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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 """Get the first element (exon / intron) from a list of transcripts"""
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32
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33 import os
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34 from optparse import OptionParser
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35 from commons.core.writer.Gff3Writer import *
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36 from SMART.Java.Python.structure.TranscriptContainer import *
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37 from SMART.Java.Python.misc.Progress import *
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38
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39
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40 if __name__ == "__main__":
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41
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42 # parse command line
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43 description = "Get Element v1.0.1: Get the first element (exon / intron) from a list of transcripts. [Category: Personnal]"
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44
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45 parser = OptionParser(description = description)
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46 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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47 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of file [compulsory] [format: transcript file format]")
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48 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in GFF3 format]")
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49 parser.add_option("-y", "--mysql", dest="mysql", action="store_true", default=False, help="mySQL output [format: bool] [default: false]")
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50 parser.add_option("-t", "--type", dest="type", action="store", type="string", help="type of the element [format: choice (exon, intron)]")
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51 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
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52 parser.add_option("-l", "--log", dest="log", action="store_true", default=False, help="write a log file [format: bool] [default: false]")
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53 (options, args) = parser.parse_args()
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54
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55 parser = TranscriptContainer(options.inputFileName, options.format, options.verbosity)
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56 writer = Gff3Writer(options.outputFileName, options.verbosity)
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57 sqlWriter = MySqlTranscriptWriter(options.outputFileName, options.verbosity)
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58
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59 nbLines = parser.getNbTranscripts()
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60 print "%i lines found" % (nbLines)
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61
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62 # treat transcripts
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63 nbWritten = 0
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64 nbUsed = 0
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65 progress = Progress(nbLines, "Analyzing transcripts of " + options.inputFileName, options.verbosity)
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66 for transcript in parser.getIterator():
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67
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68 outTranscript = Transcript()
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69 outTranscript.setName(transcript.getName())
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70 outTranscript.setDirection(transcript.getDirection())
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71 outTranscript.setChromosome(transcript.getChromosome())
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72
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73 if options.type == "exon":
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74 if len(transcript.getExons()) > 1:
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75 transcript.sortExons()
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76 outTranscript.setStart(transcript.getExons()[0].getStart())
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77 outTranscript.setEnd(transcript.getExons()[0].getEnd())
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78 writer.addTranscript(outTranscript)
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79 if options.mysql:
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80 sqlWriter.addTranscript(transcript)
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81 nbWritten += 1
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82 nbUsed += 1
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83 elif options.type == "intron":
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84 used = False
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85 for intron in transcript.getIntrons():
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86 used = True
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87 thisTranscript = Transcript()
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88 thisTranscript.copy(outTranscript)
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89 thisTranscript.setStart(intron.getStart())
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90 thisTranscript.setEnd(intron.getEnd())
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91 writer.addTranscript(thisTranscript)
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92 if options.mysql:
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93 sqlWriter.addTranscript(transcript)
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94 nbWritten += 1
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95 if used:
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96 nbUsed += 1
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97 else:
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98 sys.exit("Cannot understan type %s" % (options.type))
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99 progress.inc()
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100 progress.done()
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101
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102 if options.mysql:
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103 sqlWriter.write()
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104
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105 print "nb sequences used: %d" % (nbUsed)
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106 print "nb elements used: %d" % (nbWritten)
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