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