def get_depth_analysis(aln_filename, chrom):
# get depth from bam_stats
args = [
'-i', aln_filename, '--silent', '--depth_spacing',
str(DEPTH_SPACING)
]
bam_summaries, length_summaries, depth_summaries = bam_stats.main(args)
return depth_summaries[aln_filename][chrom][bam_stats.D_ALL_DEPTH_MAP]
def get_genome_read_depths(bam_file, args):
spacing = args.sampling_spacing
verbose = args.verbose
if not os.path.isfile(bam_file):
raise Exception("Genome bam {} does not exist!".format(bam_file))
log(bam_file)
bs_args = [
"--input_glob", bam_file, "--depth_spacing",
str(spacing), '--silent'
]
if args.filter_secondary: bs_args.append('--filter_secondary')
if args.filter_primary: bs_args.append('--filter_primary')
bam_summaries, _, depth_summaries = bam_stats.main(bs_args)
if bam_stats.GENOME_KEY in depth_summaries[bam_file]:
del depth_summaries[bam_file][bam_stats.GENOME_KEY]
positions = dict()
chromosomes = list(depth_summaries[bam_file].keys())
chromosomes.sort(key=chrom_sort)
for chromosome in chromosomes:
if verbose:
log("{}: \t{}: \tread_count: {}".format(
bam_file, chromosome, bam_summaries[bam_file][chromosome][
bam_stats.B_FILTERED_READ_COUNT]))
log("{}: \t{}: \tmax_depth: {}".format(
bam_file, chromosome,
depth_summaries[bam_file][chromosome][bam_stats.D_MAX]))
log("{}: \t{}: \tmin_depth: {}".format(
bam_file, chromosome,
depth_summaries[bam_file][chromosome][bam_stats.D_MIN]))
log("{}: \t{}: \tavg_depth: {}".format(
bam_file, chromosome,
depth_summaries[bam_file][chromosome][bam_stats.D_AVG]))
log("{}: \t{}: \tstd_depth: {}".format(
bam_file, chromosome,
depth_summaries[bam_file][chromosome][bam_stats.D_STD]))
positions[chromosome] = depth_summaries[bam_file][chromosome][
bam_stats.D_ALL_DEPTH_MAP]
pass
return positions
def main():
args = parse_args()
assert False not in [
len(args.input_bam_glob) > 0,
os.path.isfile(args.coordinate_tsv),
os.path.isdir(args.output_location)
]
coords = list()
with open(args.coordinate_tsv) as tsv_in:
for line in tsv_in:
# skip
if line.startswith("#"): continue
if len(line.strip()) == 0: continue
# get line parts
line = line.strip().split("\t")
# save relevant data
coord = {CHR: line[0]}
if len(line) >= 3:
coord[START] = int(line[1])
coord[END] = int(line[2])
if args.description_column is not None:
coord[DESC] = "_".join(line[args.description_column].split())
coords.append(coord)
for file in glob.glob(args.input_bam_glob):
for coord in coords:
out_filename = get_output_filename(file, coord)
out_location = os.path.join(args.output_location, out_filename)
region = coord[CHR] if len(coord) < 3 else "{}:{}-{}".format(
coord[CHR], coord[START], coord[END])
# log what's happening
print("{}:\n\tloc: {}\n\tdesc: {}\n\tout: {}".format(
file, region, coord[DESC] if DESC in coord else '',
out_location),
file=sys.stderr)
# get the region and index
samtools_args = ['samtools', 'view', '-hb', file, region]
with open(out_location, 'w') as output:
subprocess.check_call(samtools_args, stdout=output)
subprocess.check_call(['samtools', 'index', out_location])
# maybe make stats
if args.produce_bam_stats:
stats_filename = "{}.stats.txt".format(out_filename)
stats_location = os.path.join(args.output_location,
stats_filename)
bam_stats_args = [
'-i', out_location, '-g', '-l', '-d', '-v', '-o',
stats_location
]
if len(coord) >= 3:
bam_stats_args.extend(
['-r', '{}-{}'.format(coord[START], coord[END])])
# get summaries
generic_summaries, _, depth_summaries = bam_stats.main(
bam_stats_args)
# are we flagging output based on depth?
if args.min_depth_threshold is not None:
# find depth
generic_summary = generic_summaries[out_location][
bam_stats.GENOME_KEY]
depth_summary = depth_summaries[out_location][
bam_stats.GENOME_KEY]
depth_summary_value = int(
max(depth_summary[bam_stats.D_MED],
depth_summary[bam_stats.D_AVG]))
print("\tsection_depth:{}".format(depth_summary_value),
file=sys.stderr)
# handle min depth
if args.min_depth_threshold <= depth_summary_value:
print("\tFLAGGED!", file=sys.stderr)
# also try to get stats for only primary reads
bam_stats_args_prim = [
'-i', out_location, '-d', '-V',
'--filter_secondary', '--filter_supplementary',
'-r', '{}-{}'.format(coord[START], coord[END])
]
_, _, prim_depth_summaries = bam_stats.main(
bam_stats_args_prim)
prim_depth_summary = prim_depth_summaries[
out_location][bam_stats.GENOME_KEY]
prim_depth_summary_value = int(
max(prim_depth_summary[bam_stats.D_MED],
prim_depth_summary[bam_stats.D_AVG]))
# document depths in flagged filename
flag_filename = "FLAGGED.DEPTH_{:04d}_p{:04d}.{}.stats.txt".format(
depth_summary_value, prim_depth_summary_value,
out_filename)
with open(
os.path.join(args.output_location,
flag_filename), 'w') as flag_out:
print("####################################",
file=flag_out)
print("bam_file:{}".format(out_filename),
file=flag_out)
print("bam_stats_file:{}".format(stats_filename),
file=flag_out)
print("depth_threshold:{}".format(
args.min_depth_threshold),
file=flag_out)
print("median_depth:{}".format(
depth_summary[bam_stats.D_MED]),
file=flag_out)
print("mean_depth:{}".format(
depth_summary[bam_stats.D_AVG]),
file=flag_out)
print("total_reads:{}".format(
generic_summary[bam_stats.B_READ_COUNT]),
file=flag_out)
print("filtered_reads:{}".format(
generic_summary[bam_stats.B_SECONDARY_COUNT] +
generic_summary[
bam_stats.B_SUPPLEMENTARY_COUNT]),
file=flag_out)
print("primary_median_depth:{}".format(
prim_depth_summary[bam_stats.D_MED]),
file=flag_out)
print("primary_mean_depth:{}".format(
prim_depth_summary[bam_stats.D_AVG]),
file=flag_out)
print("Fin.", file=sys.stderr)