def bam_innerdist(bam1, bam2, summaryout=None):
iter1 = bam_iter(bam1)
iter2 = bam_iter(bam2, quiet=True)
distances = {}
total = 0
proper = 0
orientation_count = {"+/-": 0, "-/+": 0, "+/+": 0, "-/-": 0}
read1_last = None
read2_last = None
read1 = None
read2 = None
while True:
try:
while not read1 or read1_last == read1.qname:
read1 = iter1.next()
while not read2 or read2_last == read2.qname:
read2 = iter2.next()
except StopIteration:
break
if read1.qname != read2.qname:
raise ValueError("Error: BAM files aren't properly paired! (%s, %s)\n" % (read1.qname, read2.qname))
read1_last = read1.qname
read2_last = read2.qname
total += 1
if read1.is_unmapped or read2.is_unmapped or read1.tid != read2.tid:
continue
proper += 1
if read1.pos < read2.pos:
dist = read2.pos - read1.aend
else:
dist = read1.pos - read2.aend
if summaryout:
summaryout.write("%s\n" % dist)
if not dist in distances:
distances[dist] = 1
else:
distances[dist] += 1
orientation = "%s/%s" % ("-" if read1.is_reverse else "+", "-" if read2.is_reverse else "+")
orientation_count[orientation] += 1
mean, stdev = counts_mean_stdev(distances)
return total, proper, mean, stdev, orientation_count
def bam_innerdist(bam1, bam2, summaryout=None):
iter1 = bam_iter(bam1)
iter2 = bam_iter(bam2, quiet=True)
distances = {}
total = 0
proper = 0
orientation_count = {
'+/-': 0,
'-/+': 0,
'+/+': 0,
'-/-': 0,
}
read1_last = None
read2_last = None
read1 = None
read2 = None
while True:
try:
while not read1 or read1_last == read1.qname:
read1 = iter1.next()
while not read2 or read2_last == read2.qname:
read2 = iter2.next()
except StopIteration:
break
if read1.qname != read2.qname:
raise ValueError(
"Error: BAM files aren't properly paired! (%s, %s)\n" %
(read1.qname, read2.qname))
read1_last = read1.qname
read2_last = read2.qname
total += 1
if read1.is_unmapped or read2.is_unmapped or read1.tid != read2.tid:
continue
proper += 1
if read1.pos < read2.pos:
dist = read2.pos - read1.aend
else:
dist = read1.pos - read2.aend
if summaryout:
summaryout.write('%s\n' % dist)
if not dist in distances:
distances[dist] = 1
else:
distances[dist] += 1
orientation = '%s/%s' % ('-' if read1.is_reverse else '+',
'-' if read2.is_reverse else '+')
orientation_count[orientation] += 1
mean, stdev = counts_mean_stdev(distances)
return total, proper, mean, stdev, orientation_count
def bam_stats(infiles, gtf_file=None, region=None, delim=None, tags=[], show_all=False, fillin_stats=True):
if gtf_file:
gtf = GTF(gtf_file)
else:
gtf = None
sys.stderr.write('Calculating Read stats...\n')
stats = [BamStats(bam_open(x), gtf, region, delim, tags, show_all=show_all) for x in infiles]
sys.stdout.write('\t')
for fname, stat in zip(infiles, stats):
sys.stdout.write('%s\t\t' % fname)
sys.stdout.write('\n')
sys.stdout.write('Reads:\t')
for stat in stats:
sys.stdout.write('%s\t\t' % stat.total)
sys.stdout.write('\n')
sys.stdout.write('Mapped:\t')
for stat in stats:
sys.stdout.write('%s\t\t' % stat.mapped)
sys.stdout.write('\n')
sys.stdout.write('Unmapped:\t')
for stat in stats:
sys.stdout.write('%s\t\t' % stat.unmapped)
sys.stdout.write('\n')
sys.stdout.write('\nFlag distribution\n')
validflags = set()
maxsize = 0
for flag in flag_descriptions:
for stat in stats:
if stat.flag_counts.counts[flag] > 0:
validflags.add(flag)
maxsize = max(maxsize, len(flag_descriptions[flag]))
for flag in sorted(validflags):
sys.stdout.write("[0x%03x] %-*s" % (flag, maxsize, flag_descriptions[flag]))
for stat in stats:
sys.stdout.write('\t%s\t%0.2f%%' % (stat.flag_counts.counts[flag], (float(stat.flag_counts.counts[flag]) * 100 / stat.total)))
sys.stdout.write('\n')
sys.stdout.write('\n')
if stats[0].tlen_counts:
sys.stdout.write('Template length:')
for stat in stats:
mean, stdev = counts_mean_stdev(stat.tlen_counts)
sys.stdout.write('\t%0.2f\t+/- %0.2f' % (mean, stdev))
sys.stdout.write('\n')
sys.stdout.write('\n')
stat_tags = {}
for tag in stats[0].tagbins:
stat_tags[tag] = []
for stat in stats:
stat_tags[tag].append(stat.tagbins[tag])
for tag in stat_tags:
asc = stats[0].tagbins[tag].asc
sys.stdout.write("Ave %s:" % tag)
for i, tagbin in enumerate(stat_tags[tag]):
sys.stdout.write('\t%s' % tagbin.mean)
if i != len(stats):
sys.stdout.write('\t')
sys.stdout.write('\n')
sys.stdout.write("Max %s:" % tag)
for i, tagbin in enumerate(stat_tags[tag]):
sys.stdout.write('\t%s' % tagbin.max)
if i != len(stats):
sys.stdout.write('\t')
sys.stdout.write('\n')
sys.stdout.write('%s distribution:\n' % tag)
gens = []
gen_vals = []
last_pcts = []
for stat in stats:
gens.append(stat.distribution_gen(tag))
gen_vals.append(None)
last_pcts.append(0.0)
good = True
last = None
while good:
good = False
for i, stat in enumerate(stats):
if not gen_vals[i]:
try:
gen_vals[i] = gens[i].next()
except StopIteration:
pass
vals = [tup[0] for tup in gen_vals if tup]
if not vals:
continue
if asc:
minval = min(vals)
else:
minval = max(vals)
if last and type(last) == int and fillin_stats:
if asc:
last += 1
# fill in missing values
while last < minval:
sys.stdout.write('%s' % last)
for i, stat in enumerate(stats):
sys.stdout.write('\t0\t%s' % last_pcts[i])
sys.stdout.write('\n')
last += 1
else:
last -= 1
# fill in missing values
while last > minval:
sys.stdout.write('%s' % last)
for i, stat in enumerate(stats):
sys.stdout.write('\t0\t%s' % last_pcts[i])
sys.stdout.write('\n')
last -= 1
last = minval
sys.stdout.write(str(minval))
for i, tup in enumerate(gen_vals):
if tup and tup[0] == minval:
sys.stdout.write('\t%s\t%s' % (tup[1], tup[2]))
last_pcts[i] = tup[2]
gen_vals[i] = None
good = True
else:
sys.stdout.write('\t0\t%s' % (last_pcts[i]))
sys.stdout.write('\n')
sys.stdout.write('\n')
sys.stdout.write('Reference counts')
for stat in stats:
sys.stdout.write('\tcount\t')
sys.stdout.write('\n')
for k in sorted([x for x in stats[0].refs]):
sys.stdout.write('%s' % k)
for stat in stats:
sys.stdout.write('\t%s\t' % stat.refs[k])
sys.stdout.write('\n')
if gtf_file:
sys.stdout.write('Mapping regions')
for stat in stats:
sys.stdout.write('\tcount\tCPM')
sys.stdout.write('\n')
sorted_keys = [x for x in stats[0].regiontagger.counts]
sorted_keys.sort()
for k in sorted_keys:
sys.stdout.write('%s' % k)
for stat in stats:
sys.stdout.write('\t%s\t%s' % (stat.regiontagger.counts[k], float(stat.regiontagger.counts[k]) / stat.mapped / 1000000))
sys.stdout.write('\n')
def bam_stats(infiles, gtf_file=None, region=None, delim=None, tags=[], show_all=False, fillin_stats=True):
if gtf_file:
gtf = GTF(gtf_file)
else:
gtf = None
sys.stderr.write('Calculating Read stats...\n')
stats = [BamStats(bam_open(x), gtf, region, delim, tags, show_all=show_all) for x in infiles]
sys.stdout.write('\t')
for fname, stat in zip(infiles, stats):
sys.stdout.write('%s\t\t' % fname)
sys.stdout.write('\n')
sys.stdout.write('Reads:\t')
for stat in stats:
sys.stdout.write('%s\t\t' % stat.total)
sys.stdout.write('\n')
sys.stdout.write('Mapped:\t')
for stat in stats:
sys.stdout.write('%s\t\t' % stat.mapped)
sys.stdout.write('\n')
sys.stdout.write('Unmapped:\t')
for stat in stats:
sys.stdout.write('%s\t\t' % stat.unmapped)
sys.stdout.write('\n')
sys.stdout.write('\nFlag distribution\n')
validflags = set()
maxsize = 0
for flag in flag_descriptions:
for stat in stats:
if stat.flag_counts.counts[flag] > 0:
validflags.add(flag)
maxsize = max(maxsize, len(flag_descriptions[flag]))
for flag in sorted(validflags):
sys.stdout.write("[0x%03x] %-*s" % (flag, maxsize, flag_descriptions[flag]))
for stat in stats:
sys.stdout.write('\t%s\t%0.2f%%' % (stat.flag_counts.counts[flag], (float(stat.flag_counts.counts[flag]) * 100 / stat.total)))
sys.stdout.write('\n')
sys.stdout.write('\n')
if stats[0].tlen_counts:
sys.stdout.write('Template length:')
for stat in stats:
mean, stdev = counts_mean_stdev(stat.tlen_counts)
sys.stdout.write('\t%0.2f\t+/- %0.2f' % (mean, stdev))
sys.stdout.write('\n')
sys.stdout.write('\n')
stat_tags = {}
for tag in stats[0].tagbins:
stat_tags[tag] = []
for stat in stats:
stat_tags[tag].append(stat.tagbins[tag])
for tag in stat_tags:
asc = stats[0].tagbins[tag].asc
sys.stdout.write("Ave %s:" % tag)
for i, tagbin in enumerate(stat_tags[tag]):
sys.stdout.write('\t%s' % tagbin.mean)
if i != len(stats):
sys.stdout.write('\t')
sys.stdout.write('\n')
sys.stdout.write("Max %s:" % tag)
for i, tagbin in enumerate(stat_tags[tag]):
sys.stdout.write('\t%s' % tagbin.max)
if i != len(stats):
sys.stdout.write('\t')
sys.stdout.write('\n')
sys.stdout.write('%s distribution:\n' % tag)
gens = []
gen_vals = []
last_pcts = []
for stat in stats:
gens.append(stat.distribution_gen(tag))
gen_vals.append(None)
last_pcts.append(0.0)
good = True
last = None
while good:
good = False
for i, stat in enumerate(stats):
if not gen_vals[i]:
try:
gen_vals[i] = gens[i].next()
except StopIteration:
pass
vals = [tup[0] for tup in gen_vals if tup]
if not vals:
continue
if asc:
minval = min(vals)
else:
minval = max(vals)
if last and type(last) == int and fillin_stats:
if asc:
last += 1
# fill in missing values
while last < minval:
sys.stdout.write('%s' % last)
for i, stat in enumerate(stats):
sys.stdout.write('\t0\t%s' % last_pcts[i])
sys.stdout.write('\n')
last += 1
else:
last -= 1
# fill in missing values
while last > minval:
sys.stdout.write('%s' % last)
for i, stat in enumerate(stats):
sys.stdout.write('\t0\t%s' % last_pcts[i])
sys.stdout.write('\n')
last -= 1
last = minval
sys.stdout.write(str(minval))
for i, tup in enumerate(gen_vals):
if tup and tup[0] == minval:
sys.stdout.write('\t%s\t%s' % (tup[1], tup[2]))
last_pcts[i] = tup[2]
gen_vals[i] = None
good = True
else:
sys.stdout.write('\t0\t%s' % (last_pcts[i]))
sys.stdout.write('\n')
sys.stdout.write('\n')
sys.stdout.write('Reference counts')
for stat in stats:
sys.stdout.write('\tcount\t')
sys.stdout.write('\n')
for k in sorted([x for x in stats[0].refs]):
sys.stdout.write('%s' % k)
for stat in stats:
sys.stdout.write('\t%s\t' % stat.refs[k])
sys.stdout.write('\n')
if gtf_file:
sys.stdout.write('Mapping regions')
for stat in stats:
sys.stdout.write('\tcount\tCPM')
sys.stdout.write('\n')
sorted_keys = [x for x in stats[0].regiontagger.counts]
sorted_keys.sort()
for k in sorted_keys:
sys.stdout.write('%s' % k)
for stat in stats:
sys.stdout.write('\t%s\t%s' % (stat.regiontagger.counts[k], float(stat.regiontagger.counts[k]) / stat.mapped / 1000000))
sys.stdout.write('\n')