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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 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.Transcript import Transcript
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35 from SMART.Java.Python.misc.Progress import Progress
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36
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37 zeroBaseToOneBaseConvertor = (lambda x: x - 1 if x > 0 else x)
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38
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39 class GetExons(object):
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40
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41 def __init__(self, verbosity):
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42 self.verbosity = verbosity
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43 self.selection = False
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44
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45 def setInputFile(self, fileName, format):
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46 chooser = ParserChooser(self.verbosity)
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47 chooser.findFormat(format)
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48 self.parser = chooser.getParser(fileName)
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49
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50 def setSelection(self, selection):
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51 if selection == None:
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52 return
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53 self.selection = True
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54 self.selectionItems = []
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55 self.selectionIntervals = []
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56 for part in selection.split(","):
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57 try:
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58 splittedPart = map(int, part.split(".."))
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59 except Exception:
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60 raise Exception("Elements '" + splittedPart + "' of selection '" + selection + "' do no seem to be integers!")
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61 if len(splittedPart) == 1:
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62 self.selectionItems.append(splittedPart[0])
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63 elif len(splittedPart) == 2:
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64 self.selectionIntervals.append((splittedPart[0], splittedPart[1]))
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65 else:
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66 raise Exception("Cannot parse elements '" + splittedPart + "' of selection '" + selection + "'!")
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67
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68 def getSelectionExonIndices(self, nbExons):
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69 if not self.selection:
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70 return range(nbExons)
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71 indices = []
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72 for item in self.selectionItems:
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73 indices.append(range(nbExons)[zeroBaseToOneBaseConvertor(item)])
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74 for start, end in self.selectionIntervals:
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75 start, end = map(zeroBaseToOneBaseConvertor, (start, end))
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76 if end > 0:
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77 end += 1
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78 indices.extend(range(nbExons)[start:end])
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79 return indices
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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 run(self):
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85 progress = Progress(self.parser.getNbTranscripts(), "Reading input file", self.verbosity)
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86 nbExons = 0
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87 for cpt1, transcript in enumerate(self.parser.getIterator()):
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88 selectedExons = self.getSelectionExonIndices(transcript.getNbExons())
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89 transcript.sortExons()
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90 for cpt2, exon in enumerate(transcript.getExons()):
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91 if cpt2 not in selectedExons:
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92 continue
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93 exonTranscript = Transcript()
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94 exonTranscript.copy(exon)
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95 if "Parent" in exonTranscript.tags:
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96 del exonTranscript.tags["Parent"]
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97 exonTranscript.tags["feature"] = "transcript"
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98 if "ID" not in exonTranscript.tags or exonTranscript.tags["ID"] == "unnamed transcript":
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99 exonTranscript.tags["ID"] = "exon_%d-%d" % (cpt1+1, cpt2+1)
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100 if exonTranscript.getName() == "unnamed transcript":
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101 exonTranscript.setName("exon_%d-%d" % (cpt1+1, cpt2+1))
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102 self.writer.addTranscript(exonTranscript)
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103 nbExons += 1
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104 progress.inc()
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105 self.writer.write()
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106 self.writer.close()
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107 progress.done()
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108 if self.verbosity > 1:
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109 print "%d transcripts read" % (self.parser.getNbTranscripts())
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110 print "%d exons written" % (nbExons)
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111
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112 if __name__ == "__main__":
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113
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114 description = "Get Exons v1.0.1: Get the exons of a set of transcripts. [Category: Data Modification]"
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115
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116 parser = OptionParser(description = description)
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117 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in transcript format given by -f]")
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118 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of file [compulsory] [format: transcript file format]")
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119 parser.add_option("-s", "--select", dest="select", action="store", default=None, type="string", help="select some of the exons (like '1,2,5..-3,-1') [format: string]")
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120 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [format: output file in GFF3 format]")
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121 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
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122 (options, args) = parser.parse_args()
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123
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124 ge = GetExons(options.verbosity)
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125 ge.setInputFile(options.inputFileName, options.format)
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126 ge.setSelection(options.select)
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127 ge.setOutputFile(options.outputFileName)
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128 ge.run()
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