Mercurial > repos > yufei-luo > s_mart
diff smart_toolShed/commons/core/parsing/NCListParser.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/smart_toolShed/commons/core/parsing/NCListParser.py Thu Jan 17 10:52:14 2013 -0500 @@ -0,0 +1,125 @@ +# +# 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