def count_bigwig_total(bw_file):
bw = open_bigwig(bw_file)
result = sum(l * bw.stats(ch, 0, l, "mean")[0]
for ch, l in bw.chroms().items())
assert (
abs(result) > 0
) ## BigWig could have negative values, e.g. the negative-strand GroCAP bigwigs
return result
def count_bigwig_total(bw_file, tmpdir):
download_file(bw_file, tmpdir, overwrite_ok=True)
bw_file = join(tmpdir, basename(bw_file))
from pyBigWig import open as open_bigwig
bw = open_bigwig(bw_file)
result = sum(l * bw.stats(ch, 0, l, "mean")[0]
for ch, l in bw.chroms().items())
assert (
abs(result) > 0
) ## BigWig could have negative values, e.g. the negative-strand GroCAP bigwigs
return result
def count_bigwig(target, bed_file, output):
from pyBigWig import open as open_bigwig
bw = open_bigwig(target)
bed = read_bed(bed_file)
with open(output, "wb") as outfp:
for chr, start, end, *rest in bed.itertuples(index=False, name=None):
# if isinstance(name, np.float):
# name = ""
try:
val = bw.stats(chr, int(start), int(max(end, start + 1)), "mean")[0] or 0
except RuntimeError:
print("Failed on", chr, start, end)
raise
val *= abs(end - start) # convert to total coverage
output = ("\t".join([chr, str(start), str(end), str(val)]) + "\n").encode('ascii')
outfp.write(output)