def calc_coverage(bamfile, regions=None, mtchr=None):
depths = []
for region in regions:
output_dir = OrderedDict()
if type(region) == Interval:
# Add one to start as starts are 0 based; ends are 1 based.
chrom, start, end = str(region.chrom), region.start + 1, region.stop
output_dir["name"] = region.name
else:
chrom, start, end = re.split("[:-]", region)
start, end = int(start), int(end)
output_dir["chrom"] = chrom
output_dir["start"] = start
output_dir["end"] = end
# If end extends to far, adjust for chrom
chrom_len = bamfile.lengths[bamfile.gettid(chrom)]
if end > chrom_len:
with indent(4):
puts_err(
colored.yellow(
"\nSpecified chromosome end extends beyond chromosome length. Set to max of: "
+ str(chrom_len)
+ "\n"
)
)
end = chrom_len
region = bamfile.pileup(chrom, start, end + 1, truncate=True, max_depth=1e8)
cum_depth = 0
pos_covered = 0
for n, i in enumerate(region):
pos_covered += 1
cum_depth += i.nsegments
length = end - start + 1
coverage = cum_depth / float(length)
breadth = pos_covered / float(length)
output_dir["ATTR"] = "bases_mapped"
print eav(bam_name, output_dir, cum_depth, args["--tsv"], args["--header"])
output_dir["ATTR"] = "depth_of_coverage"
print eav(bam_name, output_dir, coverage, args["--tsv"])
output_dir["ATTR"] = "breadth_of_coverage"
print eav(bam_name, output_dir, breadth, args["--tsv"])
output_dir["ATTR"] = "length"
print eav(bam_name, output_dir, length, args["--tsv"])
output_dir["ATTR"] = "pos_mapped"
print eav(bam_name, output_dir, pos_covered, args["--tsv"])
depths.append(
{"chrom": chrom, "bases_mapped": cum_depth, "pos_covered": pos_covered, "depth_of_coverage": coverage}
)
return depths
else:
mtchr = mtchr[0]
with indent(4):
puts_err(colored.blue("\nGuessing Mitochondrial Chromosome: " + mtchr + "\n"))
depths = []
cov = calc_coverage(bamfile, chroms, mtchr)
# Genomewide depth
output_dir = {}
genome_length = sum([x for x in bamfile.lengths], args["--tsv"])
output_dir["length"] = genome_length
output_dir["chrom"] = "genome"
bases_mapped = sum([x["bases_mapped"] for x in cov])
output_dir["ATTR"] = "bases_mapped"
print eav(bam_name, output_dir, bases_mapped, args["--tsv"])
output_dir["ATTR"] = "depth_of_coverage"
coverage = bases_mapped / float(genome_length)
print eav(bam_name, output_dir, coverage, args["--tsv"])
output_dir["ATTR"] = "breadth_of_coverage"
breadth = sum([x["pos_covered"] for x in cov]) / float(genome_length)
print eav(bam_name, output_dir, breadth, args["--tsv"])
output_dir["ATTR"] = "positions_mapped"
pos_mapped = sum([x["pos_covered"] for x in cov])
print eav(bam_name, output_dir, pos_mapped, args["--tsv"])
if mtchr:
# Nuclear
