comparison smart_toolShed/SMART/Java/Python/CleanTranscriptFile.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
1 #! /usr/bin/env python
2 #
3 # Copyright INRA-URGI 2009-2011
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 SMART.Java.Python.cleaning.CleanerChooser import CleanerChooser
33
34
35 class CleanTranscriptFile(object):
36
37 def __init__(self, verbosity):
38 self.verbosity = verbosity
39 self.chooser = CleanerChooser(self.verbosity)
40
41 def setInputFile(self, fileName, format):
42 self.chooser.findFormat(format)
43 self.cleaner = self.chooser.getCleaner()
44 self.cleaner.setInputFileName(fileName)
45
46 def setOutputFile(self, fileName):
47 self.cleaner.setOutputFileName(fileName)
48
49 def setAcceptedTypes(self, types):
50 if types != None:
51 self.cleaner.setAcceptedTypes(types)
52
53 def run(self):
54 self.cleaner.clean()
55
56
57 if __name__ == "__main__":
58
59 description = "Clean Transcript File v1.0.1: Clean a transcript file so that it is useable for S-MART. [Category: Other]"
60
61 parser = OptionParser(description = description)
62 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="query input file [compulsory] [format: file in transcript format given by -f]")
63 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of previous file [compulsory] [format: transcript file format]")
64 parser.add_option("-t", "--types", dest="acceptedTypes", action="store", default=None, type="string", help="name of the types you want to keep in GFF/GTF (list separated by commas) [format: string] [default: None]")
65 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [format: output file in GFF3 format]")
66 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
67 (options, args) = parser.parse_args()
68
69 ctf = CleanTranscriptFile(options.verbosity)
70 ctf.setInputFile(options.inputFileName, options.format)
71 ctf.setOutputFile(options.outputFileName)
72 ctf.setAcceptedTypes(None if options.acceptedTypes == None else options.acceptedTypes.split(","))
73 ctf.run()
74