6
+ − 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, struct, time, random
+ − 32 from optparse import OptionParser
+ − 33 from commons.core.parsing.ParserChooser import ParserChooser
+ − 34 from commons.core.writer.Gff3Writer import Gff3Writer
+ − 35 from SMART.Java.Python.structure.Transcript import Transcript
+ − 36 from SMART.Java.Python.structure.Interval import Interval
+ − 37 from SMART.Java.Python.ncList.NCList import NCList
+ − 38 from SMART.Java.Python.ncList.NCListCursor import NCListCursor
+ − 39 from SMART.Java.Python.ncList.NCListFilePickle import NCListFilePickle, 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 from SMART.Java.Python.misc import Utils
+ − 44 try:
+ − 45 import cPickle as pickle
+ − 46 except:
+ − 47 import pickle
+ − 48
+ − 49 REFERENCE = 0
+ − 50 QUERY = 1
+ − 51 TYPES = (REFERENCE, QUERY)
+ − 52 TYPETOSTRING = {0: "reference", 1: "query"}
+ − 53
+ − 54 class RestrictFromCoverage(object):
+ − 55
+ − 56 def __init__(self, verbosity = 1):
+ − 57 self._verbosity = verbosity
+ − 58 self._randomNumber = random.randint(0, 100000)
+ − 59 self._nbWritten = 0
+ − 60 self._nbLines = dict([type, 0] for type in TYPES)
+ − 61 self._splittedFileNames = dict([type, {}] for type in TYPES)
+ − 62 self._nbElementsPerChromosome = dict([type, {}] for type in TYPES)
+ − 63 self._nbElements = dict([type, 0] for type in TYPES)
+ − 64
+ − 65 def __del__(self):
+ − 66 pass
+ − 67
+ − 68 def _close(self):
+ − 69 self._writer.close()
+ − 70
+ − 71 def setInputFileName(self, fileName, format, type):
+ − 72 chooser = ParserChooser(self._verbosity)
+ − 73 chooser.findFormat(format)
+ − 74 parser = chooser.getParser(fileName)
+ − 75 sortedFileName = "%s_%d_%d_sorted.pkl" % (os.path.splitext(fileName)[0], self._randomNumber, type)
+ − 76 if self._verbosity > 2:
+ − 77 print "Preparing %s file..." % (TYPETOSTRING[type])
+ − 78 startTime = time.time()
+ − 79 fs = FileSorter(parser, self._verbosity-1)
+ − 80 fs.perChromosome(True)
+ − 81 fs.setOutputFileName(sortedFileName)
+ − 82 fs.sort()
+ − 83 self._nbLines[type] = fs.getNbElements()
+ − 84 self._splittedFileNames[type] = fs.getOutputFileNames()
+ − 85 self._nbElementsPerChromosome[type] = fs.getNbElementsPerChromosome()
+ − 86 self._nbElements[type] = fs.getNbElements()
+ − 87 endTime = time.time()
+ − 88 if self._verbosity > 2:
+ − 89 print " ...done (%ds)" % (endTime - startTime)
+ − 90
+ − 91 def setOutputFileName(self, outputFileName):
+ − 92 self._writer = Gff3Writer(outputFileName)
+ − 93
+ − 94 def setPercent(self, minPercent, maxPercent):
+ − 95 self._minPercent = minPercent
+ − 96 self._maxPercent = maxPercent
+ − 97
+ − 98 def setNbNucleotides(self, minNb, maxNb):
+ − 99 self._minNucleotides = minNb
+ − 100 self._maxNucleotides = maxNb
+ − 101
+ − 102 def setOverlap(self, minOverlap, maxOverlap):
+ − 103 self._minOverlap = minOverlap
+ − 104 self._maxOverlap = maxOverlap
+ − 105
+ − 106 def setStrands(self, boolean):
+ − 107 self._twoStrands = boolean
+ − 108
+ − 109 def _compareChromosome(self, chromosome):
+ − 110 firstOverlap = 0
+ − 111 parser1 = NCListFileUnpickle(self._splittedFileNames[QUERY][chromosome], self._verbosity)
+ − 112 parser2 = NCListFileUnpickle(self._splittedFileNames[REFERENCE][chromosome], self._verbosity)
+ − 113 progress = Progress(self._nbElementsPerChromosome[QUERY][chromosome], "Analyzing %s" % (chromosome), self._verbosity)
+ − 114 for transcript1 in parser1.getIterator():
+ − 115 firstOverlap = self._compareList(transcript1, parser2)
+ − 116 parser2.setInitAddress(firstOverlap)
+ − 117 progress.inc()
+ − 118 progress.done()
+ − 119
+ − 120 def _compareList(self, transcript1, parser2):
+ − 121 values = []
+ − 122 for exon in transcript1.getExons():
+ − 123 values.append([0.0] * exon.getSize())
+ − 124 firstOverlap = None
+ − 125 for transcript2 in parser2.getIterator():
+ − 126 address = parser2.getCurrentTranscriptAddress()
+ − 127 nbElements = float(transcript2.getTagValue("nbElements")) if "nbElements" in transcript2.getTagNames() else 1.0
+ − 128 nbOccurrences = float(transcript2.getTagValue("nbOccurrences")) if "nbOccurrences" in transcript2.getTagNames() else 1.0
+ − 129 nbElements /= nbOccurrences
+ − 130 if transcript2.getStart() > transcript1.getEnd():
+ − 131 if firstOverlap == None:
+ − 132 firstOverlap = address
+ − 133 if self._checkValues(values):
+ − 134 self._printTranscript(transcript1)
+ − 135 return firstOverlap
+ − 136 elif transcript1.overlapWith(transcript2):
+ − 137 if firstOverlap == None:
+ − 138 firstOverlap = address
+ − 139 values = self._compareTranscript(transcript1, transcript2, values, nbElements)
+ − 140 if self._checkValues(values):
+ − 141 self._printTranscript(transcript1)
+ − 142 return firstOverlap
+ − 143
+ − 144 def _compareTranscript(self, transcript1, transcript2, values, nbElements):
+ − 145 if not transcript1.overlapWith(transcript2) or ((self._twoStrands) and transcript1.getDirection() != transcript2.getDirection()):
+ − 146 return values
+ − 147 for id1, exon1 in enumerate(transcript1.getExons()):
+ − 148 for exon2 in transcript2.getExons():
+ − 149 values[id1] = map(sum, zip(values[id1], self._compareExon(exon1, exon2, nbElements)))
+ − 150 return values
+ − 151
+ − 152 def _compareExon(self, exon1, exon2, nbElements):
+ − 153 array = [0.0] * exon1.getSize()
+ − 154 if not exon1.overlapWith(exon2) or ((self._twoStrands) and exon1.getDirection() != exon2.getDirection()):
+ − 155 return array
+ − 156 for pos in range(max(exon1.getStart(), exon2.getStart()) - exon1.getStart(), min(exon1.getEnd(), exon2.getEnd()) - exon1.getStart()+1):
+ − 157 array[pos] += nbElements
+ − 158 return array
+ − 159
+ − 160 def _filter(self, value):
+ − 161 if self._minOverlap and self._maxOverlap:
+ − 162 return self._minOverlap <= value <= self._maxOverlap
+ − 163 if self._minOverlap:
+ − 164 return self._minOverlap <= value
+ − 165 if self._maxOverlap:
+ − 166 return value <= self._maxOverlap
+ − 167 return True
+ − 168
+ − 169 def _checkValues(self, values):
+ − 170 nbValues = sum(map(len, values))
+ − 171 nbPosValues = sum(map(len, [filter(self._filter, valuePart) for valuePart in values]))
+ − 172 ratio = float(nbPosValues) / nbValues * 100
+ − 173 if self._minNucleotides and nbPosValues < self._minNucleotides:
+ − 174 return False
+ − 175 if self._maxNucleotides and nbPosValues > self._maxNucleotides:
+ − 176 return False
+ − 177 if self._minPercent and ratio < self._minPercent:
+ − 178 return False
+ − 179 if self._maxPercent and ratio > self._maxPercent:
+ − 180 return False
+ − 181 return True
+ − 182
+ − 183 def _printTranscript(self, transcript):
+ − 184 self._writer.addTranscript(transcript)
+ − 185 self._nbWritten += 1
+ − 186
+ − 187 def run(self):
+ − 188 for chromosome in sorted(self._splittedFileNames[QUERY].keys()):
+ − 189 self._compareChromosome(chromosome)
+ − 190 self._close()
+ − 191 if self._verbosity > 0:
+ − 192 print "# queries: %d" % (self._nbElements[QUERY])
+ − 193 print "# refs: %d" % (self._nbElements[REFERENCE])
+ − 194 print "# written: %d (%d%%)" % (self._nbWritten, 0 if self._nbElements[QUERY] == 0 else round(float(self._nbWritten) / self._nbElements[QUERY] * 100))
+ − 195
+ − 196
+ − 197 if __name__ == "__main__":
+ − 198 description = "Restrict From Coverage v1.0.0: Select the elements from the first set which have a given coverage. [Category: Data Comparison]"
+ − 199
+ − 200 parser = OptionParser(description = description)
+ − 201 parser.add_option("-i", "--input1", dest="inputFileName1", action="store", type="string", help="input file 1 [compulsory] [format: file in transcript format given by -f]")
+ − 202 parser.add_option("-f", "--format1", dest="format1", action="store", type="string", help="format of file 1 [compulsory] [format: transcript file format]")
+ − 203 parser.add_option("-j", "--input2", dest="inputFileName2", action="store", type="string", help="input file 2 [compulsory] [format: file in transcript format given by -g]")
+ − 204 parser.add_option("-g", "--format2", dest="format2", action="store", type="string", help="format of file 2 [compulsory] [format: transcript file format]")
+ − 205 parser.add_option("-o", "--output", dest="output", action="store", default=None, type="string", help="output file [compulsory] [format: output file in GFF3 format]")
+ − 206 parser.add_option("-n", "--minNucleotides", dest="minNucleotides", action="store", default=None, type="int", help="minimum number of nucleotides overlapping to declare an overlap [format: int]")
+ − 207 parser.add_option("-N", "--maxNucleotides", dest="maxNucleotides", action="store", default=None, type="int", help="maximum number of nucleotides overlapping to declare an overlap [format: int]")
+ − 208 parser.add_option("-p", "--minPercent", dest="minPercent", action="store", default=None, type="int", help="minimum percentage of nucleotides overlapping to declare an overlap [format: int]")
+ − 209 parser.add_option("-P", "--maxPercent", dest="maxPercent", action="store", default=None, type="int", help="maximum percentage of nucleotides overlapping to declare an overlap [format: int]")
+ − 210 parser.add_option("-e", "--minOverlap", dest="minOverlap", action="store", default=None, type="int", help="minimum number of elements from 2nd file to declare an overlap [format: int]")
+ − 211 parser.add_option("-E", "--maxOverlap", dest="maxOverlap", action="store", default=None, type="int", help="maximum number of elements from 2nd file to declare an overlap [format: int]")
+ − 212 parser.add_option("-s", "--strands", dest="strands", action="store_true", default=False, help="consider the two strands separately [format: bool] [default: false]")
+ − 213 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
+ − 214 (options, args) = parser.parse_args()
+ − 215
+ − 216 rfc = RestrictFromCoverage(options.verbosity)
+ − 217 rfc.setInputFileName(options.inputFileName1, options.format1, QUERY)
+ − 218 rfc.setInputFileName(options.inputFileName2, options.format2, REFERENCE)
+ − 219 rfc.setOutputFileName(options.output)
+ − 220 rfc.setNbNucleotides(options.minNucleotides, options.maxNucleotides)
+ − 221 rfc.setPercent(options.minPercent, options.maxPercent)
+ − 222 rfc.setOverlap(options.minOverlap, options.maxOverlap)
+ − 223 rfc.setStrands(options.strands)
+ − 224 rfc.run()
