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1 #! /usr/bin/env python
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2 #
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3 # Copyright INRA-URGI 2009-2011
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4 #
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5 # This software is governed by the CeCILL license under French law and
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6 # abiding by the rules of distribution of free software. You can use,
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7 # modify and/ or redistribute the software under the terms of the CeCILL
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8 # license as circulated by CEA, CNRS and INRIA at the following URL
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9 # "http://www.cecill.info".
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10 #
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11 # As a counterpart to the access to the source code and rights to copy,
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12 # modify and redistribute granted by the license, users are provided only
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13 # with a limited warranty and the software's author, the holder of the
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14 # economic rights, and the successive licensors have only limited
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15 # liability.
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16 #
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17 # In this respect, the user's attention is drawn to the risks associated
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18 # with loading, using, modifying and/or developing or reproducing the
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19 # software by the user in light of its specific status of free software,
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20 # that may mean that it is complicated to manipulate, and that also
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21 # therefore means that it is reserved for developers and experienced
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22 # professionals having in-depth computer knowledge. Users are therefore
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23 # encouraged to load and test the software's suitability as regards their
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24 # requirements in conditions enabling the security of their systems and/or
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25 # data to be ensured and, more generally, to use and operate it in the
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26 # same conditions as regards security.
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27 #
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28 # The fact that you are presently reading this means that you have had
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29 # knowledge of the CeCILL license and that you accept its terms.
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30 #
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31 import random, os, time, MySQLdb
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32 from optparse import OptionParser
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33 from commons.core.parsing.ParserChooser import ParserChooser
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34 from commons.core.writer.TranscriptWriter import TranscriptWriter
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35 from SMART.Java.Python.structure.Transcript import Transcript
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36 from SMART.Java.Python.misc.Progress import Progress
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37 from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress
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38
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39
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40 class FindOverlapsWithSeveralIntervalsIndex(object):
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41
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42 def __init__(self, verbosity):
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43 self.verbosity = verbosity
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44 randomNumber = random.randint(0, 10000)
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45 self.dbName = "smartdb"
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46 if "SMARTTMPPATH" in os.environ:
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47 self.dbName = os.join(os.environ["SMARTTMPPATH"], self.dbName)
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48 self.db = MySQLdb.connect(db = self.dbName)
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49 self.tableName = "table_%s" % (randomNumber)
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50 self.nbQueries = 0
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51 self.nbRefs = 0
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52 self.nbOverlaps = 0
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53
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54 def __del__(self):
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55 cursor = self.db.cursor()
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56 cursor.execute("DROP TABLE IF EXISTS %s" % (self.tableName))
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57
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58
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59 def setReferenceFile(self, fileName, format):
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60 cursor = self.db.cursor()
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61 cursor.execute("CREATE TABLE %s (start INT, end INT)" % (self.tableName))
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62 cursor.execute("CREATE INDEX index_%s ON %s (start, end)" % (self.tableName, self.tableName))
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63 chooser = ParserChooser(self.verbosity)
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64 chooser.findFormat(format)
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65 parser = chooser.getParser(fileName)
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66 progress = UnlimitedProgress(1000, "Reading references", self.verbosity)
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67 for transcript in parser.getIterator():
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68 start = transcript.getStart()
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69 end = transcript.getEnd()
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70 cursor = self.db.cursor()
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71 cursor.execute("INSERT INTO %s (start, end) VALUES (%d, %d)" % (self.tableName, start, end))
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72 self.nbRefs += 1
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73 progress.inc()
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74 self.db.commit()
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75 progress.done()
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76
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77 def setQueryFile(self, fileName, format):
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78 chooser = ParserChooser(self.verbosity)
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79 chooser.findFormat(format)
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80 self.queryParser = chooser.getParser(fileName)
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81 self.nbQueries = self.queryParser.getNbTranscripts()
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82
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83 def setOutputFile(self, fileName):
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84 self.writer = TranscriptWriter(fileName, "gff3", self.verbosity)
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85
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86 def compare(self):
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87 progress = Progress(self.nbQueries, "Reading queries", self.verbosity)
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88 startTime = time.time()
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89 for queryTranscript in self.queryParser.getIterator():
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90 queryStart = queryTranscript.getStart()
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91 queryEnd = queryTranscript.getEnd()
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92 command = "SELECT 1 FROM %s WHERE start <= %d and end >= %d" % (self.tableName, queryEnd, queryStart)
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93 cursor = self.db.cursor()
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94 cursor.execute(command)
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95 overlap = False
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96 line = cursor.fetchone()
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97 while line:
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98 overlap = True
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99 line = cursor.fetchone()
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100 if overlap:
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101 self.writer.addTranscript(queryTranscript)
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102 self.nbOverlaps += 1
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103 progress.inc()
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104 progress.done()
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105 endTime = time.time()
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106 self.timeSpent = endTime - startTime
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107
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108 def displayResults(self):
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109 print "# queries: %d" % (self.nbQueries)
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110 print "# refs: %d" % (self.nbRefs)
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111 print "# overlaps: %d" % (self.nbOverlaps)
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112 print "time: %.2gs" % (self.timeSpent)
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113
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114 def run(self):
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115 self.compare()
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116 self.displayResults()
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117
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118 if __name__ == "__main__":
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119
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120 description = "Find Overlaps With Several Intervals Using Indices v1.0.1: Use MySQL to compare intervals. [Category: Personal]"
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121
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122 parser = OptionParser(description = description)
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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]")
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124 parser.add_option("-f", "--format1", dest="format1", action="store", type="string", help="format of previous file [compulsory] [format: transcript file format]")
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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]")
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126 parser.add_option("-g", "--format2", dest="format2", action="store", type="string", help="format of previous file [compulsory] [format: transcript file format]")
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127 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [format: output file in GFF3 format]")
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128 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
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129 (options, args) = parser.parse_args()
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130
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131 fowsii = FindOverlapsWithSeveralIntervalsIndex(options.verbosity)
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132 fowsii.setQueryFile(options.inputFileName1, options.format1)
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133 fowsii.setReferenceFile(options.inputFileName2, options.format2)
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134 fowsii.setOutputFile(options.outputFileName)
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135 fowsii.run()
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136
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137
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