Mercurial > repos > yufei-luo > s_mart
comparison smart_toolShed/SMART/Java/Python/fold.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
| author | yufei-luo |
|---|---|
| date | Thu, 17 Jan 2013 10:52:14 -0500 |
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| -1:000000000000 | 0:e0f8dcca02ed |
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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 """ | |
| 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() |