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1 #! /usr/bin/env python
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2 #
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3 # Copyright INRA-URGI 2009-2010
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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
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32 import os
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33 import struct
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34 from optparse import OptionParser
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35 from commons.core.parsing.GffParser import GffParser
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36 from commons.core.writer.Gff3Writer import Gff3Writer
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37
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38 LONGSIZE = struct.calcsize('l')
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39
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40 class FindOverlaps_naif(object):
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41
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42 def __init__(self, inputRefGff3FileName, inputQueryGff3FileName):
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43 self._inputRefGff3FileName = inputRefGff3FileName
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44 self._inputQueryGff3FileName = inputQueryGff3FileName
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45
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46 def close(self):
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47 self._iGff3Writer.close()
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48
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49 def setGff3FileName(self, fileName):
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50 self._inputRefGff3FileName = fileName
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51
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52 def setQueryGff3FileName(self, fileName):
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53 self._inputQueryGff3FileName = fileName
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54
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55 def setOutputGff3FileName(self, outputGff3FileName):
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56 if outputGff3FileName != '':
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57 self._outputGff3FileName = outputGff3FileName
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58 self._iGff3Writer = Gff3Writer(self._outputGff3FileName)
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59
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60 def run(self):
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61 queryParser = GffParser(self._inputQueryGff3FileName, 0)
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62 for queryTranscript in queryParser.getIterator():
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63 ids = []
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64 refParser = GffParser(self._inputRefGff3FileName, 0)
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65 for refTranscript in refParser.getIterator():
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66 if queryTranscript.overlapWith(refTranscript):
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67 ids.append(refTranscript.getTagValue('ID'))
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68 if ids:
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69 queryTranscript.setTagValue("nbOverlaps", len(ids))
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70 queryTranscript.setTagValue("overlapsWith", "--".join(ids))
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71 self._iGff3Writer.addTranscript(queryTranscript)
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72
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73 if __name__ == "__main__":
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74 description = "FindOverlapsWithSeveralInterval: Finds overlaps with several query intervals."
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75
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76 parser = OptionParser(description = description)
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77 parser.add_option("-i", "--inputRef", dest="inputRefGff3FileName", action="store", type="string", help="Reference input file [compulsory] [format: file in gff3 format]")
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78 parser.add_option("-j", "--inputQuery", dest="inputQueryGff3FileName", action="store", type="string", help="Query input file [compulsory] [format: file in gff3 format]")
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79 parser.add_option("-o", "--output", dest="outputGff3FileName", action="store", type="string", help="output file [compulsory] [format: output file in gff3 format]")
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80 (options, args) = parser.parse_args()
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81
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82 iFON = FindOverlaps_naif(options.inputRefGff3FileName, options.inputQueryGff3FileName)
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83 iFON.setOutputGff3FileName(options.outputGff3FileName)
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84 iFON.run()
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85 iFON.close()
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