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+ − 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, time, MySQLdb
+ − 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.Transcript import Transcript
+ − 36 from SMART.Java.Python.misc.Progress import Progress
+ − 37 from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress
+ − 38
+ − 39
+ − 40 class FindOverlapsWithSeveralIntervalsIndex(object):
+ − 41
+ − 42 def __init__(self, verbosity):
+ − 43 self.verbosity = verbosity
+ − 44 randomNumber = random.randint(0, 10000)
+ − 45 self.dbName = "smartdb"
+ − 46 if "SMARTTMPPATH" in os.environ:
+ − 47 self.dbName = os.join(os.environ["SMARTTMPPATH"], self.dbName)
+ − 48 self.db = MySQLdb.connect(db = self.dbName)
+ − 49 self.tableName = "table_%s" % (randomNumber)
+ − 50 self.nbQueries = 0
+ − 51 self.nbRefs = 0
+ − 52 self.nbOverlaps = 0
+ − 53
+ − 54 def __del__(self):
+ − 55 cursor = self.db.cursor()
+ − 56 cursor.execute("DROP TABLE IF EXISTS %s" % (self.tableName))
+ − 57
+ − 58
+ − 59 def setReferenceFile(self, fileName, format):
+ − 60 cursor = self.db.cursor()
+ − 61 cursor.execute("CREATE TABLE %s (start INT, end INT)" % (self.tableName))
+ − 62 cursor.execute("CREATE INDEX index_%s ON %s (start, end)" % (self.tableName, self.tableName))
+ − 63 chooser = ParserChooser(self.verbosity)
+ − 64 chooser.findFormat(format)
+ − 65 parser = chooser.getParser(fileName)
+ − 66 progress = UnlimitedProgress(1000, "Reading references", self.verbosity)
+ − 67 for transcript in parser.getIterator():
+ − 68 start = transcript.getStart()
+ − 69 end = transcript.getEnd()
+ − 70 cursor = self.db.cursor()
+ − 71 cursor.execute("INSERT INTO %s (start, end) VALUES (%d, %d)" % (self.tableName, start, end))
+ − 72 self.nbRefs += 1
+ − 73 progress.inc()
+ − 74 self.db.commit()
+ − 75 progress.done()
+ − 76
+ − 77 def setQueryFile(self, fileName, format):
+ − 78 chooser = ParserChooser(self.verbosity)
+ − 79 chooser.findFormat(format)
+ − 80 self.queryParser = chooser.getParser(fileName)
+ − 81 self.nbQueries = self.queryParser.getNbTranscripts()
+ − 82
+ − 83 def setOutputFile(self, fileName):
+ − 84 self.writer = TranscriptWriter(fileName, "gff3", self.verbosity)
+ − 85
+ − 86 def compare(self):
+ − 87 progress = Progress(self.nbQueries, "Reading queries", self.verbosity)
+ − 88 startTime = time.time()
+ − 89 for queryTranscript in self.queryParser.getIterator():
+ − 90 queryStart = queryTranscript.getStart()
+ − 91 queryEnd = queryTranscript.getEnd()
+ − 92 command = "SELECT 1 FROM %s WHERE start <= %d and end >= %d" % (self.tableName, queryEnd, queryStart)
+ − 93 cursor = self.db.cursor()
+ − 94 cursor.execute(command)
+ − 95 overlap = False
+ − 96 line = cursor.fetchone()
+ − 97 while line:
+ − 98 overlap = True
+ − 99 line = cursor.fetchone()
+ − 100 if overlap:
+ − 101 self.writer.addTranscript(queryTranscript)
+ − 102 self.nbOverlaps += 1
+ − 103 progress.inc()
+ − 104 progress.done()
+ − 105 endTime = time.time()
+ − 106 self.timeSpent = endTime - startTime
+ − 107
+ − 108 def displayResults(self):
+ − 109 print "# queries: %d" % (self.nbQueries)
+ − 110 print "# refs: %d" % (self.nbRefs)
+ − 111 print "# overlaps: %d" % (self.nbOverlaps)
+ − 112 print "time: %.2gs" % (self.timeSpent)
+ − 113
+ − 114 def run(self):
+ − 115 self.compare()
+ − 116 self.displayResults()
+ − 117
+ − 118 if __name__ == "__main__":
+ − 119
+ − 120 description = "Find Overlaps With Several Intervals Using Indices v1.0.1: Use MySQL to compare intervals. [Category: Personal]"
+ − 121
+ − 122 parser = OptionParser(description = description)
+ − 123 parser.add_option("-i", "--input1", dest="inputFileName1", action="store", type="string", help="query input file [compulsory] [format: file in transcript format given by -f]")
+ − 124 parser.add_option("-f", "--format1", dest="format1", action="store", type="string", help="format of previous file [compulsory] [format: transcript file format]")
+ − 125 parser.add_option("-j", "--input2", dest="inputFileName2", action="store", type="string", help="reference input file [compulsory] [format: file in transcript format given by -g]")
+ − 126 parser.add_option("-g", "--format2", dest="format2", action="store", type="string", help="format of previous file [compulsory] [format: transcript file format]")
+ − 127 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [format: output file in GFF3 format]")
+ − 128 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
+ − 129 (options, args) = parser.parse_args()
+ − 130
+ − 131 fowsii = FindOverlapsWithSeveralIntervalsIndex(options.verbosity)
+ − 132 fowsii.setQueryFile(options.inputFileName1, options.format1)
+ − 133 fowsii.setReferenceFile(options.inputFileName2, options.format2)
+ − 134 fowsii.setOutputFile(options.outputFileName)
+ − 135 fowsii.run()
+ − 136
+ − 137
