view smart_toolShed/commons/core/parsing/ @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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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
# "".
# 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
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# In this respect, the user's attention is drawn to the risks associated
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# software by the user in light of its specific status of free software,
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# encouraged to load and test the software's suitability as regards their
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# 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):    
    def parseLine(self, line):
        m =
        if m == None:
            sys.exit("\nLine %d '%s' does not have a map format" % (self.currentLineNb, line))
        transcript = Transcript()
        transcript.setStart(min(int("sStart")), int("sEnd"))))
        transcript.setEnd(max(int("sStart")), int("sEnd"))))

        return transcript