Mercurial > repos > yufei-luo > s_mart
view commons/core/parsing/PklParser.py @ 27:4e7ee5683ef1
Deleted selected files
author | m-zytnicki |
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date | Mon, 29 Apr 2013 03:30:11 -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 re import sys try: import cPickle as pickle except: import pickle from SMART.Java.Python.structure.Interval import Interval from commons.core.parsing.TranscriptListParser import TranscriptListParser from SMART.Java.Python.structure.Transcript import Transcript class PklParser(TranscriptListParser): """A class that parses the intern PKL file and create a transcript list""" def __init__(self, fileName, verbosity = 1): self.title = None super(PklParser, self).__init__(fileName, verbosity) self.handle = open(fileName, "rb") self.verbosity = verbosity self.initAddress = 0 self.address = self.initAddress self.over = False self.chromosome = None def __del__(self): super(PklParser, self).__del__() def getFileFormats(): return ["pkl"] getFileFormats = staticmethod(getFileFormats) def skipFirstLines(self): return def reset(self): self.handle.seek(0) self.initAddress = 0 def setChromosome(self, chromosome): self.chromosome = chromosome def gotoAddress(self, address): self.handle.seek(address) self.address = address def getNextTranscript(self): self.address = self.handle.tell() try: transcript = pickle.load(self.handle) if self.chromosome != None and transcript.getChromosome() != self.chromosome: self.over = True return False return transcript except EOFError: self.over = True return False def getIterator(self): self.gotoAddress(self.initAddress) while True: transcript = self.getNextTranscript() if not transcript: self.over = True return yield transcript def setInitAddress(self, address): self.initAddress = address def getCurrentTranscriptAddress(self): return self.address def isOver(self): return self.over