def create_het_distribution(
seqs, distrib_fhand=None, plot_fhand=None, summary_fhand=None, group_kind=None, groups=None, ploidy=2
):
"""It creates the distribution of the heterozygosity
(not takes in account ref allele)"""
title = "heterozygosity"
if groups and group_kind:
title = "heterozygosity (%s: %s)" % (group_kind, ",".join(groups))
hets = CachedArray("f")
for seq in seqs:
for snv in seq.get_features("snv"):
if not group_kind and "heterozygosity" in snv.qualifiers:
het = snv.qualifiers["heterozygosity"]
else:
het = calculate_heterozygosity(snv, ploidy, group_kind=group_kind, groups=groups)
if het is not None:
hets.append(het)
if list(hets):
create_distribution(
hets,
labels={"title": title},
distrib_fhand=distrib_fhand,
bins=None,
plot_fhand=plot_fhand,
range_=None,
summary_fhand=summary_fhand,
calculate_freqs=False,
remove_outliers=False,
)
def create_maf_distribution(
seqs, distrib_fhand=None, plot_fhand=None, summary_fhand=None, groups=None, group_kind=None
):
"It creates the distribution of the maf (not takes in account ref allele)"
title = "maf"
if groups and group_kind:
title = "maf (%s: %s)" % (group_kind, ",".join(groups))
mafs = CachedArray("f")
for seq in seqs:
for snv in seq.get_features("snv"):
maf = calculate_maf_frequency(snv, groups=groups, group_kind=group_kind)
if maf:
mafs.append(maf)
if list(mafs):
create_distribution(
mafs,
labels={"title": title},
distrib_fhand=distrib_fhand,
bins=None,
plot_fhand=plot_fhand,
range_=None,
summary_fhand=summary_fhand,
calculate_freqs=False,
remove_outliers=False,
)
def create_pic_distribution(
seqs, distrib_fhand=None, plot_fhand=None, summary_fhand=None, read_groups=None, group_kind=None, groups=None
):
"It creates the distribution of the pic (not takes in account ref allele)"
title = "pic"
if groups and group_kind:
title = "pic (%s: %s)" % (group_kind, ",".join(groups))
pics = CachedArray("f")
for seq in seqs:
for snv in seq.get_features("snv"):
if not group_kind and "pic" in snv.qualifiers:
pic = snv.qualifiers["pic"]
else:
pic = calculate_pic(snv, group_kind=group_kind, groups=groups)
if pic is not None:
pics.append(pic)
if list(pics):
create_distribution(
pics,
labels={"title": title},
distrib_fhand=distrib_fhand,
bins=None,
plot_fhand=plot_fhand,
range_=None,
summary_fhand=summary_fhand,
calculate_freqs=False,
remove_outliers=False,
)
