annotate SMART/Java/Python/CleanTranscriptFile.py @ 53:47310c4fb725

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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