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#!/usr/bin/env python
import sys
import getopt
import string
from optparse import OptionParser
import re
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())
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