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 """Compare overlap of two transcript lists"""
+ − 32 import sys
+ − 33 import os
+ − 34 from optparse import OptionParser
+ − 35 from SMART.Java.Python.misc import Utils
+ − 36 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
+ − 37 from commons.core.writer.TranscriptWriter import TranscriptWriter
+ − 38 from SMART.Java.Python.structure.TranscriptListsComparator import TranscriptListsComparator
+ − 39 from SMART.Java.Python.misc.RPlotter import RPlotter
+ − 40 from commons.core.writer.Gff3Writer import Gff3Writer
+ − 41
+ − 42 class CompareOverlapping(object):
+ − 43
+ − 44 def __init__(self):
+ − 45 self._options = None
+ − 46
+ − 47
+ − 48 def setAttributesFromCmdLine(self):
+ − 49 description = "Compare Overlapping v1.0.3: Get the data which overlap with a reference set. [Category: Data Comparison]"
+ − 50
+ − 51 parser = OptionParser(description = description)
+ − 52 parser.add_option("-i", "--input1", dest="inputFileName1", action="store", type="string", help="input file 1 [compulsory] [format: file in transcript format given by -f]")
+ − 53 parser.add_option("-f", "--format1", dest="format1", action="store", type="string", help="format of file 1 [compulsory] [format: transcript file format]")
+ − 54 parser.add_option("-j", "--input2", dest="inputFileName2", action="store", type="string", help="input file 2 [compulsory] [format: file in transcript format given by -g]")
+ − 55 parser.add_option("-g", "--format2", dest="format2", action="store", type="string", help="format of file 2 [compulsory] [format: transcript file format]")
+ − 56 parser.add_option("-o", "--output", dest="output", action="store", default=None, type="string", help="output file [compulsory] [format: output file in GFF3 format]")
+ − 57 parser.add_option("-S", "--start1", dest="start1", action="store", default=None, type="int", help="only consider the n first nucleotides of the transcripts in file 1 (do not use it with -U) [format: int]")
+ − 58 parser.add_option("-s", "--start2", dest="start2", action="store", default=None, type="int", help="only consider the n first nucleotides of the transcripts in file 2 (do not use it with -u) [format: int]")
+ − 59 parser.add_option("-U", "--end1", dest="end1", action="store", default=None, type="int", help="only consider the n last nucleotides of the transcripts in file 1 (do not use it with -S) [format: int]")
+ − 60 parser.add_option("-u", "--end2", dest="end2", action="store", default=None, type="int", help="only consider the n last nucleotides of the transcripts in file 2 (do not use it with -s) [format: int]")
+ − 61 parser.add_option("-t", "--intron", dest="introns", action="store_true", default=False, help="also report introns [format: bool] [default: false]")
+ − 62 parser.add_option("-E", "--5primeExtension1", dest="fivePrime1", action="store", default=None, type="int", help="extension towards 5' in file 1 [format: int]")
+ − 63 parser.add_option("-e", "--5primeExtension2", dest="fivePrime2", action="store", default=None, type="int", help="extension towards 5' in file 2 [format: int]")
+ − 64 parser.add_option("-N", "--3primeExtension1", dest="threePrime1", action="store", default=None, type="int", help="extension towards 3' in file 1 [format: int]")
+ − 65 parser.add_option("-n", "--3primeExtension2", dest="threePrime2", action="store", default=None, type="int", help="extension towards 3' in file 2 [format: int]")
+ − 66 parser.add_option("-c", "--colinear", dest="colinear", action="store_true", default=False, help="colinear only [format: bool] [default: false]")
+ − 67 parser.add_option("-a", "--antisense", dest="antisense", action="store_true", default=False, help="antisense only [format: bool] [default: false]")
+ − 68 parser.add_option("-d", "--distance", dest="distance", action="store", default=None, type="int", help="accept some distance between query and reference [format: int]")
+ − 69 parser.add_option("-k", "--included", dest="included", action="store_true", default=False, help="keep only elements from file 1 which are included in an element of file 2 [format: bool] [default: false]")
+ − 70 parser.add_option("-K", "--including", dest="including", action="store_true", default=False, help="keep only elements from file 2 which are included in an element of file 1 [format: bool] [default: false]")
+ − 71 parser.add_option("-m", "--minOverlap", dest="minOverlap", action="store", default=1, type="int", help="minimum number of nucleotides overlapping to declare an overlap [format: int] [default: 1]")
+ − 72 parser.add_option("-p", "--pcOverlap", dest="pcOverlap", action="store", default=None, type="int", help="minimum percentage of nucleotides to overlap to declare an overlap [format: int]")
+ − 73 parser.add_option("-O", "--notOverlapping", dest="notOverlapping", action="store_true", default=False, help="also output not overlapping data [format: bool] [default: false]")
+ − 74 parser.add_option("-x", "--exclude", dest="exclude", action="store_true", default=False, help="invert the match [format: bool] [default: false]")
+ − 75 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
+ − 76 parser.add_option("-l", "--log", dest="log", action="store_true", default=False, help="write a log file [format: bool] [default: false]")
+ − 77 (self._options, args) = parser.parse_args()
+ − 78
+ − 79
+ − 80 def run(self):
+ − 81 logHandle = None
+ − 82 if self._options.log:
+ − 83 logHandle = open(self._options.output, "w")
+ − 84
+ − 85 transcriptContainer1 = TranscriptContainer(self._options.inputFileName1, self._options.format1, self._options.verbosity)
+ − 86 transcriptContainer2 = TranscriptContainer(self._options.inputFileName2, self._options.format2, self._options.verbosity)
+ − 87 writer = TranscriptWriter(self._options.output, "gff3", self._options.verbosity)
+ − 88
+ − 89 transcriptListComparator = TranscriptListsComparator(logHandle, self._options.verbosity)
+ − 90 transcriptListComparator.restrictToStart(transcriptListComparator.QUERY, self._options.start1)
+ − 91 transcriptListComparator.restrictToStart(transcriptListComparator.REFERENCE, self._options.start2)
+ − 92 transcriptListComparator.restrictToEnd(transcriptListComparator.QUERY, self._options.end1)
+ − 93 transcriptListComparator.restrictToEnd(transcriptListComparator.REFERENCE, self._options.end2)
+ − 94 transcriptListComparator.extendFivePrime(transcriptListComparator.QUERY, self._options.fivePrime1)
+ − 95 transcriptListComparator.extendFivePrime(transcriptListComparator.REFERENCE, self._options.fivePrime2)
+ − 96 transcriptListComparator.extendThreePrime(transcriptListComparator.QUERY, self._options.threePrime1)
+ − 97 transcriptListComparator.extendThreePrime(transcriptListComparator.REFERENCE, self._options.threePrime2)
+ − 98 transcriptListComparator.acceptIntrons(transcriptListComparator.QUERY, self._options.introns)
+ − 99 transcriptListComparator.acceptIntrons(transcriptListComparator.REFERENCE, self._options.introns)
+ − 100 transcriptListComparator.getAntisenseOnly(self._options.antisense)
+ − 101 transcriptListComparator.getColinearOnly(self._options.colinear)
+ − 102 transcriptListComparator.getInvert(self._options.exclude)
+ − 103 transcriptListComparator.setMaxDistance(self._options.distance)
+ − 104 transcriptListComparator.setMinOverlap(self._options.minOverlap)
+ − 105 transcriptListComparator.setPcOverlap(self._options.pcOverlap)
+ − 106 transcriptListComparator.setIncludedOnly(self._options.included)
+ − 107 transcriptListComparator.setIncludingOnly(self._options.including)
+ − 108 transcriptListComparator.includeNotOverlapping(self._options.notOverlapping)
+ − 109 transcriptListComparator.computeOdds(True)
+ − 110 transcriptListComparator.setInputTranscriptContainer(transcriptListComparator.QUERY, transcriptContainer1)
+ − 111 transcriptListComparator.setInputTranscriptContainer(transcriptListComparator.REFERENCE, transcriptContainer2)
+ − 112 transcriptListComparator.setOutputWriter(writer)
+ − 113 transcriptListComparator.compareTranscriptList()
+ − 114
+ − 115 if self._options.log:
+ − 116 logHandle.close()
+ − 117
+ − 118 if not self._options.exclude:
+ − 119 odds = transcriptListComparator.getOdds()
+ − 120 if self._options.verbosity > 0 and odds:
+ − 121 print "min/avg/med/max transcripts: %d/%.2f/%.1f/%d" % Utils.getMinAvgMedMax(odds)
+ − 122
+ − 123 if __name__ == "__main__":
+ − 124 icompareOverlapping = CompareOverlapping()
+ − 125 icompareOverlapping.setAttributesFromCmdLine()
+ − 126 icompareOverlapping.run()
