Mercurial > repos > yufei-luo > s_mart
view commons/core/parsing/NCListParser.py @ 27:4e7ee5683ef1
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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 2009-2012 # # 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 from commons.core.parsing.TranscriptListParser import TranscriptListParser from SMART.Java.Python.structure.Transcript import Transcript from SMART.Java.Python.structure.Interval import Interval from SMART.Java.Python.ncList.NCList import NCList from SMART.Java.Python.ncList.NCListCursor import NCListCursor from SMART.Java.Python.ncList.NCListFilePickle import NCListFileUnpickle from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress try: import cPickle as pickle except: import pickle class NCListParser(TranscriptListParser): def __init__(self, fileName, verbosity = 0): self.title = None TranscriptListParser.__init__(self, fileName, verbosity) self.parse() def getFileFormats(): return ["nclist"] getFileFormats = staticmethod(getFileFormats) def skipFirstLines(self): return def parse(self): handle = open(self.fileName) self.sortedFileNames = pickle.load(handle) self.nbElements = pickle.load(handle) self.nbElementsPerChromosome = pickle.load(handle) self.ncLists = pickle.load(handle) for ncList in self.ncLists.values(): ncList._reopenFiles() handle.close() self.chromosomes = sorted(self.nbElementsPerChromosome.keys()) self.fileNames = dict([chromosome, self.ncLists[chromosome]._transcriptFileName] for chromosome in self.chromosomes) self.currentReader = None self.currentChrIndex = 0 def getSortedFileNames(self): return self._sortedFileNames def getNbElements(self): return self._nbElements def getNbElementsPerChromosome(self): return self._nbElementsPerChromosome def getNCLists(self): return self._ncLists def reset(self): self.currentChrIndex = 0 self.currentReader = None def gotoAddress(self, address): self.currentReader.gotoAddress(address) def getCurrentAddress(self): return self.getCurrentTranscriptAddress() def getCurrentTranscriptAddress(self): if self.currentReader == None: return 0 return self.currentReader.getCurrentTranscriptAddress() def getNextTranscript(self): if self.currentReader == None: self.currentReader = NCListFileUnpickle(self.fileNames[self.chromosomes[0]]) transcript = self.currentReader.getNextTranscript() if transcript == False: self.currentChrIndex += 1 if self.currentChrIndex >= len(self.chromosomes): return None self.currentReader = NCListFileUnpickle(self.fileNames[self.chromosomes[self.currentChrIndex]]) transcript = self.currentReader.getNextTranscript() return transcript def getInfos(self): self.size = 0 self.reset() progress = UnlimitedProgress(100000, "Getting information on %s." % (self.fileName), self.verbosity-9) transcript = self.getNextTranscript() for transcript in self.getIterator(): self.size += transcript.getSize() progress.inc() progress.done() self.reset() def getNbTranscripts(self): return self.nbElements