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