18
+ − 1 #! /usr/bin/env python
+ − 2 #
+ − 3 # Copyright INRA-URGI 2009-2012
+ − 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 import os, os.path, random
+ − 32 from optparse import OptionParser
+ − 33 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
+ − 34 from commons.core.parsing.GffParser import GffParser
+ − 35 from commons.core.writer.Gff3Writer import Gff3Writer
+ − 36 from commons.core.writer.TranscriptWriter import TranscriptWriter
+ − 37 from SMART.Java.Python.misc.Progress import Progress
+ − 38 from SMART.Java.Python.misc.RPlotter import RPlotter
+ − 39 from SMART.Java.Python.cleanGff import CleanGff
+ − 40 from SMART.Java.Python.CompareOverlappingSmallRef import CompareOverlappingSmallRef
+ − 41 from SMART.Java.Python.structure.TranscriptListsComparator import TranscriptListsComparator
+ − 42 from SMART.Java.Python.GetUpDownStream import GetUpDownStream
+ − 43
+ − 44 REFERENCE = 0
+ − 45 QUERY = 1
+ − 46
+ − 47 class CountLoci(object):
+ − 48
+ − 49 def __init__(self, verbosity = 1):
+ − 50 self.verbosity = verbosity
+ − 51 self.tmpFileNames = []
+ − 52
+ − 53 def __del__(self):
+ − 54 for fileName in self.tmpFileNames:
+ − 55 if os.path.exists(fileName):
+ − 56 os.remove(fileName)
+ − 57
+ − 58 def setInputFile(self, fileName, format):
+ − 59 self.inputFileName = fileName
+ − 60 self.inputFormat = format
+ − 61 self.parser = TranscriptContainer(fileName, format, self.verbosity-1)
+ − 62 if self.verbosity > 0:
+ − 63 print "%d elements in input" % (self.parser.getNbTranscripts())
+ − 64
+ − 65 def setReference(self, fileName):
+ − 66 self.referenceFileName = fileName
+ − 67
+ − 68 def setDistance(self, distance):
+ − 69 self.distance = distance
+ − 70
+ − 71 def setOutputFileName(self, fileName):
+ − 72 self.outputFileName = fileName
+ − 73 self.writer = Gff3Writer(fileName, self.verbosity-1)
+ − 74 self.outputBase = "%s_%d_" % (os.path.splitext(fileName)[0], random.randint(0, 10000))
+ − 75
+ − 76 def _writeTmpRef(self, tags, outputFileName):
+ − 77 cleanGff = CleanGff(self.verbosity-1)
+ − 78 cleanGff.setInputFileName(self.referenceFileName)
+ − 79 cleanGff.setOutputFileName(outputFileName)
+ − 80 cleanGff.setAcceptedTypes(tags)
+ − 81 cleanGff.run()
+ − 82
+ − 83 def _getReferenceFiles(self):
+ − 84 self.referenceFiles = {"CDS": "%scds.gff3" % (self.outputBase), \
+ − 85 "five_prime_UTR": "%sfive.gff3" % (self.outputBase), \
+ − 86 "three_prime_UTR": "%sthree.gff3" % (self.outputBase), \
+ − 87 "mRNA": "%smrna.gff3" % (self.outputBase), \
+ − 88 "ncRNA": "%sncRNA.gff3" % (self.outputBase), \
+ − 89 "transposable_element_gene": "%sTE.gff3" % (self.outputBase), \
+ − 90 "vic": "%svicinity.gff3" % (self.outputBase)}
+ − 91 self.tmpFileNames.extend(self.referenceFiles.values())
+ − 92 for tag, fileName in self.referenceFiles.iteritems():
+ − 93 if tag == "ncRNA":
+ − 94 self._writeTmpRef(["miRNA", "ncRNA", "rRNA", "snoRNA", "snRNA", "tRNA"], fileName)
+ − 95 elif tag == "vic":
+ − 96 continue
+ − 97 else:
+ − 98 self._writeTmpRef([tag], fileName)
+ − 99
+ − 100 def _compare(self, queryFileName, queryFormat, referenceFileName, referenceFormat, outputFileName, exclusion = False):
+ − 101 co = CompareOverlappingSmallRef(self.verbosity-1)
+ − 102 co.setQueryFile(queryFileName, queryFormat)
+ − 103 co.setReferenceFile(referenceFileName, referenceFormat)
+ − 104 co.setOutputFile(outputFileName)
+ − 105 if exclusion:
+ − 106 co.setInvert(True)
+ − 107 co.run()
+ − 108 return co.nbWritten
+ − 109
+ − 110 def _copy(self, inputFile, tag):
+ − 111 parser = GffParser(inputFile, self.verbosity-1)
+ − 112 for transcript in parser.getIterator():
+ − 113 transcript.setTagValue("locus", tag)
+ − 114 self.writer.addTranscript(transcript)
+ − 115
+ − 116 def _getCds(self):
+ − 117 outputFileName = "%sin_cds.gff3" % (self.outputBase)
+ − 118 outputNoFileName = "%sin_nocds.gff3" % (self.outputBase)
+ − 119 self.tmpFileNames.extend([outputFileName, outputNoFileName])
+ − 120 nbOverlaps = self._compare(self.inputFileName, self.inputFormat, self.referenceFiles["CDS"], "gff3", outputFileName)
+ − 121 self._compare(self.inputFileName, self.inputFormat, self.referenceFiles["CDS"], "gff3", outputNoFileName, True)
+ − 122 self._copy(outputFileName, "CDS")
+ − 123 if self.verbosity > 0:
+ − 124 print "%d overlaps in CDS" % (nbOverlaps)
+ − 125 return outputNoFileName
+ − 126
+ − 127 def _getFivePrime(self, inputFileName):
+ − 128 outputFileName = "%sin_five.gff3" % (self.outputBase)
+ − 129 outputNoFileName = "%sin_nofive.gff3" % (self.outputBase)
+ − 130 self.tmpFileNames.extend([outputFileName, outputNoFileName])
+ − 131 nbOverlaps = self._compare(inputFileName, "gff3", self.referenceFiles["five_prime_UTR"], "gff3", outputFileName)
+ − 132 self._compare(inputFileName, "gff3", self.referenceFiles["five_prime_UTR"], "gff3", outputNoFileName, True)
+ − 133 self._copy(outputFileName, "five_prime_UTR")
+ − 134 if self.verbosity > 0:
+ − 135 print "%d overlaps in 5' UTR" % (nbOverlaps)
+ − 136 return outputNoFileName
+ − 137
+ − 138 def _getThreePrime(self, inputFileName):
+ − 139 outputFileName = "%sin_three.gff3" % (self.outputBase)
+ − 140 outputNoFileName = "%sin_nothree.gff3" % (self.outputBase)
+ − 141 self.tmpFileNames.extend([outputFileName, outputNoFileName])
+ − 142 nbOverlaps = self._compare(inputFileName, "gff3", self.referenceFiles["three_prime_UTR"], "gff3", outputFileName)
+ − 143 self._compare(inputFileName, "gff3", self.referenceFiles["three_prime_UTR"], "gff3", outputNoFileName, True)
+ − 144 self._copy(outputFileName, "three_prime_UTR")
+ − 145 if self.verbosity > 0:
+ − 146 print "%d overlaps in 3' UTR" % (nbOverlaps)
+ − 147 return outputNoFileName
+ − 148
+ − 149 def _getNcRna(self, inputFileName):
+ − 150 outputFileName = "%sin_ncRna.gff3" % (self.outputBase)
+ − 151 outputNoFileName = "%sin_noNcRna.gff3" % (self.outputBase)
+ − 152 self.tmpFileNames.extend([outputFileName, outputNoFileName])
+ − 153 nbOverlaps = self._compare(inputFileName, "gff3", self.referenceFiles["ncRNA"], "gff3", outputFileName)
+ − 154 self._compare(inputFileName, "gff3", self.referenceFiles["ncRNA"], "gff3", outputNoFileName, True)
+ − 155 self._copy(outputFileName, "ncRNA")
+ − 156 if self.verbosity > 0:
+ − 157 print "%d overlaps in ncRNA" % (nbOverlaps)
+ − 158 return outputNoFileName
+ − 159
+ − 160 def _getTe(self, inputFileName):
+ − 161 outputFileName = "%sin_te.gff3" % (self.outputBase)
+ − 162 outputNoFileName = "%sin_noTe.gff3" % (self.outputBase)
+ − 163 self.tmpFileNames.extend([outputFileName, outputNoFileName])
+ − 164 nbOverlaps = self._compare(inputFileName, "gff3", self.referenceFiles["transposable_element_gene"], "gff3", outputFileName)
+ − 165 self._compare(inputFileName, "gff3", self.referenceFiles["transposable_element_gene"], "gff3", outputNoFileName, True)
+ − 166 self._copy(outputFileName, "TE")
+ − 167 if self.verbosity > 0:
+ − 168 print "%d overlaps in TE" % (nbOverlaps)
+ − 169 return outputNoFileName
+ − 170
+ − 171 def _getIntron(self, inputFileName):
+ − 172 outputFileName = "%sin_intron.gff3" % (self.outputBase)
+ − 173 outputNoFileName = "%sin_nointron.gff3" % (self.outputBase)
+ − 174 self.tmpFileNames.extend([outputFileName, outputNoFileName])
+ − 175 nbOverlaps = self._compare(inputFileName, "gff3", self.referenceFiles["mRNA"], "gff3", outputFileName)
+ − 176 self._compare(inputFileName, "gff3", self.referenceFiles["mRNA"], "gff3", outputNoFileName, True)
+ − 177 self._copy(outputFileName, "intron")
+ − 178 if self.verbosity > 0:
+ − 179 print "%d overlaps in introns" % (nbOverlaps)
+ − 180 return outputNoFileName
+ − 181
+ − 182 def _getVicinity(self, inputFileName):
+ − 183 guds = GetUpDownStream(self.verbosity-1)
+ − 184 guds.setInputFile(self.referenceFiles["mRNA"], "gff3")
+ − 185 guds.setOutputFile(self.referenceFiles["vic"])
+ − 186 guds.setDistances(self.distance, self.distance)
+ − 187 guds.run()
+ − 188 outputFileName = "%sout_vicinity.gff3" % (self.outputBase)
+ − 189 outputNoFileName = "%sout_novicinity.gff3" % (self.outputBase)
+ − 190 self.tmpFileNames.extend([outputFileName, outputNoFileName])
+ − 191 nbOverlaps = self._compare(inputFileName, "gff3", self.referenceFiles["vic"], "gff3", outputFileName)
+ − 192 nbNoOverlaps = self._compare(inputFileName, "gff3", self.referenceFiles["vic"], "gff3", outputNoFileName, True)
+ − 193 self._copy(outputFileName, "vicinity")
+ − 194 self._copy(outputNoFileName, "intergenic")
+ − 195 if self.verbosity > 0:
+ − 196 print "%d overlaps in vicinity" % (nbOverlaps)
+ − 197 print "%d elsewhere" % (nbNoOverlaps)
+ − 198
+ − 199 def run(self):
+ − 200 self._getReferenceFiles()
+ − 201 outputFileName = self._getCds()
+ − 202 outputFileName = self._getFivePrime(outputFileName)
+ − 203 outputFileName = self._getThreePrime(outputFileName)
+ − 204 outputFileName = self._getNcRna(outputFileName)
+ − 205 outputFileName = self._getTe(outputFileName)
+ − 206 outputFileName = self._getIntron(outputFileName)
+ − 207 self._getVicinity(outputFileName)
+ − 208
+ − 209
+ − 210
+ − 211 if __name__ == "__main__":
+ − 212
+ − 213 # parse command line
+ − 214 description = "Count Loci v1.0.0: Count input elements with respect to CDS, 5' UTR, 3' UTR, intron, downstream, upstream. [Category: Personal]"
+ − 215
+ − 216 parser = OptionParser(description = description)
+ − 217 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in transcript format given by -f]")
+ − 218 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of the input [compulsory] [format: transcript file format]")
+ − 219 parser.add_option("-r", "--reference", dest="reference", action="store", type="string", help="reference file [compulsory] [format: file in GFF format]")
+ − 220 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in GFF3 format]")
+ − 221 parser.add_option("-d", "--distance", dest="distance", action="store", type="int", help="distance up/down stream [compulsory] [format: output file in GFF3 format]")
+ − 222 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
+ − 223 (options, args) = parser.parse_args()
+ − 224
+ − 225 cl = CountLoci(options.verbosity)
+ − 226 cl.setInputFile(options.inputFileName, options.format)
+ − 227 cl.setDistance(options.distance)
+ − 228 cl.setReference(options.reference)
+ − 229 cl.setOutputFileName(options.outputFileName)
+ − 230 cl.run()