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
# 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 ExoParser(MapperParser):
    """A class that parses the output of Exonerate - roll your own format"""

    def __init__(self, fileName, verbosity = 0):
        super(ExoParser, self).__init__(fileName, verbosity)

    def __del__(self):
        super(ExoParser, self).__del__()

    def getFileFormats():
        return ["exo", "exonerate"]
    getFileFormats = staticmethod(getFileFormats)

    def skipFirstLines(self):
        while "Hostname" not in self.handle.readline():
            self.currentLineNb += 1

    def parseLine(self, line):
        if line == "-- completed exonerate analysis\n":
            return None
        m ="^\s*(\S+)\s+(\d+)\s+(\d+)\s+[+-]\s+(\S+)\s+(\d+)\s+(\d+)\s+([+-])\s+\d+\s+(\d+)\s+(\S.*)$", line)
        if m == None:
            sys.exit("\nLine %d '%s' does not have a RYO format" % (self.currentLineNb, line))

        mapping = Mapping()
        name =
        queryStart = min(int(, int(
        queryEnd = max(int(, int(
        chromosome =
        targetStart = min(int(, int(
        targetEnd = max(int(, int(
        direction =
        nbMismatches = int(
        rest =
        nbGaps = 0
        queryOffset = 0
        targetOffset = 0
        subMapping = None
        m ="^(\w)\s+(\d+)\s+(\d+)", rest)
        while m != None:
            queryDistance    = int(
            targetDistance = int(
            if == "M":
                if subMapping == None:
                    subMapping = SubMapping()
                    subMapping.queryInterval.setStart(queryStart + queryOffset)
                    subMapping.targetInterval.setStart(targetStart + targetOffset)
            elif == "G":
                nbGaps += max(queryDistance, targetDistance)
            elif == "I" or == "5" or == "3":
                if subMapping != None:
                    subMapping.queryInterval.setEnd(queryStart + queryOffset - 1)
                    subMapping.targetInterval.setEnd(targetStart + targetOffset - 1)
                    subMapping = None
                sys.exit("Cannot understand sign '%s' in line %s" % (, line))
            queryOffset += queryDistance
            targetOffset += targetDistance
            rest = rest[m.end():].strip()
            m ="^(\w)\s+(\d+)\s+(\d+)", rest)
        if subMapping != None:
            subMapping.queryInterval.setEnd(queryStart + queryOffset - 1)
            subMapping.targetInterval.setEnd(targetStart + targetOffset - 1)



        return mapping