Mercurial > repos > yufei-luo > s_mart
view SMART/Java/Python/cleaning/TranscriptListCleaner.py @ 9:1eb55963fe39
Updated CompareOverlappingSmall*.py
author | m-zytnicki |
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date | Thu, 14 Mar 2013 05:23:05 -0400 |
parents | 769e306b7933 |
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# # Copyright INRA-URGI 2009-2010 # # This software is governed by the CeCILL license under French law and # abiding by the rules of distribution of free software. You can use, # modify and/ or redistribute the software under the terms of the CeCILL # license as circulated by CEA, CNRS and INRIA at the following URL # "http://www.cecill.info". # # As a counterpart to the access to the source code and rights to copy, # modify and redistribute granted by the license, users are provided only # with a limited warranty and the software's author, the holder of the # economic rights, and the successive licensors have only limited # liability. # # In this respect, the user's attention is drawn to the risks associated # with loading, using, modifying and/or developing or reproducing the # software by the user in light of its specific status of free software, # that may mean that it is complicated to manipulate, and that also # therefore means that it is reserved for developers and experienced # professionals having in-depth computer knowledge. Users are therefore # encouraged to load and test the software's suitability as regards their # requirements in conditions enabling the security of their systems and/or # data to be ensured and, more generally, to use and operate it in the # same conditions as regards security. # # The fact that you are presently reading this means that you have had # knowledge of the CeCILL license and that you accept its terms. # import sys from SMART.Java.Python.structure.TranscriptList import TranscriptList from SMART.Java.Python.misc.Progress import Progress from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress class TranscriptListCleaner(object): """A (quite generic) class that cleans a file containing transcripts""" def __init__(self, verbosity = 0): self.verbosity = verbosity def setInputFileName(self, fileName): try: self.inputHandle = open(fileName) except IOError: raise Exception("Error! Transcript file '%s' does not exist! Exiting..." % (self.fileName)) def setOutputFileName(self, fileName): try: self.outputHandle = open(fileName, "w") except IOError: raise Exception("Error! Transcript file '%s' does not exist! Exiting..." % (self.fileName)) def getFileFormats(): pass getFileFormats = staticmethod(getFileFormats) def close(self): self.inputHandle.close() self.outputHandle.close() def clean(self): self._clean() self.close()