18
+ − 1 #! /usr/bin/env python
+ − 2 #
+ − 3 # Copyright INRA-URGI 2009-2011
+ − 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 optparse import OptionParser
+ − 32 from commons.core.parsing.ParserChooser import ParserChooser
+ − 33 from commons.core.writer.TranscriptWriter import TranscriptWriter
+ − 34 from SMART.Java.Python.structure.Interval import Interval
+ − 35 from SMART.Java.Python.structure.Transcript import Transcript
+ − 36 from SMART.Java.Python.structure.Mapping import Mapping
+ − 37 from SMART.Java.Python.misc.Progress import Progress
+ − 38 from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress
+ − 39
+ − 40 MINBIN = 3
+ − 41 MAXBIN = 7
+ − 42 REFERENCE = 0
+ − 43 QUERY = 1
+ − 44
+ − 45 def getBin(start, end):
+ − 46 for i in range(MINBIN, MAXBIN + 1):
+ − 47 binLevel = 10 ** i
+ − 48 if int(start / binLevel) == int(end / binLevel):
+ − 49 return int(i * 10 ** (MAXBIN + 1) + int(start / binLevel))
+ − 50 return int((MAXBIN + 1) * 10 ** (MAXBIN + 1))
+ − 51
+ − 52 def getOverlappingBins(start, end):
+ − 53 array = []
+ − 54 bigBin = int((MAXBIN + 1) * 10 ** (MAXBIN + 1))
+ − 55 for i in range(MINBIN, MAXBIN + 1):
+ − 56 binLevel = 10 ** i
+ − 57 array.append((int(i * 10 ** (MAXBIN + 1) + int(start / binLevel)), int(i * 10 ** (MAXBIN + 1) + int(end / binLevel))))
+ − 58 array.append((bigBin, bigBin))
+ − 59 return array
+ − 60
+ − 61
+ − 62 class GetIntersection(object):
+ − 63
+ − 64 def __init__(self, verbosity):
+ − 65 self.verbosity = verbosity
+ − 66 self.nbQueries = 0
+ − 67 self.nbRefs = 0
+ − 68 self.nbWritten = 0
+ − 69 self.bins = {}
+ − 70
+ − 71 def setReferenceFile(self, fileName, format):
+ − 72 chooser = ParserChooser(self.verbosity)
+ − 73 chooser.findFormat(format)
+ − 74 self.refParser = chooser.getParser(fileName)
+ − 75
+ − 76 def setQueryFile(self, fileName, format):
+ − 77 chooser = ParserChooser(self.verbosity)
+ − 78 chooser.findFormat(format)
+ − 79 self.queryParser = chooser.getParser(fileName)
+ − 80
+ − 81 def setOutputFile(self, fileName):
+ − 82 self.writer = TranscriptWriter(fileName, "gff3", self.verbosity)
+ − 83
+ − 84 def loadRef(self):
+ − 85 progress = UnlimitedProgress(10000, "Reading references", self.verbosity)
+ − 86 for transcript in self.refParser.getIterator():
+ − 87 if transcript.__class__.__name__ == "Mapping":
+ − 88 transcript = transcript.getTranscript()
+ − 89 chromosome = transcript.getChromosome()
+ − 90 bin = getBin(transcript.getStart(), transcript.getEnd())
+ − 91 if chromosome not in self.bins:
+ − 92 self.bins[chromosome] = {}
+ − 93 if bin not in self.bins[chromosome]:
+ − 94 self.bins[chromosome][bin] = []
+ − 95 self.bins[chromosome][bin].append(transcript)
+ − 96 self.nbRefs += 1
+ − 97 progress.inc()
+ − 98 progress.done()
+ − 99
+ − 100 def _compareTranscript(self, queryTranscript):
+ − 101 queryChromosome = queryTranscript.getChromosome()
+ − 102 if queryChromosome not in self.bins:
+ − 103 return None
+ − 104 queryStart = queryTranscript.getStart()
+ − 105 queryEnd = queryTranscript.getEnd()
+ − 106 bins = getOverlappingBins(queryStart, queryEnd)
+ − 107 overlaps = []
+ − 108 for binRange in bins:
+ − 109 for bin in range(binRange[0], binRange[1]+1):
+ − 110 if bin not in self.bins[queryChromosome]:
+ − 111 continue
+ − 112 for refTranscript in self.bins[queryChromosome][bin]:
+ − 113 newTranscript = queryTranscript.getIntersection(refTranscript)
+ − 114 if newTranscript != None:
+ − 115 overlaps.append(newTranscript)
+ − 116 if not overlaps:
+ − 117 return None
+ − 118 newTranscript = overlaps[0]
+ − 119 for transcript in overlaps[1:]:
+ − 120 newTranscript.merge(transcript)
+ − 121 return newTranscript
+ − 122
+ − 123 def compare(self):
+ − 124 progress = UnlimitedProgress(10000, "Comparing queries", self.verbosity)
+ − 125 for queryTranscript in self.queryParser.getIterator():
+ − 126 if queryTranscript.__class__.__name__ == "Mapping":
+ − 127 queryTranscript = queryTranscript.getTranscript()
+ − 128 progress.inc()
+ − 129 self.nbQueries += 1
+ − 130 newTranscript = self._compareTranscript(queryTranscript)
+ − 131 if newTranscript != None:
+ − 132 self.writer.addTranscript(queryTranscript)
+ − 133 self.nbWritten += 1
+ − 134 progress.done()
+ − 135 self.writer.close()
+ − 136
+ − 137 def displayResults(self):
+ − 138 print "# queries: %d" % (self.nbQueries)
+ − 139 print "# refs: %d" % (self.nbRefs)
+ − 140 print "# written: %d" % (self.nbWritten)
+ − 141
+ − 142 def run(self):
+ − 143 self.loadRef()
+ − 144 self.compare()
+ − 145 self.displayResults()
+ − 146
+ − 147 if __name__ == "__main__":
+ − 148
+ − 149 description = "Get Intersection v1.0.0: Shrink the first data set so that all bases covered by the first data set is also covered by the second data set. [Category: Data Comparison]"
+ − 150
+ − 151 parser = OptionParser(description = description)
+ − 152 parser.add_option("-i", "--input1", dest="inputFileName1", action="store", type="string", help="query input file [compulsory] [format: file in transcript format given by -f]")
+ − 153 parser.add_option("-f", "--format1", dest="format1", action="store", type="string", help="format of previous file [compulsory] [format: transcript file format]")
+ − 154 parser.add_option("-j", "--input2", dest="inputFileName2", action="store", type="string", help="reference input file [compulsory] [format: file in transcript format given by -g]")
+ − 155 parser.add_option("-g", "--format2", dest="format2", action="store", type="string", help="format of previous file [compulsory] [format: transcript file format]")
+ − 156 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [format: output file in GFF3 format]")
+ − 157 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
+ − 158 (options, args) = parser.parse_args()
+ − 159
+ − 160 gi = GetIntersection(options.verbosity)
+ − 161 gi.setQueryFile(options.inputFileName1, options.format1)
+ − 162 gi.setReferenceFile(options.inputFileName2, options.format2)
+ − 163 gi.setOutputFile(options.outputFileName)
+ − 164 gi.run()
