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 """
+ − 32 Merge sliding windows of two different clusterings
+ − 33 """
+ − 34
+ − 35 import sys
+ − 36 import re
+ − 37 import os
+ − 38 from optparse import OptionParser
+ − 39 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
+ − 40 from commons.core.writer.Gff3Writer import Gff3Writer
+ − 41 from SMART.Java.Python.misc.Progress import Progress
+ − 42 from SMART.Java.Python.structure.Transcript import Transcript
+ − 43
+ − 44 class MergeSlidingWindowsClusters(object):
+ − 45 """
+ − 46 Merge the ouptput of several sets of sliding windows
+ − 47 """
+ − 48
+ − 49 def __init__(self, verbosity = 0):
+ − 50 self.verbosity = verbosity
+ − 51 self.inputs = []
+ − 52 self.outputData = {}
+ − 53 self.nbData = 0
+ − 54 self.nbWrittenData = 0
+ − 55 self.chromosomes = []
+ − 56 self.writer = None
+ − 57
+ − 58 def __del__(self):
+ − 59 if self.writer != None:
+ − 60 self.writer.close()
+ − 61
+ − 62 def addInput(self, fileName, fileFormat):
+ − 63 self.inputs.append(TranscriptContainer(fileName, fileFormat, self.verbosity))
+ − 64 self.chromosomes = list(set(self.chromosomes).union(set(self.inputs[-1].getChromosomes())))
+ − 65
+ − 66 def setOutput(self, fileName):
+ − 67 self.writer = Gff3Writer(fileName, self.verbosity)
+ − 68
+ − 69 def readInput(self, i, chromosome):
+ − 70 progress = Progress(self.inputs[i].getNbTranscripts(), "Reading file #%d -- chromosome %s" % (i+1, chromosome), self.verbosity)
+ − 71 for transcript in self.inputs[i].getIterator():
+ − 72 progress.inc()
+ − 73 if chromosome != transcript.getChromosome(): continue
+ − 74 start = transcript.getStart()
+ − 75 end = transcript.getEnd()
+ − 76 direction = transcript.getDirection()
+ − 77 tags = transcript.tags
+ − 78 if chromosome not in self.outputData:
+ − 79 self.outputData[chromosome] = {}
+ − 80 if direction not in self.outputData[chromosome]:
+ − 81 self.outputData[chromosome][direction] = {}
+ − 82 if start not in self.outputData[chromosome][direction]:
+ − 83 self.outputData[chromosome][direction][start] = {}
+ − 84 if end in self.outputData[chromosome][direction][start]:
+ − 85 ends = self.outputData[chromosome][direction][start].keys()
+ − 86 if ends[0] != end:
+ − 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))
+ − 88 self.outputData[chromosome][direction][start][end].update(tags)
+ − 89 else:
+ − 90 self.outputData[chromosome][direction][start][end] = tags
+ − 91 self.nbData += 1
+ − 92 progress.done()
+ − 93
+ − 94
+ − 95 def writeOutput(self, chromosome):
+ − 96 progress = Progress(self.nbData - self.nbWrittenData, "Writing output for chromosome %s" % (chromosome), self.verbosity)
+ − 97 for direction in self.outputData[chromosome]:
+ − 98 for start in self.outputData[chromosome][direction]:
+ − 99 for end in self.outputData[chromosome][direction][start]:
+ − 100 transcript = Transcript()
+ − 101 transcript.setChromosome(chromosome)
+ − 102 transcript.setStart(start)
+ − 103 transcript.setEnd(end)
+ − 104 transcript.setDirection(direction)
+ − 105 transcript.tags = self.outputData[chromosome][direction][start][end]
+ − 106 transcript.setName("region_%d" % (self.nbWrittenData + 1))
+ − 107 tags = transcript.getTagNames()
+ − 108 for tag in tags:
+ − 109 if tag.startswith("Name_") or tag.startswith("ID_"):
+ − 110 del transcript.tags[tag]
+ − 111 self.nbWrittenData += 1
+ − 112 self.writer.addTranscript(transcript)
+ − 113 progress.inc()
+ − 114 self.writer.write()
+ − 115 progress.done()
+ − 116 self.outputData = {}
+ − 117
+ − 118 def merge(self):
+ − 119 for chromosome in self.chromosomes:
+ − 120 for i, input in enumerate(self.inputs):
+ − 121 self.readInput(i, chromosome)
+ − 122 self.writeOutput(chromosome)
+ − 123 self.writer.close()
+ − 124
+ − 125
+ − 126 if __name__ == "__main__":
+ − 127
+ − 128 # parse command line
+ − 129 description = "Merge Sliding Windows Clusters v1.0.2: Merge two files containing the results of a sliding windows clustering. [Category: Sliding Windows]"
+ − 130
+ − 131 parser = OptionParser(description = description)
+ − 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]")
+ − 133 parser.add_option("-f", "--inputFormat1", dest="inputFormat1", action="store", type="string", help="format of the input file 1 [compulsory] [format: transcript file format]")
+ − 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]")
+ − 135 parser.add_option("-g", "--inputFormat2", dest="inputFormat2", action="store", type="string", help="format of the input file 2 [compulsory] [format: transcript file format]")
+ − 136 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in GFF3 format]")
+ − 137 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
+ − 138 (options, args) = parser.parse_args()
+ − 139
+ − 140 merger = MergeSlidingWindowsClusters(options.verbosity)
+ − 141 merger.addInput(options.inputFileName1, options.inputFormat1)
+ − 142 merger.addInput(options.inputFileName2, options.inputFormat2)
+ − 143 merger.setOutput(options.outputFileName)
+ − 144 merger.merge()
