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
+ − 32 import struct
+ − 33 import math
+ − 34 import os
+ − 35 from optparse import OptionParser
+ − 36 from commons.core.writer.Gff3Writer import Gff3Writer
+ − 37 from SMART.Java.Python.ncList.NCList import NCList
+ − 38 from SMART.Java.Python.ncList.FileSorter import FileSorter
+ − 39 from commons.core.parsing.ParserChooser import ParserChooser
+ − 40 from SMART.Java.Python.ncList.NCListCursor import NCListCursor
+ − 41 from SMART.Java.Python.structure.Transcript import Transcript
+ − 42
+ − 43 LONGSIZE = struct.calcsize('l')
+ − 44
+ − 45 class FindOverlapsWithOneInterval(object):
+ − 46
+ − 47 def __init__(self, verbosity):
+ − 48 self._sortedFileName = None
+ − 49 self._verbosity = verbosity
+ − 50 self._overlappingNames = []
+ − 51 self._nbOverlaps = 0
+ − 52 self._nbWritten = 0
+ − 53
+ − 54 def __del__(self):
+ − 55 if self._sortedFileName and os.path.exists(self._sortedFileName):
+ − 56 os.remove(self._sortedFileName)
+ − 57
+ − 58 def close(self):
+ − 59 self._iWriter.close()
+ − 60
+ − 61 def setOutputFileName(self, fileName):
+ − 62 self._iWriter = Gff3Writer(fileName)
+ − 63
+ − 64 def setFileName(self, fileName, format):
+ − 65 chooser = ParserChooser(self._verbosity)
+ − 66 chooser.findFormat(format)
+ − 67 self._parser = chooser.getParser(fileName)
+ − 68 self._sortedFileName = "%s_sorted.pkl" % (os.path.splitext(fileName)[0])
+ − 69
+ − 70 def setInterval(self, chromosome, start, end):
+ − 71 self._chromosome = chromosome
+ − 72 self._start = start
+ − 73 self._end = end
+ − 74 self._transcript = Transcript()
+ − 75 self._transcript.setChromosome(chromosome)
+ − 76 self._transcript.setStart(start)
+ − 77 self._transcript.setEnd(end)
+ − 78 self._transcript.setDirection("+")
+ − 79
+ − 80 def setTranscript(self, transcript):
+ − 81 if transcript.__class__.__name__ == "Mapping":
+ − 82 transcript = transcript.getTranscript()
+ − 83 self._chromosome = transcript.getChromosome()
+ − 84 self._start = transcript.getStart()
+ − 85 self._end = transcript.getEnd()
+ − 86 self._transcript = transcript
+ − 87
+ − 88 def prepareIntermediateFiles(self):
+ − 89 fs = FileSorter(self._parser, self._verbosity-4)
+ − 90 fs.selectChromosome(self._chromosome)
+ − 91 fs.perChromosome(False)
+ − 92 fs.setOutputFileName(self._sortedFileName)
+ − 93 fs.sort()
+ − 94 self._nbTotalLines = fs.getNbElements()
+ − 95 self._nbLines = fs.getNbElementsPerChromosome()[self._chromosome]
+ − 96
+ − 97 def createNCList(self):
+ − 98 if self._verbosity > 2:
+ − 99 print "Creating NC-list..."
+ − 100 ncList = NCList(self._verbosity)
+ − 101 ncList.createIndex(True)
+ − 102 ncList.setChromosome(self._chromosome)
+ − 103 ncList.setFileName(self._sortedFileName)
+ − 104 ncList.setNbElements(self._nbTotalLines)
+ − 105 ncList.buildLists()
+ − 106 self.setNCList(ncList, ncList.getIndex())
+ − 107 if self._verbosity > 2:
+ − 108 print " ...done (%ds)" % (endTime - startTime)
+ − 109
+ − 110 def setNCList(self, ncList, index):
+ − 111 self._ncList = ncList
+ − 112 self._indix = index
+ − 113
+ − 114 def binarySearch(self, cursor, startL, endL):
+ − 115 if startL > endL:
+ − 116 return None
+ − 117 middleL = (startL + endL) / 2
+ − 118 cursor.moveSibling(middleL)
+ − 119 overlap = self.isOverlapping(cursor)
+ − 120 if overlap == 0:
+ − 121 if middleL == startL:
+ − 122 return cursor
+ − 123 else:
+ − 124 return self.binarySearch(cursor, startL, middleL)
+ − 125 if overlap == -1:
+ − 126 return self.binarySearch(cursor, middleL + 1, endL)
+ − 127 return self.binarySearch(cursor, startL, middleL - 1)
+ − 128
+ − 129 def compare(self, cursor = None):
+ − 130 self._ncList.openFiles()
+ − 131 if cursor == None:
+ − 132 dump = True
+ − 133 cursor = NCListCursor(None, self._ncList, 0, self._verbosity)
+ − 134 cursor._getSiblingData()
+ − 135 cursor = self.binarySearch(cursor, cursor._firstSiblingLIndex, cursor._lastSiblingLIndex)
+ − 136 if cursor == None:
+ − 137 return
+ − 138 while not cursor.isOut() and self.isOverlapping(cursor) == 0:
+ − 139 self.write(cursor)
+ − 140 newCursor = NCListCursor(cursor)
+ − 141 if newCursor.hasChildren():
+ − 142 newCursor.moveDown()
+ − 143 self.compare(newCursor)
+ − 144 if cursor.isLast():
+ − 145 return
+ − 146 cursor.moveRight()
+ − 147
+ − 148 def isOverlapping(self, cursor):
+ − 149 if self._end < cursor.getStart():
+ − 150 return 1
+ − 151 if self._start > cursor.getEnd():
+ − 152 return -1
+ − 153 return 0
+ − 154
+ − 155 def write(self, cursor):
+ − 156 self._nbOverlaps += 1
+ − 157 refTranscript = cursor.getTranscript()
+ − 158 self._overlappingNames.append(refTranscript.getName())
+ − 159
+ − 160 def dumpWriter(self):
+ − 161 if (not self._overlappingNames) or self._transcript == None:
+ − 162 return
+ − 163 self._transcript.setTagValue("nbOverlaps", len(self._overlappingNames))
+ − 164 self._transcript.setTagValue("overlapsWith", "--".join(self._overlappingNames))
+ − 165 self._iWriter.addTranscript(self._transcript)
+ − 166 self._nbWritten += 1
+ − 167 self._overlappingNames = []
+ − 168
+ − 169 def run(self):
+ − 170 self.prepareIntermediateFiles()
+ − 171 self.createNCList()
+ − 172 self.compare()
+ − 173 self.dumpWriter()
+ − 174 self.close()
+ − 175 if self._verbosity > 0:
+ − 176 print "# refs: %d" % (self._nbLines)
+ − 177 print "# written: %d (%d overlaps)" % (self._nbOverlappingQueries, self._nbOverlaps)
+ − 178
+ − 179
+ − 180 if __name__ == "__main__":
+ − 181 description = "FindOverlapsWithOneInterval: Finds overlaps with one query interval."
+ − 182
+ − 183 parser = OptionParser(description = description)
+ − 184 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="Input file [compulsory] [format: file in transcript format given by -f]")
+ − 185 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="Format of previous file [compulsory] [format: transcript file format]")
+ − 186 parser.add_option("-s", "--start", dest="start", action="store", type="int", help="The start of the query interval [compulsory] [format: int]")
+ − 187 parser.add_option("-e", "--end", dest="end", action="store", type="int", help="The end of the query interval [compulsory] [format: int]")
+ − 188 parser.add_option("-c", "--chromosome", dest="chromosome", action="store", type="string", help="Chromosome of the query interval [compulsory] [format: string]")
+ − 189 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="Output file [compulsory] [format: output file in GFF3 format]")
+ − 190 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="Trace level [format: int] [default: 1]")
+ − 191 (options, args) = parser.parse_args()
+ − 192
+ − 193 iFOWOI = FindOverlapsWithOneInterval(options.verbosity)
+ − 194 iFOWOI.setFileName(options.inputFileName, options.format)
+ − 195 iFOWOI.setInterval(options.chromosome, options.start, options.end)
+ − 196 iFOWOI.setOutputFileName(options.outputFileName)
+ − 197 iFOWOI.run()
