annotate smart_toolShed/commons/core/parsing/SamParser.py @ 0:e0f8dcca02ed

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

#
# Copyright INRA-URGI 2009-2010
# 
# This software is governed by the CeCILL license under French law and
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# modify and/ or redistribute the software under the terms of the CeCILL
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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
from SMART.Java.Python.structure.Interval import Interval

class SamParser(MapperParser):
    """A class that parses SAM format (as given by BWA)"""

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


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


    def getFileFormats():
        return ["sam"]
    getFileFormats = staticmethod(getFileFormats)


    def skipFirstLines(self):
        pass


    def getInfos(self):
        self.chromosomes = set()
        self.nbMappings  = 0
        self.size        = 0
        self.reset()
        if self.verbosity >= 10:
            print "Getting information on SAM file"
        self.reset()
        for line in self.handle:
            line = line.strip()
            if line == "" or line[0] == "@":
                continue
            parts      = line.split("\t")
            chromosome = parts[2]
            if chromosome != "*":
                self.chromosomes.add(chromosome)
            self.nbMappings += 1
            self.size += len(parts[8])
            if self.verbosity >= 10 and self.nbMappings % 100000 == 0:
                sys.stdout.write("    %d mappings read\r" % (self.nbMappings))
                sys.stdout.flush()
        self.reset()
        if self.verbosity >= 10:
            print "    %d mappings read" % (self.nbMappings)
            print "Done."


    def parseLine(self, line):

        line = line.strip()
        if line[0] == "@":
            return

        fields = line.split("\t")
        if len(fields) < 11:
            raise Exception("Line %d '%s' does not look like a SAM line (number of fields is %d instead of 11)" % (self.currentLineNb, line, len(fields)))

        name = fields[0]
        flag = int(fields[1])

        if (flag & 0x4) == 0x4:
            return None

        direction       = 1 if (flag & 0x10) == 0x0 else -1
        chromosome      = fields[2]
        genomeStart     = int(fields[3])
        quality         = fields[4]
        cigar           = fields[5]
        mate            = fields[6]
        mateGenomeStart = fields[7]
        gapSize         = fields[8]
        sequence        = fields[9]
        quality         = fields[10]
        tags            = fields[11:]

        if mateGenomeStart != "*":
            mateGenomeStart = int(mateGenomeStart)

        mapping       = Mapping()
        nbOccurrences = 1
        nbMismatches  = 0
        nbMatches     = 0
        nbGaps        = 0
        subMapping    = None
        queryOffset   = 0
        targetOffset  = 0
        currentNumber = 0
        readStart     = None

        for tag in tags:
            key = tag[:2]
            if key == "X0":
                nbOccurrences = int(tag[5:])
            elif key == "X1":
                nbOccurrences += int(tag[5:])
            elif key == "XM":
                nbMismatches = int(tag[5:])
        mapping.setTagValue("nbOccurrences", nbOccurrences)
        mapping.setTagValue("quality", int(fields[4]))

        for char in cigar:
            m = re.match(r"[0-9]", char)
            if m != None:
                currentNumber = currentNumber * 10 + (ord(char) - ord("0"))
                continue
            # match
            m = re.match(r"[M]", char)
            if m != None:
                if readStart == None:
                    readStart = queryOffset
                if subMapping == None:
                    subMapping = SubMapping()
                    subMapping.setSize(currentNumber)
                    subMapping.setDirection(direction)
                    subMapping.queryInterval.setName(name)
                    subMapping.queryInterval.setStart(queryOffset)
                    subMapping.queryInterval.setDirection(direction)
                    subMapping.targetInterval.setChromosome(chromosome)
                    subMapping.targetInterval.setStart(genomeStart + targetOffset)
                    subMapping.targetInterval.setDirection(1)
                nbMatches    += currentNumber
                targetOffset += currentNumber
                queryOffset  += currentNumber
                currentNumber = 0
                continue
            # insertion on the read
            m = re.match(r"[I]", char)
            if m != None:
                nbGaps       += 1
                queryOffset  += currentNumber
                currentNumber = 0
                continue
            # insertion on the genome
            m = re.match(r"[D]", char)
            if m != None:
                if subMapping != None:
                    subMapping.queryInterval.setEnd(queryOffset - 1)
                    subMapping.targetInterval.setEnd(genomeStart + targetOffset - 1)
                    mapping.addSubMapping(subMapping)
                subMapping    = None
                nbGaps       += 1
                targetOffset += currentNumber
                currentNumber = 0
                continue
            # intron
            m = re.match(r"[N]", char)
            if m != None:
                if subMapping != None:
                    subMapping.queryInterval.setEnd(queryOffset - 1)
                    subMapping.targetInterval.setEnd(genomeStart + targetOffset - 1)
                    mapping.addSubMapping(subMapping)
                subMapping    = None
                targetOffset += currentNumber
                currentNumber = 0
                continue
            # soft clipping (substitution)
            m = re.match(r"[S]", char)
            if m != None:
                nbMismatches += currentNumber
                targetOffset += currentNumber
                queryOffset  += currentNumber
                currentNumber = 0
                continue
            # hard clipping
            m = re.match(r"[H]", char)
            if m != None:
                targetOffset += currentNumber
                queryOffset  += currentNumber
                currentNumber = 0
                continue
            # padding
            m = re.match(r"[P]", char)
            if m != None:
                continue
            raise Exception("Do not understand paramer '%s' in line %s" % (char, line))

        if subMapping != None:
            subMapping.queryInterval.setEnd(queryOffset - 1)
            subMapping.targetInterval.setEnd(genomeStart + targetOffset - 1)
            mapping.addSubMapping(subMapping)

        mapping.queryInterval.setStart(readStart)
        mapping.queryInterval.setEnd(queryOffset - 1)
        mapping.targetInterval.setEnd(genomeStart + targetOffset - 1)
        mapping.setNbMismatches(nbMismatches)
        mapping.setNbGaps(nbGaps)

        mapping.queryInterval.setName(name)
        mapping.queryInterval.setDirection(direction)
        mapping.targetInterval.setChromosome(chromosome)
        mapping.targetInterval.setStart(genomeStart)
        mapping.targetInterval.setDirection(direction)
        mapping.setSize(len(sequence))
        mapping.setDirection(direction)

        return mapping