Mercurial > repos > yufei-luo > s_mart
diff SMART/Java/Python/ncList/NCListParser.py @ 6:769e306b7933
Change the repository level.
author | yufei-luo |
---|---|
date | Fri, 18 Jan 2013 04:54:14 -0500 |
parents | |
children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SMART/Java/Python/ncList/NCListParser.py Fri Jan 18 04:54:14 2013 -0500 @@ -0,0 +1,74 @@ +#! /usr/bin/env python +# +# 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 random, os, time +from optparse import OptionParser +from commons.core.parsing.ParserChooser import ParserChooser +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 +try: + import cPickle as pickle +except: + import pickle + +class NCListParser(object): + + def __init__(self, fileName, verbosity = 1): + self._fileName = fileName + self._ncLists = {} + self._sortedFileNames = {} + self._nbElements = 0 + self._nbElementsPerChromosome = {} + self._verbosity = verbosity + + 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() + + def getSortedFileNames(self): + return self._sortedFileNames + + def getNbElements(self): + return self._nbElements + + def getNbElementsPerChromosome(self): + return self._nbElementsPerChromosome + + def getNCLists(self): + return self._ncLists