comparison extractSplitReads_BwaMem.py @ 0:a1225091082c draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit 6a109f553d1691e243372258ad564244586875c3"

0:a1225091082c

#!/usr/bin/env python

import re
import sys
from optparse import OptionParser


def extractSplitsFromBwaMem(inFile, numSplits, includeDups, minNonOverlap):
    if inFile == "stdin":
        data = sys.stdin
    else:
        data = open(inFile, 'r')
    for line in data:
        split = 0
        if line[0] == '@':
            print(line.strip())
            continue
        samList = line.strip().split('\t')
        sam = SAM(samList)
        if includeDups == 0 and (1024 & sam.flag) == 1024:
            continue
        for el in sam.tags:
            if "SA:" in el:
                if(len(el.split(";"))) <= numSplits:
                    split = 1
                    mate = el.split(",")
                    mateCigar = mate[3]
                    mateFlag = int(0)
                    if mate[2] == "-":
                        mateFlag = int(16)
        if split:
            read1 = sam.flag & 64
            if read1 == 64:
                tag = "_1"
            else:
                tag = "_2"
            samList[0] = sam.query + tag
            readCigar = sam.cigar
            readCigarOps = extractCigarOps(readCigar, sam.flag)
            readQueryPos = calcQueryPosFromCigar(readCigarOps)
            mateCigarOps = extractCigarOps(mateCigar, mateFlag)
            mateQueryPos = calcQueryPosFromCigar(mateCigarOps)
            overlap = calcQueryOverlap(readQueryPos.qsPos, readQueryPos.qePos,
                                       mateQueryPos.qsPos, mateQueryPos.qePos)
            nonOverlap1 = 1 + readQueryPos.qePos - readQueryPos.qsPos - overlap
            nonOverlap2 = 1 + mateQueryPos.qePos - mateQueryPos.qsPos - overlap
            mno = min(nonOverlap1, nonOverlap2)
            if mno >= minNonOverlap:
                print("\t".join(samList))

# -----------------------------------------------------------------------
# functions
# -----------------------------------------------------------------------


class SAM (object):
    """
    __very__ basic class for SAM input.
    """
    def __init__(self, samList=[]):
        if len(samList) > 0:
            self.query = samList[0]
            self.flag = int(samList[1])
            self.ref = samList[2]
            self.pos = int(samList[3])
            self.mapq = int(samList[4])
            self.cigar = samList[5]
            self.matRef = samList[6]
            self.matePos = int(samList[7])
            self.iSize = int(samList[8])
            self.seq = samList[9]
            self.qual = samList[10]
            self.tags = samList[11:]
            # tags is a list of each tag:vtype:value sets
            self.valid = 1
        else:
            self.valid = 0
            self.query = 'null'

    def extractTagValue(self, tagID):
        for tag in self.tags:
            tagParts = tag.split(':', 2)
            if (tagParts[0] == tagID):
                if (tagParts[1] == 'i'):
                    return int(tagParts[2])
                elif (tagParts[1] == 'H'):
                    return int(tagParts[2], 16)
                return tagParts[2]
        return None


cigarPattern = '([0-9]+[MIDNSHP])'
cigarSearch = re.compile(cigarPattern)
atomicCigarPattern = '([0-9]+)([MIDNSHP])'
atomicCigarSearch = re.compile(atomicCigarPattern)


def extractCigarOps(cigar, flag):
    if (cigar == "*"):
        cigarOps = []
    elif (flag & 0x0010):
        cigarOpStrings = cigarSearch.findall(cigar)
        cigarOps = []
        for opString in cigarOpStrings:
            cigarOpList = atomicCigarSearch.findall(opString)
#            print cigarOpList
            # "struct" for the op and it's length
            cigar = cigarOp(cigarOpList[0][0], cigarOpList[0][1])
            # add to the list of cigarOps
            cigarOps.append(cigar)
            cigarOps = cigarOps
        cigarOps.reverse()
        # do in reverse order because negative strand
    else:
        cigarOpStrings = cigarSearch.findall(cigar)
        cigarOps = []
        for opString in cigarOpStrings:
            cigarOpList = atomicCigarSearch.findall(opString)
            # "struct" for the op and it's length
            cigar = cigarOp(cigarOpList[0][0], cigarOpList[0][1])
            # add to the list of cigarOps
            cigarOps.append(cigar)
#            cigarOps = cigarOps
    return(cigarOps)


def calcQueryPosFromCigar(cigarOps):
    qsPos = 0
    qePos = 0
    qLen = 0
    # if first op is a H, need to shift start position
    # the opPosition counter sees if the for loop is looking
    # at the first index of the cigar object
    opPosition = 0
    for cigar in cigarOps:
        if opPosition == 0 and (cigar.op == 'H' or cigar.op == 'S'):
            qsPos += cigar.length
            qePos += cigar.length
            qLen += cigar.length
        elif opPosition > 0 and (cigar.op == 'H' or cigar.op == 'S'):
            qLen += cigar.length
        elif cigar.op == 'M' or cigar.op == 'I':
            qePos += cigar.length
            qLen += cigar.length
            opPosition += 1
    d = queryPos(qsPos, qePos, qLen)
    return d


class cigarOp (object):
    """
    sturct to store a discrete CIGAR operations
    """
    def __init__(self, opLength, op):
        self.length = int(opLength)
        self.op = op


class queryPos (object):
    """
    struct to store the start and end positions of query CIGAR operations
    """
    def __init__(self, qsPos, qePos, qLen):
        self.qsPos = int(qsPos)
        self.qePos = int(qePos)
        self.qLen = int(qLen)


def calcQueryOverlap(s1, e1, s2, e2):
    o = 1 + min(e1, e2) - max(s1, s2)
    return max(0, o)

###############################################


class Usage(Exception):
    def __init__(self, msg):
        self.msg = msg


def main():
    usage = """%prog -i <file>

extractSplitReads_BwaMem v0.1.0
Author: Ira Hall
Description: Get split-read alignments from bwa-mem in lumpy compatible
format. Ignores reads marked as duplicates.
Works on read or position sorted SAM input. Tested on bwa mem v0.7.5a-r405.
    """
    parser = OptionParser(usage)

    parser.add_option("-i", "--inFile", dest="inFile",
                      help="A SAM file or standard input (-i stdin).",
                      metavar="FILE")
    parser.add_option("-n", "--numSplits", dest="numSplits", default=2,
                      type="int",
                      help='''The maximum number of split-read mappings to
                      allow per read. Reads with more are excluded.
                      Default=2''', metavar="INT")
    parser.add_option("-d", "--includeDups", dest="includeDups",
                      action="store_true", default=0,
                      help='''Include alignments marked as duplicates.
                      Default=False''')
    parser.add_option("-m", "--minNonOverlap", dest="minNonOverlap",
                      default=20, type="int", help='''minimum non-overlap between
                      split alignments on the query (default=20)''',
                      metavar="INT")
    (opts, args) = parser.parse_args()
    if opts.inFile is None:
        parser.print_help()
        print
    else:
        try:
            extractSplitsFromBwaMem(opts.inFile, opts.numSplits,
                                    opts.includeDups, opts.minNonOverlap)
        except IOError as err:
            sys.stderr.write("IOError " + str(err) + "\n")
            return


if __name__ == "__main__":
    sys.exit(main())