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comparison SMART/Java/Python/fold.py @ 6:769e306b7933

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author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
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5:ea3082881bf8 6:769e306b7933
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()