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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 from optparse import OptionParser
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32 from commons.core.parsing.ParserChooser import ParserChooser
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33 from commons.core.writer.TranscriptWriter import TranscriptWriter
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34 from SMART.Java.Python.structure.Interval import Interval
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35 from SMART.Java.Python.structure.Transcript import Transcript
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36 from SMART.Java.Python.structure.Mapping import Mapping
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37 from SMART.Java.Python.misc.Progress import Progress
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38 from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress
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39
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40 MINBIN = 3
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41 MAXBIN = 7
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42 REFERENCE = 0
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43 QUERY = 1
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44
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45 def getBin(start, end):
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46 for i in range(MINBIN, MAXBIN + 1):
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47 binLevel = 10 ** i
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48 if int(start / binLevel) == int(end / binLevel):
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49 return int(i * 10 ** (MAXBIN + 1) + int(start / binLevel))
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50 return int((MAXBIN + 1) * 10 ** (MAXBIN + 1))
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51
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52 def getOverlappingBins(start, end):
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53 array = []
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54 bigBin = int((MAXBIN + 1) * 10 ** (MAXBIN + 1))
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55 for i in range(MINBIN, MAXBIN + 1):
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56 binLevel = 10 ** i
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57 array.append((int(i * 10 ** (MAXBIN + 1) + int(start / binLevel)), int(i * 10 ** (MAXBIN + 1) + int(end / binLevel))))
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58 array.append((bigBin, bigBin))
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59 return array
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60
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61
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62 class GetIntersection(object):
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63
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64 def __init__(self, verbosity):
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65 self.verbosity = verbosity
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66 self.nbQueries = 0
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67 self.nbRefs = 0
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68 self.nbWritten = 0
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69 self.bins = {}
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70
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71 def setReferenceFile(self, fileName, format):
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72 chooser = ParserChooser(self.verbosity)
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73 chooser.findFormat(format)
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74 self.refParser = chooser.getParser(fileName)
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75
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76 def setQueryFile(self, fileName, format):
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77 chooser = ParserChooser(self.verbosity)
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78 chooser.findFormat(format)
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79 self.queryParser = chooser.getParser(fileName)
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80
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81 def setOutputFile(self, fileName):
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82 self.writer = TranscriptWriter(fileName, "gff3", self.verbosity)
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83
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84 def loadRef(self):
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85 progress = UnlimitedProgress(10000, "Reading references", self.verbosity)
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86 for transcript in self.refParser.getIterator():
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87 if transcript.__class__.__name__ == "Mapping":
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88 transcript = transcript.getTranscript()
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89 chromosome = transcript.getChromosome()
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90 bin = getBin(transcript.getStart(), transcript.getEnd())
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91 if chromosome not in self.bins:
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92 self.bins[chromosome] = {}
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93 if bin not in self.bins[chromosome]:
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94 self.bins[chromosome][bin] = []
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95 self.bins[chromosome][bin].append(transcript)
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96 self.nbRefs += 1
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97 progress.inc()
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98 progress.done()
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99
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100 def _compareTranscript(self, queryTranscript):
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101 queryChromosome = queryTranscript.getChromosome()
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102 if queryChromosome not in self.bins:
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103 return None
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104 queryStart = queryTranscript.getStart()
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105 queryEnd = queryTranscript.getEnd()
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106 bins = getOverlappingBins(queryStart, queryEnd)
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107 overlaps = []
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108 for binRange in bins:
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109 for bin in range(binRange[0], binRange[1]+1):
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110 if bin not in self.bins[queryChromosome]:
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111 continue
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112 for refTranscript in self.bins[queryChromosome][bin]:
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113 newTranscript = queryTranscript.getIntersection(refTranscript)
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114 if newTranscript != None:
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115 overlaps.append(newTranscript)
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116 if not overlaps:
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117 return None
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118 newTranscript = overlaps[0]
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119 for transcript in overlaps[1:]:
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120 newTranscript.merge(transcript)
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121 return newTranscript
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122
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123 def compare(self):
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124 progress = UnlimitedProgress(10000, "Comparing queries", self.verbosity)
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125 for queryTranscript in self.queryParser.getIterator():
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126 if queryTranscript.__class__.__name__ == "Mapping":
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127 queryTranscript = queryTranscript.getTranscript()
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128 progress.inc()
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129 self.nbQueries += 1
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130 newTranscript = self._compareTranscript(queryTranscript)
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131 if newTranscript != None:
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132 self.writer.addTranscript(queryTranscript)
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133 self.nbWritten += 1
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134 progress.done()
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135 self.writer.close()
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136
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137 def displayResults(self):
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138 print "# queries: %d" % (self.nbQueries)
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139 print "# refs: %d" % (self.nbRefs)
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140 print "# written: %d" % (self.nbWritten)
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141
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142 def run(self):
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143 self.loadRef()
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144 self.compare()
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145 self.displayResults()
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146
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147 if __name__ == "__main__":
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148
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149 description = "Get Intersection v1.0.0: Shrink the first data set so that all bases covered by the first data set is also covered by the second data set. [Category: Data Comparison]"
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150
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151 parser = OptionParser(description = description)
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152 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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153 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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154 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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155 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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156 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [format: output file in GFF3 format]")
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157 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
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158 (options, args) = parser.parse_args()
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159
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160 gi = GetIntersection(options.verbosity)
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161 gi.setQueryFile(options.inputFileName1, options.format1)
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162 gi.setReferenceFile(options.inputFileName2, options.format2)
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163 gi.setOutputFile(options.outputFileName)
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164 gi.run()
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