6
+ − 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
+ − 32
+ − 33 """Convert files with some mapping format to coordinates format"""
+ − 34
+ − 35 import os
+ − 36 from optparse import OptionParser
+ − 37 from commons.core.parsing.PslParser import PslParser
+ − 38 from commons.core.parsing.AxtParser import AxtParser
+ − 39 from commons.core.writer.Gff3Writer import Gff3Writer
+ − 40 from commons.core.writer.MySqlTranscriptWriter import MySqlTranscriptWriter
+ − 41 from SMART.Java.Python.structure.TranscriptListsComparator import TranscriptListsComparator
+ − 42 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
+ − 43 from SMART.Java.Python.misc.Progress import Progress
+ − 44
+ − 45
+ − 46 class MappingToCoordinates(object):
+ − 47 def __init__(self,verbosity=1, inputFileName=None, format = None, output=None,galaxy = False, title="S-MART"):
+ − 48 self.verbosity = verbosity
+ − 49 self.inputFileName = inputFileName
+ − 50 self.format = format
+ − 51 self.output = output
+ − 52 self.galaxy = galaxy
+ − 53 self.title = title
+ − 54
+ − 55 def setAttributesFromCmdLine(self):
+ − 56 description = "Mapping To Coordinates v1.0.1: Convert a set of mappings (given by a mapping tool) to a set of transcripts. [Category: Conversion]"
+ − 57 parser = OptionParser(description = description)
+ − 58 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in mapping format given by -f]")
+ − 59 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of file [compulsory] [format: mapping file format]")
+ − 60 parser.add_option("-o", "--output", dest="output", action="store", default=None, type="string", help="output file [compulsory] [format: output file in GFF3 format]")
+ − 61 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
+ − 62 parser.add_option("-G", "--galaxy", dest="galaxy", action="store_true", default=False, help="used for galaxy [format: bool] [default: False]")
+ − 63 (options, args) = parser.parse_args()
+ − 64
+ − 65 self.verbosity = options.verbosity
+ − 66 self.inputFileName = options.inputFileName
+ − 67 self.format = options.format
+ − 68 self.output = options.output
+ − 69 self.galaxy = options.galaxy
+ − 70
+ − 71 def run(self):
+ − 72 if self.verbosity > 0:
+ − 73 print "Reading input file..."
+ − 74 parser = TranscriptContainer(self.inputFileName, self.format, self.verbosity)
+ − 75 if self.verbosity > 0:
+ − 76 print "... done"
+ − 77 writer = Gff3Writer(self.output, self.verbosity, self.title)
+ − 78
+ − 79 progress = Progress(parser.getNbTranscripts(), "Reading %s" % (self.inputFileName), self.verbosity)
+ − 80 for transcript in parser.getIterator():
+ − 81 writer.addTranscript(transcript)
+ − 82 progress.inc()
+ − 83 progress.done()
+ − 84
+ − 85 if self.galaxy:
+ − 86 os.rename("%s.gff3" % (self.output), self.output)
+ − 87
+ − 88 if __name__ == '__main__':
+ − 89 launcher = MappingToCoordinates()
+ − 90 launcher.setAttributesFromCmdLine()
+ − 91 launcher.run()