def __init__(self, args):
self.args = args
self.stats = stats.Stats('')
self.samfile = pysam.Samfile(args.input)
self.amplicons = amplicon.load_amplicons_from_header(self.samfile.header, self.stats, self.samfile)
self.amplicons = dict([(x.external_id, x) for x in self.amplicons])
def __init__(self, args):
self.args = args
self.stats = stats.Stats('')
self.samfile = pysam.Samfile(args.input)
self.amplicons = amplicon.load_amplicons_from_header(
self.samfile.header, self.stats, self.samfile)
self.amplicons = dict([(x.external_id, x) for x in self.amplicons])
def coverage(args):
counts = {}
inp = pysam.Samfile(args.input)
uniq = {}
reads = {}
total = 0
stats = Stats("")
amplicons = amplicon.load_amplicons_from_header(inp.header, stats, None)
libs = {}
for rg in inp.header["RG"]:
for amp in amplicons:
key = rg["ID"], amp.external_id
reads[key] = uniq[key] = 0
libs[rg["ID"]] = rg.get("LB", None)
for r in inp:
total += 1
tags = dict(r.tags)
try:
key = tags["RG"], tags["ea"]
except KeyError:
continue
try:
reads[key] += 1
if not r.is_duplicate:
uniq[key] += 1
except KeyError:
logging.debug("unexpected key")
total_ot = sum(reads.values())
total_uniq = sum(uniq.values())
total_ot_p = (100.0 * total_ot) / total
try:
reads_per_counter = float(total_ot) / total_uniq
except ZeroDivisionError:
reads_per_counter = 0
print("total %(total)s reads, on target %(total_ot)s, uniq %(total_uniq)s" % locals(), file=sys.stderr)
print("on target %3.2f%%" % total_ot_p, file=sys.stderr)
print("on target reads per counter: %2.2f" % reads_per_counter, file=sys.stderr)
if args.control:
total_control = sum([reads[x] for x in reads if x[0] == args.control])
control_p = (100 * total_control) / total
print("control reads %(total_control)s, %(control_p)f%%" % locals(), file=sys.stderr)
out = csv.writer(sys.stdout)
out.writerow(["rg", "lib", "amp", "unique", "reads"])
for (rg, amp) in sorted(reads):
if rg != args.control:
key = (rg, amp)
out.writerow(map(str, (rg, libs[rg], amp, uniq[key], reads[key])))
def coverage(args):
counts = {}
inp = pysam.Samfile(args.input)
uniq = {}
reads = {}
total = 0
stats = Stats('')
amplicons = amplicon.load_amplicons_from_header(inp.header, stats, None)
libs = {}
for rg in inp.header['RG']:
for amp in amplicons:
key = rg['ID'], amp.external_id
reads[key] = uniq[key] = 0
libs[rg['ID']] = rg.get('LB', None)
for r in inp:
total += 1
tags = dict(r.tags)
try:
key = tags['RG'], tags['ea']
except KeyError:
continue
try:
reads[key] += 1
if not r.is_duplicate:
uniq[key] += 1
except KeyError:
logging.debug('unexpected key')
total_ot = sum(reads.values())
total_uniq = sum(uniq.values())
total_ot_p = (100.0 * total_ot) / total
try:
reads_per_counter = float(total_ot) / total_uniq
except ZeroDivisionError:
reads_per_counter = 0
print(
'total %(total)s reads, on target %(total_ot)s, uniq %(total_uniq)s' %
locals(),
file=sys.stderr)
print('on target %3.2f%%' % total_ot_p, file=sys.stderr)
print('on target reads per counter: %2.2f' % reads_per_counter,
file=sys.stderr)
if args.control:
total_control = sum([reads[x] for x in reads if x[0] == args.control])
control_p = (100 * total_control) / total
print('control reads %(total_control)s, %(control_p)f%%' % locals(),
file=sys.stderr)
out = csv.writer(sys.stdout)
out.writerow(['rg', 'lib', 'amp', 'unique', 'reads'])
for (rg, amp) in sorted(reads):
if rg != args.control:
key = (rg, amp)
out.writerow(map(str, (rg, libs[rg], amp, uniq[key], reads[key])))
