Mercurial > repos > yufei-luo > s_mart
diff commons/core/parsing/MapperParser.py @ 36:44d5973c188c
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author | m-zytnicki |
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date | Tue, 30 Apr 2013 15:02:29 -0400 |
parents | 769e306b7933 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/commons/core/parsing/MapperParser.py Tue Apr 30 15:02:29 2013 -0400 @@ -0,0 +1,129 @@ +# +# 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 sys +from SMART.Java.Python.structure.Mapping import Mapping + + +class MapperParser(object): + """An interface that parses the output of a generic mapper""" + + def __init__(self, fileName, verbosity = 0): + super(MapperParser, self).__init__() + self.verbosity = verbosity + self.nbMappings = None + self.chromosomes = None + self.size = None + self.currentMapping = Mapping() + self.handle = open(fileName) + self.currentLineNb = 0 + self.skipFirstLines() + self.fileName = fileName + self.startingPoint = self.handle.tell() + + + def __del__(self): + self.handle.close() + + + def reset(self): + self.handle.seek(self.startingPoint) + self.currentLineNb = 0 + + + def getNextMapping(self): + for line in self.handle: + mapping = self.parseLine(line) + self.currentLineNb += 1 + if mapping != None: + return mapping + return False + + + def getIterator(self): + self.reset() + mapping = self.getNextMapping() + while mapping: + yield mapping + mapping = self.getNextMapping() + + + def getInfos(self): + self.chromosomes = set() + self.nbMappings = 0 + self.size = 0 + self.reset() + if self.verbosity >= 10: + print "Getting information." + for mapping in self.getIterator(): + transcript = mapping.getTranscript() + self.chromosomes.add(transcript.getChromosome()) + self.nbMappings += 1 + self.size += transcript.getSize() + if self.verbosity >= 10 and self.nbMappings % 100000 == 0: + sys.stdout.write(" %d mappings read\r" % (self.nbMappings)) + sys.stdout.flush() + self.reset() + if self.verbosity >= 10: + print " %d mappings read" % (self.nbMappings) + print "Done." + + + def getNbMappings(self): + if self.nbMappings != None: + return self.nbMappings + self.getInfos() + return self.nbMappings + + + def getNbItems(self): + return self.getNbMappings() + + + def getChromosomes(self): + if self.chromosomes != None: + return self.chromosomes + self.getInfos() + return self.chromosomes + + + def getSize(self): + if self.size != None: + return self.size + self.getInfos() + return self.size + + + def getNbNucleotides(self): + return self.getSize() + + + def setDefaultTagValue(self, name, value): + for mapping in self.getIterator(): + mapping.setTagValue(name, value)