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1 #! /usr/bin/env python
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2 #
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3 # Copyright INRA-URGI 2009-2010
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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
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32 from optparse import OptionParser
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33 from commons.core.parsing.FastaParser import FastaParser
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34 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
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35 from SMART.Java.Python.misc.Progress import Progress
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36 from SMART.Java.Python.misc.RPlotter import RPlotter
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37 from SMART.Java.Python.misc.Utils import *
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38
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39
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40 class GetGenomeCoverage(object):
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41
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42 def __init__(self, verbosity = 1):
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43 self.verbosity = verbosity
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44 self.inputContainer = None
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45 self.referenceParser = None
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46 self.outputFileName = None
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47 self.genomeSize = None
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48 self.coverage = {}
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49 self.distribution = {}
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50
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51
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52 def setInputFile(self, fileName, format):
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53 self.inputContainer = TranscriptContainer(fileName, format, self.verbosity)
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54
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55
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56 def setOutputFile(self, fileName):
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57 self.outputFileName = fileName
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58
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59
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60 def setReference(self, fileName):
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61 self.referenceParser = FastaParser(fileName, self.verbosity)
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62
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63
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64 def getReferenceSizes(self):
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65 self.genomeSize = 0
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66 for chromosome in self.referenceParser.getRegions():
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67 self.genomeSize += self.referenceParser.getSizeOfRegion(chromosome)
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68
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69
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70 def getCoverage(self):
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71 progress = Progress(self.inputContainer.getNbTranscripts(), "Reading reads", self.verbosity)
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72 for transcript in self.inputContainer.getIterator():
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73 chromosome = transcript.getChromosome()
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74 if chromosome not in self.coverage:
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75 self.coverage[chromosome] = {}
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76 for exon in transcript.getExons():
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77 for pos in range(exon.getStart(), exon.getEnd() + 1):
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78 if pos not in self.coverage[chromosome]:
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79 self.coverage[chromosome][pos] = 1
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80 else:
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81 self.coverage[chromosome][pos] += 1
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82 progress.inc()
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83 progress.done()
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84
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85
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86 def getDistribution(self):
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87 nbNucleotides = sum([len(self.coverage[chromosome].keys()) for chromosome in self.coverage])
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88 progress = Progress(nbNucleotides, "Building distribution", self.verbosity)
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89 for chromosome in self.coverage:
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90 for num in self.coverage[chromosome].values():
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91 if num not in self.distribution:
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92 self.distribution[num] = 1
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93 else:
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94 self.distribution[num] += 1
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95 progress.inc()
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96 progress.done()
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97 self.distribution[0] = self.genomeSize - nbNucleotides
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98
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99
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100 def plotDistribution(self):
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101 plotter = RPlotter(self.outputFileName, self.verbosity)
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102 plotter.setFill(0)
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103 plotter.addLine(self.distribution)
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104 plotter.plot()
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105 print "min/avg/med/max reads per base: %d/%.2f/%.1f/%d" % getMinAvgMedMax(self.distribution)
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106
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107
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108 def run(self):
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109 self.getReferenceSizes()
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110 self.getCoverage()
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111 self.getDistribution()
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112 self.plotDistribution()
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113
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114
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115 if __name__ == "__main__":
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116
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117 # parse command line
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118 description = "Plot Genome Coverage v1.0.1: Get the coverage of a genome. [Category: Personal]"
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119
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120 parser = OptionParser(description = description)
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121 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="reads file [compulsory] [format: file in transcript format given by -f]")
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122 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of file [compulsory] [format: transcript file format]")
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123 parser.add_option("-r", "--reference", dest="reference", action="store", type="string", help="sequences file [compulsory] [format: file in FASTA format]")
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124 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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125 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
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126 (options, args) = parser.parse_args()
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127
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128 getGenomeCoverage = GetGenomeCoverage(options.verbosity)
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129 getGenomeCoverage.setInputFile(options.inputFileName, options.format)
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130 getGenomeCoverage.setOutputFile(options.outputFileName)
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131 getGenomeCoverage.setReference(options.reference)
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132 getGenomeCoverage.run()
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