Mercurial > repos > yufei-luo > s_mart
view commons/core/parsing/MummerParser.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 commons.core.parsing.MapperParser import MapperParser from SMART.Java.Python.structure.Mapping import Mapping from SMART.Java.Python.structure.SubMapping import SubMapping class MummerParser(MapperParser): """A class that parses the output of Mummer format""" def __init__(self, fileName, verbosity = 0): super(MummerParser, self).__init__(fileName, verbosity) def __del__(self): super(MummerParser, self).__del__() def getFileFormats(): return ["mummer"] getFileFormats = staticmethod(getFileFormats) def skipFirstLines(self): pass def parseLine(self, line): mapping = Mapping() subMapping = SubMapping() # handle header m = re.search(r"^>\s+(\S+)\s+Reverse\s+Len\s+=\s+(\d+)$", line) if m != None: subMapping.queryInterval.setName(m.group(1)) subMapping.queryInterval.setSize(int(m.group(2))) subMapping.queryInterval.setDirection(-1) else: m = re.search(r"^>\s+(\S+)\s+Len\s+=\s+(\d+)$", line) if m != None: subMapping.queryInterval.setName(m.group(1)) subMapping.queryInterval.setSize(int(m.group(2))) subMapping.queryInterval.setDirection(1) else : sys.exit("Header line %d '%s' is strange in Mummer file" % (self.currentLineNb, line)) for line in self.handle: self.currentLineNb += 1 break line = line.strip() # handle line m = re.search(r"^(\w+)\s+(\d+)\s+(\d+)\s+(\d+)$", line) if m != None: subMapping.targetInterval.setName(m.group(1)) subMapping.targetInterval.setStart(int(m.group(2))) subMapping.queryInterval.setStart(int(m.group(3))) subMapping.targetInterval.setSize(int(m.group(4))) else: sys.exit("Line %d '%s' is strange in Mummer file" % (self.currentLineNb, line)) mapping.addSubMapping(subMapping) return mapping