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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 Merge sliding windows of two different clusterings
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33 """
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34
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35 import sys
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36 import re
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37 import os
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38 from optparse import OptionParser
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39 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
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40 from commons.core.writer.Gff3Writer import Gff3Writer
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41 from SMART.Java.Python.misc.Progress import Progress
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42 from SMART.Java.Python.structure.Transcript import Transcript
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43
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44 class MergeSlidingWindowsClusters(object):
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45 """
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46 Merge the ouptput of several sets of sliding windows
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47 """
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48
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49 def __init__(self, verbosity = 0):
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50 self.verbosity = verbosity
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51 self.inputs = []
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52 self.outputData = {}
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53 self.nbData = 0
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54 self.nbWrittenData = 0
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55 self.chromosomes = []
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56 self.writer = None
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57
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58 def __del__(self):
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59 if self.writer != None:
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60 self.writer.close()
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61
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62 def addInput(self, fileName, fileFormat):
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63 self.inputs.append(TranscriptContainer(fileName, fileFormat, self.verbosity))
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64 self.chromosomes = list(set(self.chromosomes).union(set(self.inputs[-1].getChromosomes())))
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65
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66 def setOutput(self, fileName):
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67 self.writer = Gff3Writer(fileName, self.verbosity)
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68
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69 def readInput(self, i, chromosome):
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70 progress = Progress(self.inputs[i].getNbTranscripts(), "Reading file #%d -- chromosome %s" % (i+1, chromosome), self.verbosity)
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71 for transcript in self.inputs[i].getIterator():
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72 progress.inc()
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73 if chromosome != transcript.getChromosome(): continue
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74 start = transcript.getStart()
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75 end = transcript.getEnd()
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76 direction = transcript.getDirection()
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77 tags = transcript.tags
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78 if chromosome not in self.outputData:
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79 self.outputData[chromosome] = {}
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80 if direction not in self.outputData[chromosome]:
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81 self.outputData[chromosome][direction] = {}
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82 if start not in self.outputData[chromosome][direction]:
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83 self.outputData[chromosome][direction][start] = {}
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84 if end in self.outputData[chromosome][direction][start]:
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85 ends = self.outputData[chromosome][direction][start].keys()
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86 if ends[0] != end:
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87 sys.exit("Error! Two regions starting at %d end are not consistent (%d and %d) in %s on strand %d" % (start, end, ends[0], chromosome, direction))
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88 self.outputData[chromosome][direction][start][end].update(tags)
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89 else:
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90 self.outputData[chromosome][direction][start][end] = tags
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91 self.nbData += 1
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92 progress.done()
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93
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94
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95 def writeOutput(self, chromosome):
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96 progress = Progress(self.nbData - self.nbWrittenData, "Writing output for chromosome %s" % (chromosome), self.verbosity)
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97 for direction in self.outputData[chromosome]:
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98 for start in self.outputData[chromosome][direction]:
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99 for end in self.outputData[chromosome][direction][start]:
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100 transcript = Transcript()
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101 transcript.setChromosome(chromosome)
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102 transcript.setStart(start)
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103 transcript.setEnd(end)
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104 transcript.setDirection(direction)
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105 transcript.tags = self.outputData[chromosome][direction][start][end]
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106 transcript.setName("region_%d" % (self.nbWrittenData + 1))
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107 tags = transcript.getTagNames()
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108 for tag in tags:
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109 if tag.startswith("Name_") or tag.startswith("ID_"):
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110 del transcript.tags[tag]
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111 self.nbWrittenData += 1
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112 self.writer.addTranscript(transcript)
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113 progress.inc()
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114 self.writer.write()
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115 progress.done()
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116 self.outputData = {}
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117
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118 def merge(self):
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119 for chromosome in self.chromosomes:
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120 for i, input in enumerate(self.inputs):
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121 self.readInput(i, chromosome)
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122 self.writeOutput(chromosome)
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123 self.writer.close()
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124
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125
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126 if __name__ == "__main__":
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127
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128 # parse command line
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129 description = "Merge Sliding Windows Clusters v1.0.2: Merge two files containing the results of a sliding windows clustering. [Category: Sliding Windows]"
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130
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131 parser = OptionParser(description = description)
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132 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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133 parser.add_option("-f", "--inputFormat1", dest="inputFormat1", action="store", type="string", help="format of the input file 1 [compulsory] [format: transcript file format]")
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134 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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135 parser.add_option("-g", "--inputFormat2", dest="inputFormat2", action="store", type="string", help="format of the input file 2 [compulsory] [format: transcript file format]")
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136 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in GFF3 format]")
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137 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
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138 (options, args) = parser.parse_args()
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139
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140 merger = MergeSlidingWindowsClusters(options.verbosity)
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141 merger.addInput(options.inputFileName1, options.inputFormat1)
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142 merger.addInput(options.inputFileName2, options.inputFormat2)
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143 merger.setOutput(options.outputFileName)
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144 merger.merge()
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