Mercurial > repos > yufei-luo > s_mart
view commons/core/parsing/MapParser.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.Mapping import Mapping from commons.core.parsing.MapperParser import MapperParser from SMART.Java.Python.structure.SubMapping import SubMapping from SMART.Java.Python.misc import Utils from SMART.Java.Python.structure.Transcript import Transcript from commons.core.parsing.TranscriptListParser import TranscriptListParser class MapParser(TranscriptListParser): """A class that parses the repet .map files""" def __init__(self, fileName, verbosity = 0): self._lineParseRe = re.compile(r"(?P<seqName>\w+)\s(?P<chrName>\w+)\s(?P<sStart>\d+)\s(?P<sEnd>\d+)") TranscriptListParser.__init__(self, fileName, verbosity) def getFileFormats(): return ["map"] getFileFormats = staticmethod(getFileFormats) def skipFirstLines(self): return def parseLine(self, line): m = self._lineParseRe.search(line) if m == None: sys.exit("\nLine %d '%s' does not have a map format" % (self.currentLineNb, line)) transcript = Transcript() transcript.setChromosome(m.group("chrName")) transcript.setStart(min(int(m.group("sStart")), int(m.group("sEnd")))) transcript.setEnd(max(int(m.group("sStart")), int(m.group("sEnd")))) transcript.setName(m.group("seqName")) transcript.setDirection(1) return transcript