Mercurial > repos > yufei-luo > s_mart
view commons/core/parsing/NucmerParser.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 re import sys from SMART.Java.Python.structure.SubMapping import SubMapping from SMART.Java.Python.structure.Mapping import Mapping from SMART.Java.Python.structure.Interval import Interval from commons.core.parsing.MapperParser import MapperParser class NucmerParser(MapperParser): """A class that parses the output of Nucmer""" def __init__(self, fileName, verbosity = 0): super(NucmerParser, self).__init__(fileName, verbosity) def __del__(self): super(NucmerParser, self).__del__() def getFileFormats(): return ["nucmer"] getFileFormats = staticmethod(getFileFormats) def skipFirstLines(self): pass def parseLine(self, line): if not line: return None if line[0] == ">": self.currentChromosome = line[1:].split()[0] return None splittedLine = line.strip().split() if len(splittedLine) != 8: raise Exception("Line %d '%s' does not have a NucMer format" % (self.currentLineNb, line)) subMapping = SubMapping() subMapping.targetInterval.setChromosome(self.currentChromosome) subMapping.targetInterval.setName(self.currentChromosome) subMapping.targetInterval.setStart(min(int(splittedLine[0]), int(splittedLine[1]))) subMapping.targetInterval.setEnd(max(int(splittedLine[0]), int(splittedLine[1]))) subMapping.targetInterval.setDirection(splittedLine[6]) subMapping.queryInterval.setChromosome(splittedLine[7]) subMapping.queryInterval.setName(splittedLine[7]) subMapping.queryInterval.setStart(1) subMapping.queryInterval.setEnd(int(splittedLine[3])) subMapping.queryInterval.setDirection("+") mapping = Mapping() mapping.addSubMapping(subMapping) mapping.setDirection(splittedLine[6]) mapping.setIdentity(float(splittedLine[5])) mapping.setSize(int(splittedLine[3])) return mapping