comparison smart_toolShed/commons/core/parsing/ExoParser.py @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

0:e0f8dcca02ed

#
# 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.
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# 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,
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#
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
            pass


    def parseLine(self, line):
        
        if line == "-- completed exonerate analysis\n":
            return None
        
        m = re.search(r"^\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 = m.group(1)
        queryStart = min(int(m.group(2)), int(m.group(3)))
        queryEnd = max(int(m.group(2)), int(m.group(3)))-1
        chromosome = m.group(4)
        targetStart = min(int(m.group(5)), int(m.group(6)))
        targetEnd = max(int(m.group(5)), int(m.group(6)))-1
        direction = m.group(7)
        nbMismatches = int(m.group(8))
        rest = m.group(9).strip()
        
        nbGaps = 0
        queryOffset = 0
        targetOffset = 0
        
        subMapping = None
        m = re.search(r"^(\w)\s+(\d+)\s+(\d+)", rest)
        while m != None:
            queryDistance    = int(m.group(2))
            targetDistance = int(m.group(3))
            if m.group(1) == "M":
                if subMapping == None:
                    subMapping = SubMapping()
    
                    subMapping.setSize(queryDistance)
                    subMapping.setDirection(direction)
        
                    subMapping.queryInterval.setName(name)
                    subMapping.queryInterval.setStart(queryStart + queryOffset)
                    subMapping.queryInterval.setDirection(direction)
        
                    subMapping.targetInterval.setChromosome(chromosome)
                    subMapping.targetInterval.setStart(targetStart + targetOffset)
                    subMapping.targetInterval.setDirection(1)
    
            elif m.group(1) == "G":
                nbGaps += max(queryDistance, targetDistance)
                
            elif m.group(1) == "I" or m.group(1) == "5" or m.group(1) == "3":
                if subMapping != None:
                    subMapping.queryInterval.setEnd(queryStart + queryOffset - 1)
                    subMapping.targetInterval.setEnd(targetStart + targetOffset - 1)
                    mapping.addSubMapping(subMapping)
                    subMapping = None
            else:
                sys.exit("Cannot understand sign '%s' in line %s" % (m.group(1), line))
            
            queryOffset += queryDistance
            targetOffset += targetDistance
            rest = rest[m.end():].strip()
            m = re.search(r"^(\w)\s+(\d+)\s+(\d+)", rest)
            
        if subMapping != None:
            subMapping.queryInterval.setEnd(queryStart + queryOffset - 1)
            subMapping.targetInterval.setEnd(targetStart + targetOffset - 1)
            mapping.addSubMapping(subMapping)
                        
        mapping.setNbMismatches(nbMismatches)
        mapping.setNbGaps(nbGaps)
        mapping.setDirection(direction)

        mapping.queryInterval.setName(name)
        mapping.queryInterval.setStart(queryStart)
        mapping.queryInterval.setEnd(queryEnd)

        mapping.targetInterval.setChromosome(chromosome)
        mapping.targetInterval.setStart(targetStart)
        mapping.targetInterval.setEnd(targetEnd)

        return mapping