def worker(self,i,j,k):
samfile = pysam.Samfile(self.samfiles[i], "rb")
assert samfile._hasIndex(), "Cannot open BAM index for file %s"%sf
chrommap = self.chrreg.chrommap(self.samfiles[i])
# blocksize = int(math.ceil(len(self.loci)/self.tpb))
# for l in range(j*blocksize,min((j+1)*blocksize,len(self.loci))):
for l in range(j,len(self.loci),self.tpb):
snvchr, snvpos, ref, alt, snvextra = self.loci[l]
cnts = Counter()
total = Counter()
reads = []
snvpos1 = snvpos - 1
try:
snvlabel = chrommap(snvchr)
if snvlabel != None:
for pileupcolumn in samfile.pileup(snvlabel, snvpos1, snvpos1 + 1, truncate=True):
total[i] += pileupcolumn.n
for pileupread in pileupcolumn.pileups:
try:
al, pos, base, nseg = self.filter.test(pileupread)
except BadRead, e:
cnts[(i, e.message)] += 1
continue
reads.append((al, pos, base, i))
cnts[(i, 'Good')] += 1
except ValueError, e:
pass # raise e
total[i] -= cnts[(i,"GapInQueryAtSNVLocus")]
# del cnts[(i,"GapInQueryAtSNVLocus")]
# print >>sys.stderr, (snvchr, snvpos, ref, alt, total, cnts)
self._queue[k].put((snvchr, snvpos, ref, alt, total, reads, cnts))
def iterator(self):
samfiles = []
chrommap = []
for al in self.samfiles:
samfile = pysam.Samfile(al, "rb")
assert samfile._hasIndex(), "Cannot open BAM index for file %s"%sf
samfiles.append(samfile)
chrommap.append(self.chrreg.chrommap(al))
for snvchr, snvpos, ref, alt, snvextra in self.loci:
cnts = Counter()
total = Counter()
reads = []
snvpos1 = snvpos - 1
for i, samfile in enumerate(samfiles):
try:
snvlabel = chrommap[i](snvchr)
if snvlabel != None:
for pileupcolumn in samfile.pileup(snvlabel, snvpos1, snvpos1 + 1, truncate=True):
total[i] += pileupcolumn.n
for pileupread in pileupcolumn.pileups:
try:
al, pos, base, nseg = self.filter.test(pileupread)
except BadRead, e:
cnts[(i, e.message)] += 1
continue
reads.append((al, pos, base, i))
cnts[(i, 'Good')] += 1
except ValueError:
pass
total[i] -= cnts[(i,"GapInQueryAtSNVLocus")]
# del cnts[(i,"GapInQueryAtSNVLocus")]
yield (snvchr, snvpos, ref, alt, total, reads, cnts)
def iterator(self):
samfiles = []
chrommap = []
for al in self.samfiles:
samfile = pysam.Samfile(al, "rb")
assert samfile.has_index(
), "Cannot open BAM index for file %s" % sf
samfiles.append(samfile)
chrommap.append(self.chrreg.chrommap(al))
pileup_kwargs = self.filter.pileup_kwargs()
for snvchr, snvpos, ref, alt, snvextra in self.loci:
cnts = Counter()
total = Counter()
reads = []
snvpos1 = snvpos - 1
for i, samfile in enumerate(samfiles):
try:
snvlabel = chrommap[i](snvchr)
if snvlabel != None:
for pileupcolumn in samfile.pileup(snvlabel,
snvpos1,
snvpos1 + 1,
truncate=True,
**pileup_kwargs):
self.filter.pileup_start(pileupcolumn)
total[i] = pileupcolumn.n
for pileupread in pileupcolumn.pileups:
if self.readgroups != None:
grp = (i,
self.readgroups.group(
pileupread.alignment))
if grp[1] == None:
continue
total[grp] += 1
else:
grp = i
try:
al, pos, base = self.filter.extract_base(
pileupread)
except BadRead as e:
cnts[(grp, e.args[0])] += 1
continue
reads.append((al, pos, base, grp))
cnts[(grp, 'Good')] += 1
self.filter.pileup_end(pileupcolumn)
except ValueError:
pass
yield (snvchr, snvpos, ref, alt, total, reads, cnts)
def worker(self, i, j, k):
samfile = pysam.Samfile(self.samfiles[i], "rb")
assert samfile.has_index(), "Cannot open BAM index for file %s" % sf
chrommap = self.chrreg.chrommap(self.samfiles[i])
# blocksize = int(math.ceil(len(self.loci)/self.tpb))
# for l in range(j*blocksize,min((j+1)*blocksize,len(self.loci))):
pileup_kwargs = self.filter.pileup_kwargs()
for l in range(j, len(self.loci), self.tpb):
snvchr, snvpos, ref, alt, snvextra = self.loci[l]
cnts = Counter()
total = Counter()
reads = []
snvpos1 = snvpos - 1
try:
snvlabel = chrommap(snvchr)
if snvlabel != None:
for pileupcolumn in samfile.pileup(snvlabel,
snvpos1,
snvpos1 + 1,
truncate=True,
**pileup_kwargs):
self.filter.pileup_start(pileupcolumn)
total[i] += pileupcolumn.n
for pileupread in pileupcolumn.pileups:
if self.readgroups != None:
grp = (i,
self.readgroups.group(
pileupread.alignment))
total[grp] += 1
else:
grp = i
try:
al, pos, base = self.filter.extract_base(
pileupread)
except BadRead as e:
cnts[(i, e.args[0])] += 1
continue
reads.append(
(PileupAlignment(al.seq, al.is_reverse), pos,
base, grp))
cnts[(i, 'Good')] += 1
self.filter.pileup_end(pileupcolumn)
except ValueError as e:
pass
self._queue[k].put((snvchr, snvpos, ref, alt, total, reads, cnts))
return
#!/bin/env python2.7
import sys
from os.path import join, dirname, realpath
try:
sys.path.append(join(dirname(realpath(__file__)),
'..', '..', 'common', 'src'))
except NameError:
pass
from pysamimport import pysam
for filename in sys.argv[1:]:
samfile = pysam.Samfile(filename, "rb")
assert samfile.has_index(), "Cannot open BAM index for file %s"%filename
print(filename,"\n "+", ".join(samfile.references)+".")
usedsnvheaders.add(h)
cannonr = (",".join(["%s:%s" % t for t in sorted(r.items())]))
snvkey = (chr, locus, ref, alt, cannonr)
if snvkey not in snvdata:
snvdata[snvkey] = (chr, locus, ref, alt, r)
progress.update()
progress.done()
snvdata = sorted(snvdata.values())
extrasnvheaders = [h for h in extrasnvheaders if h in usedsnvheaders]
progress.message("SNVs: %d" % len(snvdata))
samfiles = []
for al in opt.alignments:
if al.lower().endswith('.bam'):
samfile = pysam.Samfile(al, "rb")
elif al.lower().endswith('.sam'):
samfile = pysam.Samfile(al, "r")
else:
raise RuntimeError("Unexpected alignments file extension: %s." % al)
samfiles.append(samfile)
outheaders = snvheaders + [
_f for _f in """
SNVCount
NoSNVCount
Prob
LogOdds
P-Value
Bonferroni
FDR
def add_bamlabels(self,filename):
samfile = pysam.Samfile(filename, "rb")
assert samfile._hasIndex(), "Cannot open BAM index for file %s"%filename
self._reg[filename] = ChromLabels(samfile.references)
self._bam.append(filename)