Mercurial > repos > yufei-luo > s_mart
view commons/core/parsing/MapperParser.py @ 14:c79b9ae3f65f
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author | m-zytnicki |
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date | Fri, 19 Apr 2013 10:13:11 -0400 |
parents | 769e306b7933 |
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# # 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)