def make_ambiguity_bigwig_by_readname(prefix, bam_filenames, stop_after=None, subsample=1):
#import pysam
#alf = pysam.AlignmentFile(bam_filenames[0])
#header = alf.header
header = sam.parsed_bam_headers(bam_filenames[0])
with open(prefix+"-chrom.sizes","wb") as f:
for entry in header["SQ"]:
f.write("{}\t{}\n".format(entry["SN"],entry["LN"]))
chrom_names = [ entry["SN"] for entry in header["SQ"] ]
chrom_sizes = [ int(entry["LN"]) for entry in header["SQ"] ]
#alf.close()
unambiguous = dict([ (i,Piler(j)) for i,j in zip(chrom_names,chrom_sizes) ])
total = dict([ (i,Piler(j)) for i,j in zip(chrom_names,chrom_sizes) ])
old = grace.status("Ambiguity bigwig")
for filename in bam_filenames:
#alf = pysam.AlignmentFile(filename)
alf = sam.Bam_reader(filename)
n = 0
sub = subsample-1
for (key,items) in itertools.groupby(alf, lambda item: item.query_name):
sub = (sub + 1) % subsample
if sub: continue
items = [ item for item in items if not item.is_unmapped and not item.is_supplementary ]
if not items:
continue
# Only use top scoring alignments
AS = [ item.get_AS() for item in items ]
best_AS = max(AS)
items = [ item for item, this_AS in zip(items,AS) if this_AS >= best_AS ]
for item in items:
#spanner = fragment_split_coverage([item])
spanner = fragment_coverage([item]) #TODO fixme when blocks available
spanner = scale_spanner(1.0/len(items), spanner)
total[item.reference_name].add(spanner)
if len(items) == 1:
unambiguous[item.reference_name].add(spanner)
n += 1
if stop_after is not None and n > stop_after: break
if n % 1000000 == 0: grace.status(os.path.basename(prefix)+" "+filename+" "+grace.pretty_number(n))
alf.close()
ambiguities = [ ]
for i in xrange(len(total)):
u = unambiguous[chrom_names[i]].get()
t = map_spanner(lambda x: x*1j, total[chrom_names[i]].get())
c = pile([u,t],initial=0.0)
c = map_spanner(lambda x: max(0.0,x.imag-x.real)/max(x.imag,1.0), c)
ambiguities.append(c)
bedgraph(prefix+".bedgraph", zip(chrom_names, [ item for item in ambiguities ]))
subprocess.check_call([
"wigToBigWig",prefix+".bedgraph",prefix+"-chrom.sizes",prefix+".bw"])
os.unlink(prefix+".bedgraph")
os.unlink(prefix+"-chrom.sizes")
grace.status(old)
def make_ambiguity_bigwig(prefix, bam_filenames, stop_after=None, subsample=1):
#import pysam
#alf = pysam.AlignmentFile(bam_filenames[0])
#header = alf.header
header = sam.parsed_bam_headers(bam_filenames[0])
with open(prefix+"-chrom.sizes","wb") as f:
for entry in header["SQ"]:
f.write("{}\t{}\n".format(entry["SN"],entry["LN"]))
chrom_names = [ entry["SN"] for entry in header["SQ"] ]
chrom_sizes = [ int(entry["LN"]) for entry in header["SQ"] ]
#alf.close()
unambiguous = dict([ (i,Piler(j)) for i,j in zip(chrom_names,chrom_sizes) ])
total = dict([ (i,Piler(j)) for i,j in zip(chrom_names,chrom_sizes) ])
for filename in bam_filenames:
#alf = pysam.AlignmentFile(filename)
alf = sam.Bam_reader(filename)
n = 0
sub = subsample-1
for item in alf:
if item.is_unmapped or item.is_supplementary:
continue
sub = (sub + 1) % subsample
if sub: continue
#spanner = fragment_split_coverage([item])
spanner = fragment_coverage([item]) #TODO fixme when blocks available
total[item.reference_name].add(spanner)
NH = 1
for item2 in item.extra:
if item2.startswith("NH:i:"):
NH = int(item2[5:])
if NH == 1:
unambiguous[item.reference_name].add(spanner)
n += 1
if stop_after is not None and n > stop_after: break
if n % 1000000 == 0: print prefix, filename, grace.pretty_number(n)
alf.close()
ambiguities = [ ]
for i in xrange(len(total)):
u = unambiguous[chrom_names[i]].get()
t = map_spanner(lambda x: x*1j, total[chrom_names[i]].get())
c = pile([u,t],initial=0.0)
c = map_spanner(lambda x: max(0.0,x.imag-x.real)/max(x.imag,1.0), c)
ambiguities.append(c)
bedgraph(prefix+".bedgraph", zip(chrom_names, [ item for item in ambiguities ]))
subprocess.check_call([
"wigToBigWig",prefix+".bedgraph",prefix+"-chrom.sizes",prefix+".bw"])
os.unlink(prefix+".bedgraph")
os.unlink(prefix+"-chrom.sizes")
def make_bigwig(prefix, bam_filenames, make_spanner, fragments=False, stop_after=None, scale=1.0, polya=False):
have_pysam = False
try:
import pysam
have_pysam = True
except ImportError:
pass
#alf = pysam.AlignmentFile(bam_filenames[0])
#header = alf.header
header = sam.parsed_bam_headers(bam_filenames[0])
with open(prefix+"-chrom.sizes","wb") as f:
for entry in header["SQ"]:
f.write("{}\t{}\n".format(entry["SN"],entry["LN"]))
chrom_names = [ entry["SN"] for entry in header["SQ"] ]
chrom_sizes = [ int(entry["LN"]) for entry in header["SQ"] ]
#alf.close()
forward = dict([ (i,Piler(j)) for i,j in zip(chrom_names,chrom_sizes) ])
reverse = dict([ (i,Piler(j)) for i,j in zip(chrom_names,chrom_sizes) ])
old = grace.status("Bigwig")
for filename in bam_filenames:
if have_pysam:
alf = pysam.AlignmentFile(filename)
else:
alf = sam.Bam_reader(filename)
n = 0
if not fragments:
for item in alf:
if item.is_unmapped or item.is_secondary or item.is_supplementary:
continue
if polya and not alignment_is_polya(item):
continue
# Assume --> <-- oriented read pairs
which = forward if bool(item.is_reverse) == bool(item.is_read2) else reverse
which[item.reference_name].add( make_spanner(item) )
n += 1
if stop_after is not None and n > stop_after: break
if n % 1000000 == 0: grace.status(os.path.basename(prefix)+" "+filename+" "+grace.pretty_number(n))
else:
for item in iter_fragments(alf):
if polya and not any(alignment_is_polya(al) for al in item):
continue
# Assume --> <-- oriented read pairs
which = forward if bool(item[0].is_reverse) == bool(item[0].is_read2) else reverse
which[item[0].reference_name].add( make_spanner(item) )
n += 1
if stop_after is not None and n > stop_after: break
if n % 1000000 == 0: grace.status(os.path.basename(prefix)+" "+filename+" "+grace.pretty_number(n))
if have_pysam:
alf.close()
bedgraph(prefix+"-fwd.bedgraph", zip(chrom_names, [ scale_spanner(scale, forward[item].get()) for item in chrom_names ]))
subprocess.check_call([
"wigToBigWig",prefix+"-fwd.bedgraph",prefix+"-chrom.sizes",prefix+"-fwd.bw"])
os.unlink(prefix+"-fwd.bedgraph")
bedgraph(prefix+"-rev.bedgraph", zip(chrom_names, [ scale_spanner(scale, reverse[item].get()) for item in chrom_names ]))
subprocess.check_call([
"wigToBigWig",prefix+"-rev.bedgraph",prefix+"-chrom.sizes",prefix+"-rev.bw"])
os.unlink(prefix+"-rev.bedgraph")
os.unlink(prefix+"-chrom.sizes")
grace.status(old)
def make_ambiguity_bigwig_by_readname(prefix,
bam_filenames,
stop_after=None,
subsample=1):
#import pysam
#alf = pysam.AlignmentFile(bam_filenames[0])
#header = alf.header
header = sam.parsed_bam_headers(bam_filenames[0])
with open(prefix + "-chrom.sizes", "wb") as f:
for entry in header["SQ"]:
f.write("{}\t{}\n".format(entry["SN"], entry["LN"]))
chrom_names = [entry["SN"] for entry in header["SQ"]]
chrom_sizes = [int(entry["LN"]) for entry in header["SQ"]]
#alf.close()
unambiguous = dict([(i, Piler(j))
for i, j in zip(chrom_names, chrom_sizes)])
total = dict([(i, Piler(j)) for i, j in zip(chrom_names, chrom_sizes)])
old = grace.status("Ambiguity bigwig")
for filename in bam_filenames:
#alf = pysam.AlignmentFile(filename)
alf = sam.Bam_reader(filename)
n = 0
sub = subsample - 1
for (key, items) in itertools.groupby(alf,
lambda item: item.query_name):
sub = (sub + 1) % subsample
if sub: continue
items = [
item for item in items
if not item.is_unmapped and not item.is_supplementary
]
if not items:
continue
# Only use top scoring alignments
AS = [item.get_AS() for item in items]
best_AS = max(AS)
items = [
item for item, this_AS in zip(items, AS) if this_AS >= best_AS
]
for item in items:
#spanner = fragment_split_coverage([item])
spanner = fragment_coverage(
[item]) #TODO fixme when blocks available
spanner = scale_spanner(1.0 / len(items), spanner)
total[item.reference_name].add(spanner)
if len(items) == 1:
unambiguous[item.reference_name].add(spanner)
n += 1
if stop_after is not None and n > stop_after: break
if n % 1000000 == 0:
grace.status(
os.path.basename(prefix) + " " + filename + " " +
grace.pretty_number(n))
alf.close()
ambiguities = []
for i in xrange(len(total)):
u = unambiguous[chrom_names[i]].get()
t = map_spanner(lambda x: x * 1j, total[chrom_names[i]].get())
c = pile([u, t], initial=0.0)
c = map_spanner(lambda x: max(0.0, x.imag - x.real) / max(x.imag, 1.0),
c)
ambiguities.append(c)
bedgraph(prefix + ".bedgraph",
zip(chrom_names, [item for item in ambiguities]))
subprocess.check_call([
"wigToBigWig", prefix + ".bedgraph", prefix + "-chrom.sizes",
prefix + ".bw"
])
os.unlink(prefix + ".bedgraph")
os.unlink(prefix + "-chrom.sizes")
grace.status(old)
def make_ambiguity_bigwig(prefix, bam_filenames, stop_after=None, subsample=1):
#import pysam
#alf = pysam.AlignmentFile(bam_filenames[0])
#header = alf.header
header = sam.parsed_bam_headers(bam_filenames[0])
with open(prefix + "-chrom.sizes", "wb") as f:
for entry in header["SQ"]:
f.write("{}\t{}\n".format(entry["SN"], entry["LN"]))
chrom_names = [entry["SN"] for entry in header["SQ"]]
chrom_sizes = [int(entry["LN"]) for entry in header["SQ"]]
#alf.close()
unambiguous = dict([(i, Piler(j))
for i, j in zip(chrom_names, chrom_sizes)])
total = dict([(i, Piler(j)) for i, j in zip(chrom_names, chrom_sizes)])
for filename in bam_filenames:
#alf = pysam.AlignmentFile(filename)
alf = sam.Bam_reader(filename)
n = 0
sub = subsample - 1
for item in alf:
if item.is_unmapped or item.is_supplementary:
continue
sub = (sub + 1) % subsample
if sub: continue
#spanner = fragment_split_coverage([item])
spanner = fragment_coverage([item
]) #TODO fixme when blocks available
total[item.reference_name].add(spanner)
NH = 1
for item2 in item.extra:
if item2.startswith("NH:i:"):
NH = int(item2[5:])
if NH == 1:
unambiguous[item.reference_name].add(spanner)
n += 1
if stop_after is not None and n > stop_after: break
if n % 1000000 == 0: print prefix, filename, grace.pretty_number(n)
alf.close()
ambiguities = []
for i in xrange(len(total)):
u = unambiguous[chrom_names[i]].get()
t = map_spanner(lambda x: x * 1j, total[chrom_names[i]].get())
c = pile([u, t], initial=0.0)
c = map_spanner(lambda x: max(0.0, x.imag - x.real) / max(x.imag, 1.0),
c)
ambiguities.append(c)
bedgraph(prefix + ".bedgraph",
zip(chrom_names, [item for item in ambiguities]))
subprocess.check_call([
"wigToBigWig", prefix + ".bedgraph", prefix + "-chrom.sizes",
prefix + ".bw"
])
os.unlink(prefix + ".bedgraph")
os.unlink(prefix + "-chrom.sizes")
def make_bigwig(prefix,
bam_filenames,
make_spanner,
fragments=False,
stop_after=None,
scale=1.0,
polya=False):
have_pysam = False
try:
import pysam
have_pysam = True
except ImportError:
pass
#alf = pysam.AlignmentFile(bam_filenames[0])
#header = alf.header
header = sam.parsed_bam_headers(bam_filenames[0])
with open(prefix + "-chrom.sizes", "wb") as f:
for entry in header["SQ"]:
f.write("{}\t{}\n".format(entry["SN"], entry["LN"]))
chrom_names = [entry["SN"] for entry in header["SQ"]]
chrom_sizes = [int(entry["LN"]) for entry in header["SQ"]]
#alf.close()
forward = dict([(i, Piler(j)) for i, j in zip(chrom_names, chrom_sizes)])
reverse = dict([(i, Piler(j)) for i, j in zip(chrom_names, chrom_sizes)])
old = grace.status("Bigwig")
for filename in bam_filenames:
if have_pysam:
alf = pysam.AlignmentFile(filename)
else:
alf = sam.Bam_reader(filename)
n = 0
if not fragments:
for item in alf:
if item.is_unmapped or item.is_secondary or item.is_supplementary:
continue
if polya and not alignment_is_polya(item):
continue
# Assume --> <-- oriented read pairs
which = forward if bool(item.is_reverse) == bool(
item.is_read2) else reverse
which[item.reference_name].add(make_spanner(item))
n += 1
if stop_after is not None and n > stop_after: break
if n % 1000000 == 0:
grace.status(
os.path.basename(prefix) + " " + filename + " " +
grace.pretty_number(n))
else:
for item in iter_fragments(alf):
if polya and not any(alignment_is_polya(al) for al in item):
continue
# Assume --> <-- oriented read pairs
which = forward if bool(item[0].is_reverse) == bool(
item[0].is_read2) else reverse
which[item[0].reference_name].add(make_spanner(item))
n += 1
if stop_after is not None and n > stop_after: break
if n % 1000000 == 0:
grace.status(
os.path.basename(prefix) + " " + filename + " " +
grace.pretty_number(n))
if have_pysam:
alf.close()
bedgraph(
prefix + "-fwd.bedgraph",
zip(chrom_names, [
scale_spanner(scale, forward[item].get()) for item in chrom_names
]))
subprocess.check_call([
"wigToBigWig", prefix + "-fwd.bedgraph", prefix + "-chrom.sizes",
prefix + "-fwd.bw"
])
os.unlink(prefix + "-fwd.bedgraph")
bedgraph(
prefix + "-rev.bedgraph",
zip(chrom_names, [
scale_spanner(scale, reverse[item].get()) for item in chrom_names
]))
subprocess.check_call([
"wigToBigWig", prefix + "-rev.bedgraph", prefix + "-chrom.sizes",
prefix + "-rev.bw"
])
os.unlink(prefix + "-rev.bedgraph")
os.unlink(prefix + "-chrom.sizes")
grace.status(old)
