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|
# SAM line parser
class Sam:
import re
SAMSTR = re.compile("^(\S+)\t(\d+)\t(\S+)\t(\d+)\t(\d+)\t(\S+)\t(\S+)\t"\
"(\d+)\t([\+\-]*\d+)\t(\S+)\t(\S+)"\
"(\t.+)?")
TAGSTR = re.compile("^(\S{2}):([iZ]):(\S+)")
# SAMSTR = re.compile("^(\S+)\s+(\d+)\s+(\S+)\s+(\d+)\s+(\d+)\s+(\S+)\s+(\S+)\s+"\
# "(\d+)\s+([\+\-]*\d+)\s+(\S+)\s+(\S+)(\s+AS:i:\d+){0,1}"\
# ".*(\s+NM:i:\d+){0,1}")
QNAMSTR = re.compile("^(\S+)\/([12])$")
ALISCOR = re.compile("\tAS:i:(\d+)")
CLIPSTART = re.compile("^(\d+)([HS])")
CLIPEND = re.compile("(\d+)([HS])$")
QEXT = re.compile("/([12])$")
FLAG_PAIRED = 0x0001
FLAG_PROPER = 0x0002
FLAG_NOMAP = 0x0004
FLAG_MATENOMAP = 0x0008
FLAG_STRAND = 0x0010 # reverse complemented
FLAG_MATESTRAND = 0x0020
FLAG_1stMATE = 0x0040
FLAG_2ndMATE = 0x0080
FLAG_NOTPRIMARY = 0x0100
FLAG_CHECKFAIL = 0x0200
FLAG_DUPLICATE = 0x0400
DEFAULT_SWSCOR = 0
MAPQ_NONRANDOM = 4
FASTQ_FORMAT = '@%s\n%s\n+\n%s\n'
COMPLEMENTOR = {'A':'T', 'C':'G', 'G':'C', 'T':'A',
'a':'t', 'c':'g', 'g':'c', 't':'a',
'N':'N', 'n':'n'}
def __init__(self):
self.blank()
def blank(self):
self.ok = False
self.qname = ""
self.flag = 0
self.rname = ""
self.pos = 0
self.mapq = 0
self.cigar = ""
self.mrnm = ""
self.mpos = 0
self.isize = 0
self.swscor = 0
self.nt = "" # nucleotide sequence
self.qual = "" # base qualities
self.tags = {}
def parse(self, lin, is_verbose=True):
self.blank()
m = Sam.SAMSTR.match(lin)
if m:
#print m.groups()
#print "GROUPS: %i" % len(m.groups())
self.qname = m.group(1)
self.flag = int(m.group(2))
self.rname = m.group(3)
self.pos = int(m.group(4))
self.mapq = int(m.group(5))
self.cigar = m.group(6)
self.mrnm = m.group(7)
self.mpos = int(m.group(8))
self.isize = int(m.group(9))
self.nt = m.group(10)
self.qual = m.group(11)
self.tags = {}
if len(m.groups()) > 11:
tags = m.group(12).split('\t')
#print "TAGS", tags
for tag in tags:
n = Sam.TAGSTR.match(tag)
if n:
(tagnam, typ, fld) = n.groups()
self.tags[tagnam] = (typ, fld)
self.ok = True
else:
if is_verbose: print("NOT PARSED '%s'" % lin)
self.blank()
def clip(self):
s = 0
e = 0
typ = 'H'
isCorrect = False
ms = Sam.CLIPSTART.match(self.cigar)
if ms:
s = int(ms.group(1))
typ = ms.group(2)
me = Sam.CLIPSTART.search(self.cigar)
if me:
e = int(me.group(1))
if ms and ms.group(2) == me.group(2):
isCorrect = True
return (typ, isCorrect, s, e)
def strand(self):
print("(%i, %s)" % (self.flag, bool(self.flag & Sam.FLAG_STRAND)))
return bool(self.flag & Sam.FLAG_STRAND)
def calcUnclippedStart(self):
rs = self.pos
(typ, ok, s, e) = self.clip()
#print rs
#print (typ, ok, s, e)
if typ == 'H' and ok:
rs = rs - s
return rs
def cmpFlags(self, other):
rv = True
if self.flag != other.flag:
f = Sam.FLAG_PROPER | Sam.FLAG_MATENOMAP | Sam.FLAG_MATESTRAND
if (self.flag & (~f)) != (other.flag & (~f)):
rv = False
return rv
def strFlags(self):
s = "FLAG:\n"
if self.flag & Sam.FLAG_PAIRED:
i = 1
else:
i = 0
s = s + '[%1i] Paired Read\n' % i
if self.flag & Sam.FLAG_PROPER:
i = 1
else:
i = 0
s = s + '[%1i] Proper Read\n' % i
if self.flag & Sam.FLAG_1stMATE:
i = 1
else:
i = 0
s = s + '[%1i] 1st mate of a pair\n' % i
if self.flag & Sam.FLAG_2ndMATE:
i = 1
else:
i = 0
s = s + '[%1i] 2nd mate of a pair\n' % i
return s
def isMapped(self):
return self.name != '*'
def getMateNam(self):
#print "getMateNam:%s" % (self.qname)
m = Sam.QNAMSTR.search(self.qname)
if m:
rv = (m.group(1), int(m.group(2)))
else:
flg = int(self.flag)
if flg & Sam.FLAG_1stMATE:
n = 1
elif flg & Sam.FLAG_2ndMATE:
n = 2
else:
n = 0
rv = (self.qname, n)
return rv
def compare(self, other):
rv = True
s = ""
## if self.cigar != other.cigar:
## print "CIGAR strings differ! %s::%s" % \
## (self.cigar, other.cigar)
## rv = False
spos = self.calcUnclippedStart()
opos = other.calcUnclippedStart()
if spos != opos:
if self.cigar == '*':
s = s + "%s not mapped" % self.qname
rv = False
elif other.cigar == '*':
s = s + "%s not mapped" % other.qname
rv = False
else:
s = s + "Mapping positions differ! (%i:%i, %i:%i)" % \
(self.pos, spos, other.pos, opos)
rv = False
elif not self.cmpFlags(other):
s = s + "Flags differ"
rv = False
return (rv, s)
def asFastqStr(self):
mateno = 0
seq =""
qual=""
if self.flag & Sam.FLAG_1stMATE:
namstr = '%s/1' % self.qname
elif self.flag & Sam.FLAG_2ndMATE:
namstr = '%s/2' % self.qname
else:
namstr = self.qname
if bool(self.flag & Sam.FLAG_STRAND):
(seq, qual, okflg) = self.reverseComplement()
if not okflg:
print("ERROR: when reverse complementing sequence!")
exit(1)
else:
seq = self.nt
qual = self.qual
return namstr, seq, qual
def asFastq(self, clip=0):
namstr, seq, qual = self.asFastqStr()
if clip >= len(self.nt):
print("ERROR: clipped fragment > sequence length\n%s" % (self.qname))
return Sam.FASTQ_FORMAT % (namstr, seq[clip:], qual[clip:])
def reverseComplement(self):
s = list(self.qual)
s.reverse()
qual = ""
for i in range(len(self.qual)):
qual = qual + s[i]
s = list(self.nt)
s.reverse()
seq = ""
for i in range(len(self.nt)):
try:
seq = seq + Sam.COMPLEMENTOR[s[i]]
except:
seq = seq + 'N'
return (seq, qual, len(self.nt) == len(self.qual))
def next(self, infil, is_verbose=False):
while 1:
lin = infil.readline()
if not lin: break
self.parse(lin, is_verbose)
if self.ok: break
if is_verbose: print("not parsed: %s" % lin)
return not lin # True if EOF
def fetchNextRead(infil, read):
isEOF = False
currnam = read.qname
while 1:
lin = infil.readline()
if not lin:
isEOF = True
break
read.parse(lin)
if not read.ok:
print("not parsed: %s" % lin)
continue
break
#print read.target.varnum()
#if read.qname != currnam:
# break
return isEOF
def fetchNextPair(infil, samA, samB):
# assumes sorted file
from sys import exit
switch_flag = 0
isEOF = fetchNextRead(infil, samA)
if not isEOF:
isEOF = fetchNextRead(infil, samB)
if not isEOF:
errflg = False
if (samA.flag & Sam.FLAG_PAIRED) == 0 or (samB.flag & Sam.FLAG_PAIRED) == 0:
errflg = True
if (samA.flag & Sam.FLAG_1stMATE) == 0:
switch_flag = 1
if switch_flag == 0:
if (samB.flag & Sam.FLAG_2ndMATE) == 0:
errflg = True
else:
if (samB.flag & Sam.FLAG_2ndMATE) == 1:
errflg = True
if errflg:
print("ERROR: unexpected pair flags.\n%s\n%s\n%s\n%s" % \
(samA.qname, samA.strFlags(), samB.qname, samB.strFlags()))
exit(1)
return (isEOF, switch_flag)
def openFile(filnam, mode):
import gzip
is_compressed = len(filnam) > 3 and filnam[-3:] == ".gz"
try:
if is_compressed:
oufil = gzip.open(filnam, mode)
else:
oufil = open(filnam, mode)
except:
print("ERROR when opening file '%s'" % filnam)
exit(1)
return oufil
if __name__ == '__main__':
from sys import argv, exit
if len(argv) < 3:
print("usage: %s <SAM file (input)> <mapping score threshold>" % argv[0])
exit(1)
infilnam = argv[1]
mapq_min = int(argv[2])
infil = openFile(infilnam, 'r')
read = Sam()
readctr = 0
pairctr = 0
nomapctr = 0
lowqctr = 0
minqctr = 0
highqctr = 0
propctr = 0
chimictr = 0 # counter for chimeric inserts
old_qnam = ""
old_rnam = ""
isizarr = []
while 1:
if fetchNextRead(infil, read):
break;
flg = int(read.flag)
readctr = readctr + 1
if (flg & Sam.FLAG_NOMAP):
nomapctr = nomapctr + 1
else:
if int(read.mapq) >= Sam.MAPQ_NONRANDOM:
minqctr = minqctr + 1
if int(read.mapq) >= mapq_min:
highqctr = highqctr + 1
if (flg & (Sam.FLAG_PAIRED | Sam.FLAG_NOMAP | Sam.FLAG_MATENOMAP)) == Sam.FLAG_PAIRED:
pairctr = pairctr + 1
if (flg & Sam.FLAG_PROPER) == 0:
# not a proper pair
(mnam, mno) = read.getMateNam()
if mno == 1: #print mnam
old_qnam = mnam
old_rnam = read.rname
else:
if mnam == old_qnam:
if read.rname != old_rnam:
chimictr = chimictr + 1
print("[%i, %i]%s: rname1: %s, rname2: %s" % \
(readctr, chimictr, mnam, old_rnam, read.rname))
else:
# a 'proper' pair
print("%s %i %i %x" % (read.qname, abs(read.isize), read.mapq, int(read.flag)))
propctr = propctr + 1
isizarr.append(abs(read.isize))
else:
lowqctr = lowqctr + 1
if readctr % 100000 == 0:
print("%i reads ..." % readctr)
pairctr = pairctr/2
infil.close()
print("%i out of a total of %i reads (%5.2f%%) were mapped." % \
(readctr - nomapctr, readctr, 100*float(readctr - nomapctr)/readctr))
print("%i out of a total of %i reads (%5.2f%%) mapped with a mapping score > %i" % \
(minqctr, readctr, 100*float(minqctr)/readctr, Sam.MAPQ_NONRANDOM))
if Sam.MAPQ_NONRANDOM != mapq_min:
print("%i out of a total of %i reads (%5.2f%%) mapped with a mapping score > %i" % \
(highqctr, readctr, 100*float(highqctr)/readctr, mapq_min))
if pairctr > 0:
print("%i out of a total of %i reads (%5.2f%%) mapped as a proper pair with a mapping score > %i" % \
(propctr, readctr, 100*float(propctr)/readctr, mapq_min))
print("%i of %i pairs (%6.3f%%) with a mapping score >= %i mapped to different chromosomes" % \
(chimictr, pairctr, 200*float(chimictr)/pairctr, mapq_min))
else:
print("There were no reads mapped as pairs.")
exit(0)
|
