6
+ − 1 #! /usr/bin/env python
+ − 2 #
+ − 3 # Copyright INRA-URGI 2009-2011
+ − 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 random, os, os.path, time, sqlite3
+ − 32 from optparse import OptionParser
+ − 33 from commons.core.parsing.ParserChooser import ParserChooser
+ − 34 from commons.core.writer.TranscriptWriter import TranscriptWriter
+ − 35 from SMART.Java.Python.structure.Interval import Interval
+ − 36 from SMART.Java.Python.structure.Transcript import Transcript
+ − 37 from SMART.Java.Python.structure.Mapping import Mapping
+ − 38 from SMART.Java.Python.misc.Progress import Progress
+ − 39 from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress
+ − 40 try:
+ − 41 import cPickle as pickle
+ − 42 except:
+ − 43 import pickle
+ − 44
+ − 45 MINBIN = 3
+ − 46 MAXBIN = 7
+ − 47
+ − 48
+ − 49 def getBin(start, end):
+ − 50 for i in range(MINBIN, MAXBIN + 1):
+ − 51 binLevel = 10 ** i
+ − 52 if int(start / binLevel) == int(end / binLevel):
+ − 53 return int(i * 10 ** (MAXBIN + 1) + int(start / binLevel))
+ − 54 return int((MAXBIN + 1) * 10 ** (MAXBIN + 1))
+ − 55
+ − 56 def getOverlappingBins(start, end):
+ − 57 array = []
+ − 58 bigBin = int((MAXBIN + 1) * 10 ** (MAXBIN + 1))
+ − 59 for i in range(MINBIN, MAXBIN + 1):
+ − 60 binLevel = 10 ** i
+ − 61 array.append((int(i * 10 ** (MAXBIN + 1) + int(start / binLevel)), int(i * 10 ** (MAXBIN + 1) + int(end / binLevel))))
+ − 62 array.append((bigBin, bigBin))
+ − 63 return array
+ − 64
+ − 65
+ − 66 class FindOverlapsWithSeveralIntervalsBin(object):
+ − 67
+ − 68 def __init__(self, verbosity):
+ − 69 self.verbosity = verbosity
+ − 70 self.randomNumber = random.randint(0, 10000)
+ − 71 self.dbName = "smartdb%d" % (self.randomNumber)
+ − 72 if "SMARTTMPPATH" in os.environ:
+ − 73 self.dbName = os.join(os.environ["SMARTTMPPATH"], self.dbName)
+ − 74 self.connection = sqlite3.connect(self.dbName)
+ − 75 self.tableNames = {}
+ − 76 self.nbQueries = 0
+ − 77 self.nbRefs = 0
+ − 78 self.nbWritten = 0
+ − 79 self.nbOverlaps = 0
+ − 80 cursor = self.connection.cursor()
+ − 81 cursor.execute("PRAGMA journal_mode = OFF")
+ − 82 cursor.execute("PRAGMA synchronous = 0")
+ − 83 cursor.execute("PRAGMA locking_mode = EXCLUSIVE")
+ − 84 cursor.execute("PRAGMA count_change = OFF")
+ − 85 cursor.execute("PRAGMA temp_store = 2")
+ − 86
+ − 87 def __del__(self):
+ − 88 cursor = self.connection.cursor()
+ − 89 for tableName in self.tableNames.values():
+ − 90 cursor.execute("DROP TABLE IF EXISTS %s" % (tableName))
+ − 91 if os.path.exists(self.dbName):
+ − 92 os.remove(self.dbName)
+ − 93
+ − 94 def createTable(self, chromosome):
+ − 95 cursor = self.connection.cursor()
+ − 96 tableName = "tmpTable_%s_%d" % (chromosome.replace("-", "_"), self.randomNumber)
+ − 97 cursor.execute("CREATE TABLE %s (start INT, end INT, transcript BLOB, bin INT)" % (tableName))
+ − 98 cursor.execute("CREATE INDEX index_%s ON %s (bin)" % (tableName, tableName))
+ − 99 self.tableNames[chromosome] = tableName
+ − 100
+ − 101 def setReferenceFile(self, fileName, format):
+ − 102 chooser = ParserChooser(self.verbosity)
+ − 103 chooser.findFormat(format)
+ − 104 parser = chooser.getParser(fileName)
+ − 105 startTime = time.time()
+ − 106 if self.verbosity > 2:
+ − 107 print "Storing into table"
+ − 108 for transcript in parser.getIterator():
+ − 109 if transcript.__class__.__name__ == "Mapping":
+ − 110 transcript = transcript.getTranscript()
+ − 111 transcriptString = pickle.dumps(transcript)
+ − 112 chromosome = transcript.getChromosome()
+ − 113 if chromosome not in self.tableNames:
+ − 114 self.createTable(chromosome)
+ − 115 start = transcript.getStart()
+ − 116 end = transcript.getEnd()
+ − 117 bin = getBin(start, end)
+ − 118 cursor = self.connection.cursor()
+ − 119 cursor.execute("INSERT INTO %s (start, end, transcript, bin) VALUES (?, ?, ?, ?)" % (self.tableNames[chromosome]), (start, end, sqlite3.Binary(transcriptString), bin))
+ − 120 self.nbRefs += 1
+ − 121 self.connection.commit()
+ − 122 endTime = time.time()
+ − 123 if self.verbosity > 2:
+ − 124 print " ...done (%.2gs)" % (endTime - startTime)
+ − 125
+ − 126 def setQueryFile(self, fileName, format):
+ − 127 chooser = ParserChooser(self.verbosity)
+ − 128 chooser.findFormat(format)
+ − 129 self.queryParser = chooser.getParser(fileName)
+ − 130 self.nbQueries = self.queryParser.getNbItems()
+ − 131
+ − 132 def setOutputFile(self, fileName):
+ − 133 self.writer = TranscriptWriter(fileName, "gff3", self.verbosity)
+ − 134
+ − 135 def compare(self):
+ − 136 progress = Progress(self.nbQueries, "Reading queries", self.verbosity)
+ − 137 startTime = time.time()
+ − 138 for queryTranscript in self.queryParser.getIterator():
+ − 139 if queryTranscript.__class__.__name__ == "Mapping":
+ − 140 queryTranscript = queryTranscript.getTranscript()
+ − 141 progress.inc()
+ − 142 queryChromosome = queryTranscript.getChromosome()
+ − 143 if queryChromosome not in self.tableNames:
+ − 144 continue
+ − 145 queryStart = queryTranscript.getStart()
+ − 146 queryEnd = queryTranscript.getEnd()
+ − 147 bins = getOverlappingBins(queryStart, queryEnd)
+ − 148 commands = []
+ − 149 for bin in bins:
+ − 150 command = "SELECT * FROM %s WHERE bin " % (self.tableNames[queryChromosome])
+ − 151 if bin[0] == bin[1]:
+ − 152 command += "= %d" % (bin[0])
+ − 153 else:
+ − 154 command += "BETWEEN %d AND %d" % (bin[0], bin[1])
+ − 155 commands.append(command)
+ − 156 command = " UNION ".join(commands)
+ − 157 cursor = self.connection.cursor()
+ − 158 cursor.execute(command)
+ − 159 overlap = False
+ − 160 line = cursor.fetchone()
+ − 161 while line:
+ − 162 refStart, refEnd, refTranscriptString, refBin = line
+ − 163 if refStart <= queryEnd and refEnd >= queryStart:
+ − 164 refTranscript = pickle.loads(str(refTranscriptString))
+ − 165 if refTranscript.overlapWith(queryTranscript):
+ − 166 overlap = True
+ − 167 self.nbOverlaps += 1
+ − 168 line = cursor.fetchone()
+ − 169 if overlap:
+ − 170 self.writer.addTranscript(queryTranscript)
+ − 171 self.nbWritten += 1
+ − 172 progress.done()
+ − 173 endTime = time.time()
+ − 174 self.timeSpent = endTime - startTime
+ − 175
+ − 176 def displayResults(self):
+ − 177 print "# queries: %d" % (self.nbQueries)
+ − 178 print "# refs: %d" % (self.nbRefs)
+ − 179 print "# written: %d (%d overlaps)" % (self.nbWritten, self.nbOverlaps)
+ − 180 print "time: %.2gs" % (self.timeSpent)
+ − 181
+ − 182 def run(self):
+ − 183 self.compare()
+ − 184 self.displayResults()
+ − 185
+ − 186 if __name__ == "__main__":
+ − 187
+ − 188 description = "Find Overlaps With Several Intervals Using Bin v1.0.1: Use MySQL binning to compare intervals. [Category: Personal]"
+ − 189
+ − 190 parser = OptionParser(description = description)
+ − 191 parser.add_option("-i", "--input1", dest="inputFileName1", action="store", type="string", help="query input file [compulsory] [format: file in transcript format given by -f]")
+ − 192 parser.add_option("-f", "--format1", dest="format1", action="store", type="string", help="format of previous file [compulsory] [format: transcript file format]")
+ − 193 parser.add_option("-j", "--input2", dest="inputFileName2", action="store", type="string", help="reference input file [compulsory] [format: file in transcript format given by -g]")
+ − 194 parser.add_option("-g", "--format2", dest="format2", action="store", type="string", help="format of previous file [compulsory] [format: transcript file format]")
+ − 195 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [format: output file in GFF3 format]")
+ − 196 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
+ − 197 (options, args) = parser.parse_args()
+ − 198
+ − 199 fowsib = FindOverlapsWithSeveralIntervalsBin(options.verbosity)
+ − 200 fowsib.setQueryFile(options.inputFileName1, options.format1)
+ − 201 fowsib.setReferenceFile(options.inputFileName2, options.format2)
+ − 202 fowsib.setOutputFile(options.outputFileName)
+ − 203 fowsib.run()
+ − 204
