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+ − 1 #! /usr/bin/env python
+ − 2 #
+ − 3 # Copyright INRA-URGI 2009-2010
+ − 4 #
+ − 5 # This software is governed by the CeCILL license under French law and
+ − 6 # abiding by the rules of distribution of free software. You can use,
+ − 7 # modify and/ or redistribute the software under the terms of the CeCILL
+ − 8 # license as circulated by CEA, CNRS and INRIA at the following URL
+ − 9 # "http://www.cecill.info".
+ − 10 #
+ − 11 # As a counterpart to the access to the source code and rights to copy,
+ − 12 # modify and redistribute granted by the license, users are provided only
+ − 13 # with a limited warranty and the software's author, the holder of the
+ − 14 # economic rights, and the successive licensors have only limited
+ − 15 # liability.
+ − 16 #
+ − 17 # In this respect, the user's attention is drawn to the risks associated
+ − 18 # with loading, using, modifying and/or developing or reproducing the
+ − 19 # software by the user in light of its specific status of free software,
+ − 20 # that may mean that it is complicated to manipulate, and that also
+ − 21 # therefore means that it is reserved for developers and experienced
+ − 22 # professionals having in-depth computer knowledge. Users are therefore
+ − 23 # encouraged to load and test the software's suitability as regards their
+ − 24 # requirements in conditions enabling the security of their systems and/or
+ − 25 # data to be ensured and, more generally, to use and operate it in the
+ − 26 # same conditions as regards security.
+ − 27 #
+ − 28 # The fact that you are presently reading this means that you have had
+ − 29 # knowledge of the CeCILL license and that you accept its terms.
+ − 30 #
+ − 31 """Get the first element (exon / intron) from a list of transcripts"""
+ − 32
+ − 33 import os
+ − 34 from optparse import OptionParser
+ − 35 from commons.core.writer.Gff3Writer import *
+ − 36 from SMART.Java.Python.structure.TranscriptContainer import *
+ − 37 from SMART.Java.Python.misc.Progress import *
+ − 38
+ − 39
+ − 40 if __name__ == "__main__":
+ − 41
+ − 42 # parse command line
+ − 43 description = "Get Element v1.0.1: Get the first element (exon / intron) from a list of transcripts. [Category: Personnal]"
+ − 44
+ − 45 parser = OptionParser(description = description)
+ − 46 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in transcript format given by -f]")
+ − 47 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of file [compulsory] [format: transcript file format]")
+ − 48 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in GFF3 format]")
+ − 49 parser.add_option("-y", "--mysql", dest="mysql", action="store_true", default=False, help="mySQL output [format: bool] [default: false]")
+ − 50 parser.add_option("-t", "--type", dest="type", action="store", type="string", help="type of the element [format: choice (exon, intron)]")
+ − 51 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
+ − 52 parser.add_option("-l", "--log", dest="log", action="store_true", default=False, help="write a log file [format: bool] [default: false]")
+ − 53 (options, args) = parser.parse_args()
+ − 54
+ − 55 parser = TranscriptContainer(options.inputFileName, options.format, options.verbosity)
+ − 56 writer = Gff3Writer(options.outputFileName, options.verbosity)
+ − 57 sqlWriter = MySqlTranscriptWriter(options.outputFileName, options.verbosity)
+ − 58
+ − 59 nbLines = parser.getNbTranscripts()
+ − 60 print "%i lines found" % (nbLines)
+ − 61
+ − 62 # treat transcripts
+ − 63 nbWritten = 0
+ − 64 nbUsed = 0
+ − 65 progress = Progress(nbLines, "Analyzing transcripts of " + options.inputFileName, options.verbosity)
+ − 66 for transcript in parser.getIterator():
+ − 67
+ − 68 outTranscript = Transcript()
+ − 69 outTranscript.setName(transcript.getName())
+ − 70 outTranscript.setDirection(transcript.getDirection())
+ − 71 outTranscript.setChromosome(transcript.getChromosome())
+ − 72
+ − 73 if options.type == "exon":
+ − 74 if len(transcript.getExons()) > 1:
+ − 75 transcript.sortExons()
+ − 76 outTranscript.setStart(transcript.getExons()[0].getStart())
+ − 77 outTranscript.setEnd(transcript.getExons()[0].getEnd())
+ − 78 writer.addTranscript(outTranscript)
+ − 79 if options.mysql:
+ − 80 sqlWriter.addTranscript(transcript)
+ − 81 nbWritten += 1
+ − 82 nbUsed += 1
+ − 83 elif options.type == "intron":
+ − 84 used = False
+ − 85 for intron in transcript.getIntrons():
+ − 86 used = True
+ − 87 thisTranscript = Transcript()
+ − 88 thisTranscript.copy(outTranscript)
+ − 89 thisTranscript.setStart(intron.getStart())
+ − 90 thisTranscript.setEnd(intron.getEnd())
+ − 91 writer.addTranscript(thisTranscript)
+ − 92 if options.mysql:
+ − 93 sqlWriter.addTranscript(transcript)
+ − 94 nbWritten += 1
+ − 95 if used:
+ − 96 nbUsed += 1
+ − 97 else:
+ − 98 sys.exit("Cannot understan type %s" % (options.type))
+ − 99 progress.inc()
+ − 100 progress.done()
+ − 101
+ − 102 if options.mysql:
+ − 103 sqlWriter.write()
+ − 104
+ − 105 print "nb sequences used: %d" % (nbUsed)
+ − 106 print "nb elements used: %d" % (nbWritten)
