Mercurial > repos > yufei-luo > s_mart
comparison SMART/Java/Python/CleanTranscriptFile.py @ 6:769e306b7933
Change the repository level.
| author | yufei-luo |
|---|---|
| date | Fri, 18 Jan 2013 04:54:14 -0500 |
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| 5:ea3082881bf8 | 6:769e306b7933 |
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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 |