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 Read a mapping file (many formats supported) and select some of them
+ − 33 Mappings should be sorted by read names
+ − 34 """
+ − 35
+ − 36 from optparse import OptionParser
+ − 37 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
+ − 38 from SMART.Java.Python.toolLauncher.RnaFoldLauncher import RnaFoldLauncher
+ − 39 from commons.core.writer.Gff3Writer import Gff3Writer
+ − 40
+ − 41
+ − 42 class Fold(object):
+ − 43 """
+ − 44 Fold a series of transcripts
+ − 45 """
+ − 46
+ − 47 def __init__(self, verbosity = 0):
+ − 48 self.verbosity = verbosity
+ − 49 self.rnaFoldLauncher = RnaFoldLauncher(verbosity)
+ − 50 self.gff3Writer = None
+ − 51
+ − 52
+ − 53 def setInputFileName(self, fileName, format):
+ − 54 transcriptContainer = TranscriptContainer(fileName, format, options.verbosity)
+ − 55 self.rnaFoldLauncher.setTranscriptList(transcriptContainer)
+ − 56
+ − 57
+ − 58 def setOutputFileName(self, fileName):
+ − 59 self.gff3Writer = Gff3Writer("%s.gff3" % (fileName), self.verbosity)
+ − 60
+ − 61
+ − 62 def setGenomeFileName(self, fileName):
+ − 63 self.rnaFoldLauncher.setGenomeFile(fileName)
+ − 64
+ − 65
+ − 66 def setExtensions(self, fivePrime, threePrime):
+ − 67 self.rnaFoldLauncher.setExtensions(fivePrime, threePrime)
+ − 68
+ − 69
+ − 70 def start(self):
+ − 71 self.gff3Writer.addTranscriptList(self.rnaFoldLauncher.getResults())
+ − 72
+ − 73
+ − 74
+ − 75 if __name__ == "__main__":
+ − 76
+ − 77 # parse command line
+ − 78 description = "Fold v1.0.1: Fold a list of transcript and give the energy. [Category: Personal]"
+ − 79
+ − 80 parser = OptionParser(description = description)
+ − 81 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in transcript format given by -f]")
+ − 82 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of file [compulsory] [format: transcript file format]")
+ − 83 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [format: output file in GFF3 format]")
+ − 84 parser.add_option("-g", "--genome", dest="genomeFileName", action="store", type="string", help="genome file name [format: file in FASTA format]")
+ − 85 parser.add_option("-5", "--fivePrime", dest="fivePrime", action="store", type="int", help="extend towards the 5' end [format: int]")
+ − 86 parser.add_option("-3", "--threePrime", dest="threePrime", action="store", type="int", help="extend towards the 3' end [format: int]")
+ − 87 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
+ − 88 (options, args) = parser.parse_args()
+ − 89
+ − 90 folder = Fold(options.verbosity)
+ − 91 folder.setInputFileName(options.inputFileName, options.format)
+ − 92 folder.setOutputFileName(options.outputFileName)
+ − 93 folder.setExtensions(options.fivePrime, options.threePrime)
+ − 94 folder.setGenomeFileName(options.genomeFileName)
+ − 95 folder.start()
