Mercurial > repos > yufei-luo > s_mart
diff SMART/Java/Python/ncList/NCListFilePickle.py @ 36:44d5973c188c
Uploaded
author | m-zytnicki |
---|---|
date | Tue, 30 Apr 2013 15:02:29 -0400 |
parents | 769e306b7933 |
children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SMART/Java/Python/ncList/NCListFilePickle.py Tue Apr 30 15:02:29 2013 -0400 @@ -0,0 +1,123 @@ +#! /usr/bin/env python +# +# 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. +# + +try: + import cPickle as pickle +except: + import pickle +from SMART.Java.Python.structure.Transcript import Transcript + + +class NCListFilePickle(object): + + def __init__(self, fileName, verbosity = 1): + self.fileName = fileName + self.handle = open(fileName, "wb") + self.verbosity = verbosity + + def __del__(self): + if self.handle != None: + self.handle.close() + + def addTranscript(self, transcript): + pickle.dump(transcript, self.handle, -1) + + def write(self): + pass + + def close(self): + self.__del__() + + +class NCListFileUnpickle(object): + + def __init__(self, fileName, verbosity = 1): + self.handle = open(fileName, "rb") + self.verbosity = verbosity + self.initAddress = 0 + self.address = self.initAddress + self.nbTranscripts = None + self.fileName = fileName + self.over = False + self.chromosome = None + + def __del__(self): + if self.handle != None: + self.handle.close() + + def reset(self): + self.handle.seek(0) + self.initAddress = 0 + + def setChromosome(self, chromosome): + self.chromosome = chromosome + + def getNbTranscripts(self): + if self.nbTranscripts != None: + return self._nbTranscripts + self.nbTranscripts = 0 + for transcript in self.getIterator(): + self_nbTranscripts += 1 + return self.nbTranscripts + + 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