def genrefblks(readseq, chrom, start, stop, strand, cigar, nreads):
refpos = start
readpos = 0
if strand == '-':
readseq = reverse_complement(readseq)
tleftlim, trightlim = start + ENDTRIM, stop - ENDTRIM
qleftlim, qrightlim = ENDTRIM, len(readseq) - ENDTRIM
#print '==============='
#print readseq, chrom, start, stop, strand, cigar, nreads
if transcriptome:
print 'P', nreads, chrom, strand, tleftlim, trightlim
cigarcommands = cigar_pattern.findall(cigar)
if cigarcommands[0][
1] == 'S': # shift start site for the first soft clipping
start -= int(cigarcommands[0][0])
if len(cigarcommands
) > 1 and cigarcommands[-1][1] == 'S': # last soft clipping
stop += int(cigarcommands[-1][0])
for num, cmd in cigarcommands:
num = int(num)
if cmd == 'M': # match
mleft = max(qleftlim, readpos)
mright = min(qrightlim, readpos + num)
if mleft < mright:
seq = readseq[mleft:mright]
print 'M', nreads, chrom, strand, max(refpos, tleftlim), seq
refpos += num
readpos += num
elif cmd == 'S': # soft clip
readpos += num
elif cmd == 'N': # skip
refpos += num
elif cmd == 'D': # deletion
if tleftlim <= refpos < trightlim:
print 'D', nreads, chrom, strand, refpos, num
refpos += num
elif cmd == 'I': # insertion
ppos = (refpos if strand == '+' else (refpos - 1))
if tleftlim <= ppos < trightlim:
print 'I', nreads, chrom, strand, ppos, num
readpos += num
elif cmd == 'H': # hard clipping
pass
else:
print 'E', nreads, num, cmd, readseq
raise ValueError
if strand == '+':
fivep, threep = start, stop - 1
else:
fivep, threep = stop - 1, start
print '5', nreads, chrom, strand, fivep
print '3', nreads, chrom, strand, threep
def genrefblks(readseq, chrom, start, stop, strand, cigar, nreads):
refpos = start
readpos = 0
if strand == '-':
readseq = reverse_complement(readseq)
tleftlim, trightlim = start + ENDTRIM, stop - ENDTRIM
qleftlim, qrightlim = ENDTRIM, len(readseq) - ENDTRIM
#print '==============='
#print readseq, chrom, start, stop, strand, cigar, nreads
if transcriptome:
print 'P', nreads, chrom, strand, tleftlim, trightlim
cigarcommands = cigar_pattern.findall(cigar)
if cigarcommands[0][1] == 'S': # shift start site for the first soft clipping
start -= int(cigarcommands[0][0])
if len(cigarcommands) > 1 and cigarcommands[-1][1] == 'S': # last soft clipping
stop += int(cigarcommands[-1][0])
for num, cmd in cigarcommands:
num = int(num)
if cmd == 'M': # match
mleft = max(qleftlim, readpos)
mright = min(qrightlim, readpos + num)
if mleft < mright:
seq = readseq[mleft:mright]
print 'M', nreads, chrom, strand, max(refpos, tleftlim), seq
refpos += num
readpos += num
elif cmd == 'S': # soft clip
readpos += num
elif cmd == 'N': # skip
refpos += num
elif cmd == 'D': # deletion
if tleftlim <= refpos < trightlim:
print 'D', nreads, chrom, strand, refpos, num
refpos += num
elif cmd == 'I': # insertion
ppos = (refpos if strand == '+' else (refpos-1))
if tleftlim <= ppos < trightlim:
print 'I', nreads, chrom, strand, ppos, num
readpos += num
elif cmd == 'H': # hard clipping
pass
else:
print 'E', nreads, num, cmd, readseq
raise ValueError
if strand == '+':
fivep, threep = start, stop-1
else:
fivep, threep = stop-1, start
print '5', nreads, chrom, strand, fivep
print '3', nreads, chrom, strand, threep
def process(nrlist):
nucleotidetracks = [rseqarr.TRACKS.index(i) for i in 'ACGT']
for nracc in nrlist:
dbinfo = refFlat[nracc]
chrom = dbinfo['chrom']
genomeseq = ''.join(
mm9.get(chrom, blkstart, blkend)
for blkstart, blkend in dbinfo['exonBlocks']).upper()
if dbinfo['strand'] == '-':
utr3, utr5 = 'leftUtrBlocks', 'rightUtrBlocks'
else:
utr5, utr3 = 'leftUtrBlocks', 'rightUtrBlocks'
if nracc.startswith('NM_'):
utr5length = blklength(dbinfo[utr5])
cdslength = blklength(dbinfo['cdsBlocks'])
utr3length = blklength(dbinfo[utr3])
else:
exonlength = blklength(dbinfo['exonBlocks'])
cntarray = rseqarr.get_blocks(dbinfo['chrom'], dbinfo['exonBlocks'],
dbinfo['strand'])[nucleotidetracks]
depthcnt = np.array(cntarray.sum(0).clip(1), 'd')
confidentcalls = ((cntarray / depthcnt >= MINPERCENTTOCALL) *
(depthcnt >= MINREADSTOCALL))
mutatedseq = list(genomeseq)
for base, calls in zip('ACGT', confidentcalls):
for pos in np.where(calls)[0]:
mutatedseq[pos] = base
mutatedseq = ''.join(mutatedseq)
if dbinfo['strand'] == '-':
mutatedseq = reverse_complement(mutatedseq)
if nracc.startswith('NM_'):
print >> bedout, '\t'.join([
nracc,
str(utr5length),
str(utr5length + cdslength),
'%s' % dbinfo['geneName'], '.', '+'
])
else:
print >> bedout, '\t'.join([
nracc, '0',
str(exonlength),
'%s' % dbinfo['geneName'], '.', '+'
])
print >> faout, '>%s %s' % (nracc, dbinfo['geneName'])
faout.write(textwrap(mutatedseq))
def process(nrlist):
nucleotidetracks = [rseqarr.TRACKS.index(i) for i in 'ACGT']
for nracc in nrlist:
dbinfo = refFlat[nracc]
chrom = dbinfo['chrom']
genomeseq = ''.join(mm9.get(chrom, blkstart, blkend)
for blkstart, blkend in dbinfo['exonBlocks']).upper()
if dbinfo['strand'] == '-':
utr3, utr5 = 'leftUtrBlocks', 'rightUtrBlocks'
else:
utr5, utr3 = 'leftUtrBlocks', 'rightUtrBlocks'
if nracc.startswith('NM_'):
utr5length = blklength(dbinfo[utr5])
cdslength = blklength(dbinfo['cdsBlocks'])
utr3length = blklength(dbinfo[utr3])
else:
exonlength = blklength(dbinfo['exonBlocks'])
cntarray = rseqarr.get_blocks(dbinfo['chrom'], dbinfo['exonBlocks'],
dbinfo['strand'])[nucleotidetracks]
depthcnt = np.array(cntarray.sum(0).clip(1), 'd')
confidentcalls = ((cntarray/depthcnt >= MINPERCENTTOCALL) *
(depthcnt >= MINREADSTOCALL))
mutatedseq = list(genomeseq)
for base, calls in zip('ACGT', confidentcalls):
for pos in np.where(calls)[0]:
mutatedseq[pos] = base
mutatedseq = ''.join(mutatedseq)
if dbinfo['strand'] == '-':
mutatedseq = reverse_complement(mutatedseq)
if nracc.startswith('NM_'):
print >> bedout, '\t'.join([nracc, str(utr5length),
str(utr5length + cdslength),
'%s' % dbinfo['geneName'], '.', '+'])
else:
print >> bedout, '\t'.join([nracc, '0', str(exonlength),
'%s' % dbinfo['geneName'], '.', '+'])
print >> faout, '>%s %s' % (nracc, dbinfo['geneName'])
faout.write(textwrap(mutatedseq))
def iteralignments(self, strands='+-', withref=False):
geteditdist= lambda x: x[4]
for line in self.samfile:
fields = line[:-1].split('\t')
if line[0] == '@':
if line[:3] != '@SQ':
continue
sqname = fields[1][3:]
sqlen = [int(fl[3:]) for fl in fields[2:] if fl[:3] == 'LN:'][0]
self.seqlen[sqname] = sqlen
continue
qname = fields[0]
flags = int(fields[1])
rname = fields[2]
pos = int(fields[3]) # 1-based leftmost
mapq = int(fields[4]) # phred-scaled
cigar = fields[5]
seq = fields[9]
options = dict(v.split(':', 1) for v in fields[11:])
if flags & F_REVERSE_STRAND:
strand = '-'
seq = reverse_complement(seq)
else:
strand = '+'
editdist = int(options.get('NM', 'i:-1')[2:])
if rname == '*' or strand not in strands:
mapped = []
else:
reflen, _ = calculate_cigar_length(cigar)
stop = pos + reflen - 1
start = pos - 1 if self.zerobase else pos
mapped = [(rname, start, stop, strand, editdist, cigar)]
for altmatch in options.get('XA', 'Z:')[2:].split(';')[:-1]:
altfields = altmatch.split(',')
strand = altfields[1][0]
pos = int(altfields[1][1:])
rname = altfields[0]
cigar = altfields[2]
editdist = int(altfields[3])
reflen, _ = calculate_cigar_length(cigar)
stop = pos + reflen - 1
start = pos - 1 if self.zerobase else pos
if strand in strands:
mapped.append((rname, start, stop, strand, editdist,
cigar))
# search for alternative reads
for altline in self.samfile:
altfields = altline[:-1].split('\t')
altqname = altfields[0]
altflags = int(altfields[1])
if altqname != qname:
self.samfile.push(altline)
break
altrname = altfields[2]
altpos = int(altfields[3]) # 1-based leftmost
altmapq = int(altfields[4]) # phred-scaled
altcigar = altfields[5]
altseq = altfields[9]
altoptions = dict(v.split(':', 1) for v in altfields[11:])
if altflags & F_REVERSE_STRAND:
altstrand = '-'
altseq = reverse_complement(altseq)
else:
altstrand = '+'
alteditdist = int(altoptions.get('NM', 'i:-1')[2:])
if altrname != '*' and altstrand in strands:
altreflen, _ = calculate_cigar_length(altcigar)
altstop = altpos + altreflen - 1
altstart = altpos - 1 if self.zerobase else altpos
mapped.append((altrname, altstart, altstop, altstrand,
alteditdist, altcigar))
mapped.sort(key=geteditdist)
if withref:
newmapped = []
for m in mapped:
subseq = self.getsubseq(m[0], m[1]-1, m[2])
if m[3] == '-':
subseq = reverse_complement(subseq)
newmapped.append(m + (subseq,))
mapped = newmapped
yield {
'qname': qname,
'flags': flags,
'mapq': mapq,
'seq': seq,
'options': options,
'mapped': mapped, # positions are 1-based
}
