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 """Merge elements of two transcript lists with some condition"""
+ − 32
+ − 33 import os, random, shutil, glob
+ − 34 from optparse import OptionParser
+ − 35 from commons.core.parsing.SequenceListParser import SequenceListParser
+ − 36 from commons.core.parsing.BedParser import BedParser
+ − 37 from commons.core.parsing.GffParser import GffParser
+ − 38 from commons.core.writer.TranscriptWriter import TranscriptWriter
+ − 39 from SMART.Java.Python.structure.TranscriptListsComparator import TranscriptListsComparator
+ − 40 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
+ − 41 from SMART.Java.Python.misc.RPlotter import RPlotter
+ − 42 from SMART.Java.Python.misc.Progress import Progress
+ − 43
+ − 44
+ − 45
+ − 46 class MergeLists(object):
+ − 47
+ − 48 def __init__(self, verbosity):
+ − 49 self.verbosity = verbosity
+ − 50 self.seed = random.randint(0, 100000)
+ − 51 self.aggregation = False
+ − 52 self.normalization = False
+ − 53 self.distance = False
+ − 54 self.antisense = False
+ − 55 self.colinear = False
+ − 56 self.fileNames = {}
+ − 57 self.formats = {}
+ − 58 self.tmpFileNames = []
+ − 59 self.logHandle = None
+ − 60
+ − 61 # def __del__(self):
+ − 62 # for fileNameRoot in self.tmpFileNames:
+ − 63 # for fileName in glob.glob("%s*" % (fileNameRoot)):
+ − 64 # os.remove(fileName)
+ − 65 # if self.logHandle != None:
+ − 66 # self.logHandle.close()
+ − 67 # self.logHandle = None
+ − 68
+ − 69 def setLogFileName(self, fileName):
+ − 70 self.logHandle = open(fileName, "w")
+ − 71
+ − 72 def setInputFileName(self, fileName, format, id):
+ − 73 self.fileNames[id] = fileName
+ − 74 self.formats[id] = format
+ − 75
+ − 76 def setOutputFileName(self, fileName):
+ − 77 self.outputFileName = fileName
+ − 78
+ − 79 def setAggregate(self, aggregation):
+ − 80 self.aggregation = aggregation
+ − 81
+ − 82 def setNormalization(self, normalization):
+ − 83 self.normalization = normalization
+ − 84
+ − 85 def setDistance(self, distance):
+ − 86 self.distance = distance
+ − 87
+ − 88 def setAntisense(self, antisense):
+ − 89 self.antisense = antisense
+ − 90
+ − 91 def setColinear(self, colinear):
+ − 92 self.colinear = colinear
+ − 93
+ − 94 def createTmpFileName(self, root):
+ − 95 fileName = "tmp_%s_%d.gff3" % (root, self.seed)
+ − 96 self.tmpFileNames.append(fileName)
+ − 97 return fileName
+ − 98
+ − 99 def selfMerge(self, fileName, format, outputFileName):
+ − 100 transcriptListComparator = TranscriptListsComparator(self.logHandle, self.verbosity)
+ − 101 transcriptListComparator.getColinearOnly(True)
+ − 102 transcriptListComparator.setNormalization(self.normalization)
+ − 103 transcriptContainer = TranscriptContainer(fileName, format, self.verbosity)
+ − 104 writer = TranscriptWriter(outputFileName, "gff3", self.verbosity)
+ − 105 transcriptListComparator.setInputTranscriptContainer(transcriptListComparator.QUERY, transcriptContainer)
+ − 106 transcriptListComparator.setOutputWriter(writer)
+ − 107 transcriptListComparator.compareTranscriptListSelfMerge()
+ − 108
+ − 109 def keepOverlapping(self, fileNames, formats, outputFileName):
+ − 110 transcriptListComparator = TranscriptListsComparator(self.logHandle, self.verbosity)
+ − 111 transcriptListComparator.getAntisenseOnly(self.antisense)
+ − 112 transcriptListComparator.getColinearOnly(self.colinear)
+ − 113 for i in (0, 1):
+ − 114 transcriptContainer = TranscriptContainer(fileNames[i], formats[i], self.verbosity)
+ − 115 transcriptListComparator.setInputTranscriptContainer(i, transcriptContainer)
+ − 116 transcriptListComparator.aggregate(self.aggregation)
+ − 117 transcriptListComparator.setNormalization(self.normalization)
+ − 118 transcriptListComparator.setMaxDistance(self.distance)
+ − 119 writer = TranscriptWriter(outputFileName, "gff3", self.verbosity)
+ − 120 transcriptListComparator.setOutputWriter(writer)
+ − 121 transcriptListComparator.compareTranscriptList()
+ − 122
+ − 123 def mergeFiles(self, fileName1, fileName2, outputFileName):
+ − 124 outputFile = open(outputFileName, "w")
+ − 125 shutil.copyfileobj(open(fileName1, "r"), outputFile)
+ − 126 shutil.copyfileobj(open(fileName2, "r"), outputFile)
+ − 127 outputFile.close()
+ − 128
+ − 129 def run(self):
+ − 130 selectedFileQuery = self.createTmpFileName("query")
+ − 131 self.keepOverlapping({0: self.fileNames[0], 1: self.fileNames[0]}, {0: "gff3", 1: "gff3"}, selectedFileQuery)
+ − 132 mergeFileTarget = self.createTmpFileName("target")
+ − 133 self.selfMerge(self.fileNames[1], self.formats[1], mergeFileTarget)
+ − 134 if not self.aggregation:
+ − 135 overlapFile = self.createTmpFileName("overlap")
+ − 136 self.keepOverlapping({0: mergeFileTarget, 1: selectedFileQuery}, {0: "gff3", 1: "gff3"}, overlapFile)
+ − 137 mergeFileTarget = overlapFile
+ − 138 mergeFileMerged = self.createTmpFileName("merged")
+ − 139 self.mergeFiles(mergeFileTarget, selectedFileQuery, mergeFileMerged)
+ − 140 self.selfMerge(mergeFileMerged, "gff3", self.outputFileName)
+ − 141
+ − 142
+ − 143
+ − 144 if __name__ == "__main__":
+ − 145
+ − 146 # parse command line
+ − 147 description = "Merge Lists v1.0.3: Merge the elements of two lists of genomic coordinates. [Category: Merge]"
+ − 148
+ − 149 parser = OptionParser(description = description)
+ − 150 parser.add_option("-i", "--input1", dest="inputFileName1", action="store", type="string", help="input file 1 [compulsory] [format: file in transcript format given by -f]")
+ − 151 parser.add_option("-f", "--format1", dest="format1", action="store", type="string", help="format of file 1 [compulsory] [format: transcript file format]")
+ − 152 parser.add_option("-j", "--input2", dest="inputFileName2", action="store", default=None, type="string", help="input file 2 [compulsory] [format: file in transcript format given by -g]")
+ − 153 parser.add_option("-g", "--format2", dest="format2", action="store", default=None, type="string", help="format of file 2 [compulsory] [format: file in transcript format]")
+ − 154 parser.add_option("-o", "--output", dest="outputFileName", action="store", default=None, type="string", help="output file [compulsory] [format: output file in GFF3 format]")
+ − 155 parser.add_option("-k", "--all", dest="all", action="store_true", default=False, help="print all the transcripts, not only those overlapping [format: bool] [default: false]")
+ − 156 parser.add_option("-d", "--distance", dest="distance", action="store", default=0, type="int", help="max. distance between two transcripts [format: int] [default: 0]")
+ − 157 parser.add_option("-a", "--antisense", dest="antisense", action="store_true", default=False, help="antisense only [format: bool] [default: false]")
+ − 158 parser.add_option("-c", "--colinear", dest="colinear", action="store_true", default=False, help="colinear only [format: bool] [default: false]")
+ − 159 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]")
+ − 160 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
+ − 161 (options, args) = parser.parse_args()
+ − 162
+ − 163 # ml = MergeLists(logHandle, options.verbosity)
+ − 164
+ − 165 ml = MergeLists(0)
+ − 166 ml.setInputFileName(options.inputFileName1, options.format1, 0)
+ − 167 ml.setInputFileName(options.inputFileName2, options.format2, 1)
+ − 168 ml.setOutputFileName(options.outputFileName)
+ − 169 ml.setAntisense(options.antisense)
+ − 170 ml.setColinear(options.colinear)
+ − 171 ml.setAggregate(options.all)
+ − 172 ml.setNormalization(options.normalize)
+ − 173 ml.setDistance(options.distance)
+ − 174 ml.run()
