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retrieveSAM3.py
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retrieveSAM3.py
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#!/usr/bin/python
# JMG 6/13/16
# Retrieving a subset of reads from a SAM.
# Version 3: condensing just CpG methylation data.
import sys
import re
class Read():
'''
A class for representing a read's position,
seq, qual, and methylation string.
'''
def __init__(self, header, chr, pos, cigar, seq, qual, meth):
self.header = header
self.chr = chr
self.pos = pos
self.seq = seq
self.qual = qual
self.meth = meth
# convert cigar to 'M/I/D' string
cig = ''
for c in cigar:
dist = int(c[0])
cig += c[1] * dist
self.cigar = cig
def getPos(self):
return self.pos
def getCigar(self):
return self.cigar
def setCigar(self, cigar):
self.cigar = cigar
def setMeth(self, meth):
self.meth = meth
def adjustMeth(self):
'''
Remove non-CpG methylation data from methylation string.
#Convert CpG methylation data to '/' if quality is low.
'''
meth = self.meth
for c in ['h', 'H', 'x', 'X']:
meth = meth.replace(c, '.')
# remove low quality CpG bases -- min qual 30
for c in ['z', 'Z']:
idx = meth.find(c)
while idx != -1:
# convert low qual bases (< 30) to '/'
#if ord(self.qual[idx]) - 33 < 30:
# meth = meth[:idx] + '/' + meth[idx+1:]
#print c, self.qual[idx], ord(self.qual[idx]), '\n'
idx = meth.find(c, idx + 1)
self.meth = meth
def adjustCig(self, minLoc):
'''
Adjust the cigar -- add gaps to 5' end.
'''
# add gaps to 5' end
offset = self.pos - minLoc
self.cigar = 'G' * offset + self.cigar
def getMeth(self):
'''
Construct the methylation string,
including gaps.
'''
ans = ''
loc = 0 # location in self.meth
for i in range(len(self.cigar)):
# add bases from methylation string
c = self.cigar[i]
if c == 'D':
ans += '-'
elif c == 'G':
ans += ' '
elif c in ['M', 'I']:
ans += self.meth[loc]
loc += 1
else:
sys.stderr.write('Error! Unknown CIGAR base: %s\n' % c)
sys.exit(-1)
return ans
def addIns(reads):
'''
Add inserted bases to the cigars.
'''
# create matrix of cigars
mat = []
for read in reads:
mat.append(read.getCigar())
# check each position for 'I'
i = 0
while i < len(mat[-1]):
for cig in mat:
if i < len(cig) and cig[i] == 'I':
for j in range(len(mat)):
if i < len(mat[j]) and mat[j][i] != 'I':
if i == 0 or mat[j][i-1] == 'G':
mat[j] = mat[j][:i] + 'G' + mat[j][i:]
else:
mat[j] = mat[j][:i] + 'D' + mat[j][i:]
break
i += 1
# save adjusted cigars
for i in range(len(reads)):
reads[i].setCigar(mat[i])
def getInt(arg):
'''
Convert given argument to int.
'''
try:
val = int(arg)
except ValueError:
sys.stderr.write('Error! Cannot convert %s to int\n' % arg)
sys.exit(-1)
return val
def openRead(filename):
'''
Open filename for reading. '-' indicates stdin.
'''
if filename == '-':
return sys.stdin
try:
f = open(filename, 'rU')
except IOError:
sys.stderr.write('Error! Cannot open %s for reading\n' % filename)
sys.exit(-1)
return f
def openWrite(filename):
'''
Open filename for writing. '-' indicates stdout.
'''
if filename == '-':
return sys.stdout
try:
f = open(filename, 'w')
except IOError:
sys.stderr.write('Error! Cannot open %s for writing\n' % filename)
sys.exit(-1)
return f
def parseCigar(cigar):
'''
Return in/del offset, plus list of tuples for cigar.
'''
parts = re.findall(r'(\d+)([IDM])', cigar)
offset = 0
for part in parts:
if part[1] == 'D':
offset += int(part[0])
elif part[1] == 'I':
offset -= int(part[0])
return offset, parts
def getXM(lis):
'''
Get "XM" methylation string.
'''
for t in lis:
spl = t.split(':')
if spl[0] == 'XM':
return spl[-1]
sys.stderr.write('Error! Cannot find XM in SAM record\n')
sys.exit(-1)
def loadGen(fGen, chrom):
'''
Load a chromosome from the given genome file.
'''
# find chromosome
f = openRead(fGen)
seq = ''
for line in f:
if line.rstrip()[1:] == chrom:
# save sequence
for line in f:
if line[0] == '>':
return seq
seq += line.rstrip()
if seq:
return seq
sys.stderr.write('Error! Cannot find chromosome %s\n' % chrom)
sys.exit(-1)
def parseSAM(f, chrom, start, end, reads):
'''
Parse the SAM file. Select reads overlapping the
given coordinates.
'''
minLoc = 1000000000
maxLoc = 0
count = total = 0
for line in f:
if line[0] == '@':
continue
spl = line.rstrip().split('\t')
count += 1
# skip if wrong chromosome
chr = spl[2]
if chr != chrom:
continue
# write if within bounds
loc = int(spl[3])
offset, cigar = parseCigar(spl[5])
loc3 = loc + len(spl[9]) + offset
if (loc >= start and loc <= end) or \
(loc3 >= start and loc3 <= end) or \
(loc <= start and loc3 >= end):
reads.append(Read(spl[0], chr, loc, cigar, \
spl[9], spl[10], getXM(spl[11:])))
total += 1
if loc3 > maxLoc:
maxLoc = loc3
if loc < minLoc:
minLoc = loc
return count, total, minLoc, maxLoc
def main():
'''
Main.
'''
args = sys.argv[1:]
if len(args) < 6:
print 'Usage: python %s <SAMfile> <out> ' % sys.argv[0],
print '<chr> <start> <end> <genome>'
print ' Use \'-\' for stdin/stdout'
sys.exit(-1)
# open files
f = openRead(args[0])
fOut = openWrite(args[1])
# save region of interest
chr = args[2]
start = getInt(args[3])
end = getInt(args[4])
# process file
reads = []
count, total, minLoc, maxLoc = parseSAM(f, chr, \
start, end, reads)
reads = sorted(reads, key=Read.getPos) # sort by position
f.close()
# get genomic segment
if len(args) > 5:
seq = loadGen(args[5], chr)
# prepend to reads list
reads.insert(0, Read('genome', chr, minLoc-1, [(str(maxLoc - minLoc), 'M')], \
seq[minLoc-1:maxLoc-1].upper(), '', seq[minLoc-1:maxLoc-1].upper()))
# adjust reads for 5' ends, insertions
for read in reads:
read.adjustCig(minLoc)
#read.adjustMeth()
addIns(reads)
# find methylation loci
loci = []
gap = [] # running tally of deleted bases
tally = 0
gMeth = reads[0].getMeth()
for i in range(len(gMeth)):
for read in reads[1:]:
meth = read.getMeth()
if i < len(meth) and meth[i] in ['z', 'Z']:
loci.append(i)
break
if gMeth[i] == '-':
tally += 1
gap.append(tally)
# print output
#fOut.write('%s\t1-based positions:\n' % chr)
summary = {}
for read in reads[1:]:
meth = read.getMeth()
res = '' # summarized methylation string
idx = 0
while idx < len(loci):
pos = (loci[idx],)
chrPos = str(pos[0] + minLoc - gap[pos[0]]) # actual position in genome
if idx + 1 < len(loci) and loci[idx] + 1 == loci[idx + 1]:
pos += (loci[idx + 1],)
chrPos += '+1'
idx += 1
#if read == reads[1]:
# fOut.write('%d' % (chrPos))
# if len(pos) > 1:
# fOut.write('+1')
# fOut.write('\t')
if not chrPos in summary:
summary[chrPos] = [0, 0]
if pos[0] >= len(meth) or \
(len(pos) == 1 and meth[pos[0]] == ' ') or \
(len(pos) > 1 and pos[1] < len(meth) and meth[pos[1]] == ' '):
# no data: labeled '-'
res += '-'
else:
flag = 1
for i in pos:
if i >= len(meth):
# no data: labeled '-'
res += '-'
flag = 0
break
if meth[i] == 'z':
# unmethylated: labeled '0'
res += '0'
flag = 0
summary[chrPos][0] += 1
break
if meth[i] == 'Z':
# methylated: labeled '1'
res += '1'
flag = 0
summary[chrPos][1] += 1
break
if flag:
# other labeled: 'x'
res += 'x'
idx += 1
#if read == reads[1]:
# fOut.write('\n')
fOut.write('%s\n' % res)
fOut.write('\n' + '=' * 50 + '\n\n')
for i in sorted(summary):
# bismark output lists methylated before unmethylated
fOut.write('%s\t%s\t%d\t%d\n' % (chr, i, summary[i][1], summary[i][0]))
fOut.close()
sys.stderr.write('Reads analyzed: %d\n' % count)
sys.stderr.write('Reads written to %s: %d\n' % (args[1], total))
if __name__ == '__main__':
main()