
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39
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40 def __init__(self, verbosity = 0):
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41 self.verbosity = verbosity
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42 self.queryReader = None
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43 self.referenceReader = None
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44 self.outputWriter = None
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45 self.introns = False
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46 self.nbNucleotides = 0
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47 self.nbCovered = 0
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48
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49 def setInputQueryFile(self, fileName, format):
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50 self.queryReader = TranscriptContainer(fileName, format, self.verbosity-1)
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51
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52 def setInputReferenceFile(self, fileName, format):
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53 self.referenceReader = TranscriptContainer(fileName, format, self.verbosity-1)
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54
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55 def includeIntrons(self, boolean):
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56 self.introns = boolean
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57
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58 def setOutputFileName(self, fileName, title="S-MART", feature="transcript", featurePart="exon"):
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59 self.outputWriter = Gff3Writer(fileName, self.verbosity-1)
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60 self.outputWriter.setTitle(title)
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61 self.outputWriter.setFeature(feature)
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62 self.outputWriter.setFeaturePart(featurePart)
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63
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64 def readReference(self):
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65 self.coveredRegions = {}
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66 progress = Progress(self.referenceReader.getNbTranscripts(), "Reading reference file", self.verbosity-1)
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67 for transcript in self.referenceReader.getIterator():
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68 chromosome = transcript.getChromosome()
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69 if chromosome not in self.coveredRegions:
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70 self.coveredRegions[chromosome] = {}
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71 if self.introns:
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72 transcript.removeExons()
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73 for exon in transcript.getExons():
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74 for position in range(exon.getStart(), exon.getEnd()+1):
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75 self.coveredRegions[chromosome][position] = 1
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76 progress.inc()
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77 progress.done()
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78
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79 def readQuery(self):
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80 progress = Progress(self.queryReader.getNbTranscripts(), "Reading query file", self.verbosity-1)
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81 for transcript in self.queryReader.getIterator():
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82 progress.inc()
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83 chromosome = transcript.getChromosome()
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84 if chromosome not in self.coveredRegions:
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85 continue
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86 if self.introns:
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87 transcript.removeExons()
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88 for exon in transcript.getExons():
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89 for position in range(exon.getStart(), exon.getEnd()+1):
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90 self.nbNucleotides += 1
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91 self.nbCovered += self.coveredRegions[chromosome].get(position, 0)
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92 progress.done()
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93
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94 def write(self):
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95 progress = Progress(self.queryReader.getNbTranscripts(), "Writing output file", self.verbosity-1)
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96 for transcript in self.queryReader.getIterator():
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97 chromosome = transcript.getChromosome()
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98 if self.introns:
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99 transcript.removeExons()
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100 size = transcript.getSize()
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101 coverage = 0
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102 for exon in transcript.getExons():
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103 for position in range(exon.getStart(), exon.getEnd()+1):
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104 coverage += self.coveredRegions[chromosome].get(position, 0)
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105 transcript.setTagValue("coverage", 0 if size == 0 else float(coverage) / size * 100)
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106 self.outputWriter.addTranscript(transcript)
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107 progress.inc()
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108 progress.done()
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109
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110 def sumUp(self):
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111 print "%d nucleotides in query, %d (%.f%%) covered" % (self.nbNucleotides, self.nbCovered, 0 if self.nbNucleotides == 0 else float(self.nbCovered) / self.nbNucleotides * 100)
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112
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113 def run(self):
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114 self.readReference()
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115 self.readQuery()
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116 if self.outputWriter != None:
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117 self.write()
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118 self.sumUp()
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119
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120
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121 if __name__ == "__main__":
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122
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123 # parse command line
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124 description = "Compute Coverage v1.0.1: Compute the coverage of a set with respect to another set. [Category: Personal]"
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125
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126 parser = OptionParser(description = description)
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127 parser.add_option("-i", "--input1", dest="inputFileName1", action="store", type="string", help="input query file [compulsory] [format: file in transcript format given by -f]")
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128 parser.add_option("-f", "--format1", dest="format1", action="store", type="string", help="format of the first file [compulsory] [format: transcript file format]")
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129 parser.add_option("-j", "--input2", dest="inputFileName2", action="store", type="string", help="input reference file [compulsory] [format: file in transcript format given by -f]")
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130 parser.add_option("-g", "--format2", dest="format2", action="store", type="string", help="format of the second file [compulsory] [format: transcript file format]")
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131 parser.add_option("-t", "--introns", dest="introns", action="store_true", default=False, help="also include introns [format: boolean] [default: false]")
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132 parser.add_option("-o", "--output", dest="outputFileName", action="store", default=None, type="string", help="output file [format: output file in GFF3 format]")
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133 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [default: 1] [format: int]")
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134 (options, args) = parser.parse_args()
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135
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136 computer = CoverageComputer(options.verbosity)
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137 computer.setInputQueryFile(options.inputFileName1, options.format1)
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138 computer.setInputReferenceFile(options.inputFileName2, options.format2)
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139 computer.includeIntrons(options.introns)
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140 computer.setOutputFileName(options.outputFileName)
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141 computer.run()
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142
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