57
+ − 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 from optparse import OptionParser
+ − 32 from commons.core.parsing.ParserChooser import ParserChooser
+ − 33 from commons.core.writer.TranscriptWriter import TranscriptWriter
+ − 34 from SMART.Java.Python.structure.Transcript import Transcript
+ − 35 from SMART.Java.Python.misc.Progress import Progress
+ − 36
+ − 37 class RemoveExons(object):
+ − 38
+ − 39 def __init__(self, verbosity):
+ − 40 self.verbosity = verbosity
+ − 41 self.selection = False
+ − 42
+ − 43 def setInputFile(self, fileName, format):
+ − 44 chooser = ParserChooser(self.verbosity)
+ − 45 chooser.findFormat(format)
+ − 46 self.parser = chooser.getParser(fileName)
+ − 47
+ − 48 def setOutputFile(self, fileName):
+ − 49 self.writer = TranscriptWriter(fileName, "gff3", self.verbosity)
+ − 50
+ − 51 def run(self):
+ − 52 progress = Progress(self.parser.getNbTranscripts(), "Reading input file", self.verbosity)
+ − 53 for transcript in self.parser.getIterator():
+ − 54 transcript.removeExons()
+ − 55 self.writer.addTranscript(transcript)
+ − 56 progress.inc()
+ − 57 self.writer.write()
+ − 58 self.writer.close()
+ − 59 progress.done()
+ − 60
+ − 61 if __name__ == "__main__":
+ − 62
+ − 63 description = "Remove Exons v1.0.1: Excluse the exons of a set of transcripts. [Category: Data Modification]"
+ − 64
+ − 65 parser = OptionParser(description = description)
+ − 66 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in transcript format given by -f]")
+ − 67 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of file [compulsory] [format: transcript file format]")
+ − 68 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [format: output file in GFF3 format]")
+ − 69 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
+ − 70 (options, args) = parser.parse_args()
+ − 71
+ − 72 re = RemoveExons(options.verbosity)
+ − 73 re.setInputFile(options.inputFileName, options.format)
+ − 74 re.setOutputFile(options.outputFileName)
+ − 75 re.run()
