36
+ − 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 from commons.core.writer.WriterChooser import WriterChooser
+ − 32 """Clusterize a set of transcripts"""
+ − 33
+ − 34 import os, os.path, random
+ − 35 from optparse import OptionParser
+ − 36 from commons.core.parsing.ParserChooser import ParserChooser
+ − 37 from commons.core.writer.Gff3Writer import Gff3Writer
+ − 38 from SMART.Java.Python.structure.Transcript import Transcript
+ − 39 from SMART.Java.Python.ncList.NCListFilePickle import NCListFileUnpickle
+ − 40 from SMART.Java.Python.ncList.FileSorter import FileSorter
+ − 41 from SMART.Java.Python.misc.Progress import Progress
+ − 42 from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress
+ − 43
+ − 44 class Clusterize(object):
+ − 45
+ − 46 def __init__(self, verbosity):
+ − 47 self.normalize = False
+ − 48 self.presorted = False
+ − 49 self.distance = 1
+ − 50 self.colinear = False
+ − 51 self.nbWritten = 0
+ − 52 self.nbMerges = 0
+ − 53 self.verbosity = verbosity
+ − 54 self.splittedFileNames = {}
+ − 55
+ − 56 def __del__(self):
+ − 57 for fileName in self.splittedFileNames.values():
+ − 58 os.remove(fileName)
+ − 59
+ − 60 def setInputFile(self, fileName, format):
+ − 61 parserChooser = ParserChooser(self.verbosity)
+ − 62 parserChooser.findFormat(format)
+ − 63 self.parser = parserChooser.getParser(fileName)
+ − 64 self.sortedFileName = "%s_sorted_%d.pkl" % (os.path.splitext(fileName)[0], random.randint(1, 100000))
+ − 65 if "SMARTTMPPATH" in os.environ:
+ − 66 self.sortedFileName = os.path.join(os.environ["SMARTTMPPATH"], os.path.basename(self.sortedFileName))
+ − 67
+ − 68 def setOutputFileName(self, fileName, format="gff3", title="S-MART", feature="transcript", featurePart="exon"):
+ − 69 writerChooser = WriterChooser()
+ − 70 writerChooser.findFormat(format)
+ − 71 self.writer = writerChooser.getWriter(fileName)
+ − 72 self.writer.setTitle(title)
+ − 73 self.writer.setFeature(feature)
+ − 74 self.writer.setFeaturePart(featurePart)
+ − 75
+ − 76 def setDistance(self, distance):
+ − 77 self.distance = distance
+ − 78
+ − 79 def setColinear(self, colinear):
+ − 80 self.colinear = colinear
+ − 81
+ − 82 def setNormalize(self, normalize):
+ − 83 self.normalize = normalize
+ − 84
+ − 85 def setPresorted(self, presorted):
+ − 86 self.presorted = presorted
+ − 87
+ − 88 def _sortFile(self):
+ − 89 if self.presorted:
+ − 90 return
+ − 91 fs = FileSorter(self.parser, self.verbosity-4)
+ − 92 fs.perChromosome(True)
+ − 93 fs.setPresorted(self.presorted)
+ − 94 fs.setOutputFileName(self.sortedFileName)
+ − 95 fs.sort()
+ − 96 self.splittedFileNames = fs.getOutputFileNames()
+ − 97 self.nbElementsPerChromosome = fs.getNbElementsPerChromosome()
+ − 98 self.nbElements = fs.getNbElements()
+ − 99
+ − 100 def _iterate(self, chromosome):
+ − 101 if chromosome == None:
+ − 102 progress = UnlimitedProgress(10000, "Reading input file", self.verbosity)
+ − 103 parser = self.parser
+ − 104 else:
+ − 105 progress = Progress(self.nbElementsPerChromosome[chromosome], "Checking chromosome %s" % (chromosome), self.verbosity)
+ − 106 parser = NCListFileUnpickle(self.splittedFileNames[chromosome], self.verbosity)
+ − 107 transcripts = []
+ − 108 self.nbElements = 0
+ − 109 for newTranscript in parser.getIterator():
+ − 110 newTranscripts = []
+ − 111 if newTranscript.__class__.__name__ == "Mapping":
+ − 112 newTranscript = newTranscript.getTranscript()
+ − 113 for oldTranscript in transcripts:
+ − 114 if self._checkOverlap(newTranscript, oldTranscript):
+ − 115 self._merge(newTranscript, oldTranscript)
+ − 116 elif self._checkPassed(newTranscript, oldTranscript):
+ − 117 self._write(oldTranscript)
+ − 118 else:
+ − 119 newTranscripts.append(oldTranscript)
+ − 120 newTranscripts.append(newTranscript)
+ − 121 transcripts = newTranscripts
+ − 122 self.nbElements += 1
+ − 123 progress.inc()
+ − 124 for transcript in transcripts:
+ − 125 self._write(transcript)
+ − 126 progress.done()
+ − 127
+ − 128 def _merge(self, transcript1, transcript2):
+ − 129 self.nbMerges += 1
+ − 130 transcript2.setDirection(transcript1.getDirection())
+ − 131 transcript1.merge(transcript2)
+ − 132
+ − 133 def _write(self, transcript):
+ − 134 self.nbWritten += 1
+ − 135 self.writer.addTranscript(transcript)
+ − 136
+ − 137 def _checkOverlap(self, transcript1, transcript2):
+ − 138 if transcript1.getChromosome() != transcript2.getChromosome():
+ − 139 return False
+ − 140 if self.colinear and transcript1.getDirection() != transcript2.getDirection():
+ − 141 return False
+ − 142 if transcript1.getDistance(transcript2) > self.distance:
+ − 143 return False
+ − 144 return True
+ − 145
+ − 146 def _checkPassed(self, transcript1, transcript2):
+ − 147 return ((transcript1.getChromosome() != transcript2.getChromosome()) or (transcript1.getDistance(transcript2) > self.distance))
+ − 148
+ − 149 def run(self):
+ − 150 self._sortFile()
+ − 151 if self.presorted:
+ − 152 self._iterate(None)
+ − 153 else:
+ − 154 for chromosome in sorted(self.splittedFileNames.keys()):
+ − 155 self._iterate(chromosome)
+ − 156 self.writer.close()
+ − 157 if self.verbosity > 0:
+ − 158 print "# input: %d" % (self.nbElements)
+ − 159 print "# written: %d (%d%% overlaps)" % (self.nbWritten, 0 if (self.nbElements == 0) else ((float(self.nbWritten) / self.nbElements) * 100))
+ − 160 print "# merges: %d" % (self.nbMerges)
+ − 161
+ − 162
+ − 163 if __name__ == "__main__":
+ − 164 description = "Clusterize v1.0.3: clusterize the data which overlap. [Category: Merge]"
+ − 165
+ − 166 parser = OptionParser(description = description)
+ − 167 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in transcript format given by -f]")
+ − 168 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of file [format: transcript file format]")
+ − 169 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in transcript format given by -u]")
+ − 170 parser.add_option("-u", "--outputFormat", dest="outputFormat", action="store", default="gff", type="string", help="output file format [format: transcript file format]")
+ − 171 parser.add_option("-c", "--colinear", dest="colinear", action="store_true", default=False, help="merge colinear transcripts only [format: bool] [default: false]")
+ − 172 parser.add_option("-d", "--distance", dest="distance", action="store", default=0, type="int", help="max. distance between two transcripts to be merged [format: int] [default: 0]")
+ − 173 parser.add_option("-n", "--normalize", dest="normalize", action="store_true", default=False, help="normalize the number of reads per cluster by the number of mappings per read [format: bool] [default: false]")
+ − 174 parser.add_option("-s", "--sorted", dest="sorted", action="store_true", default=False, help="input is already sorted [format: bool] [default: false]")
+ − 175 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int] [default: 1]")
+ − 176 (options, args) = parser.parse_args()
+ − 177
+ − 178 c = Clusterize(options.verbosity)
+ − 179 c.setInputFile(options.inputFileName, options.format)
+ − 180 c.setOutputFileName(options.outputFileName, options.outputFormat)
+ − 181 c.setColinear(options.colinear)
+ − 182 c.setDistance(options.distance)
+ − 183 c.setNormalize(options.normalize)
+ − 184 c.setPresorted(options.sorted)
+ − 185 c.run()