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,
)
def calculate_pics_group(seqs, groups=None, group_kind=None):
'It calculates the snv heterozygosity of a given group'
pic_profile = {}
for seq in seqs:
for snv in seq.get_features('snv'):
pic = calculate_pic(snv, group_kind=group_kind, groups=groups)
if pic is not None:
location = snv.location.start.position
seq_name = seq.name
if seq_name not in pic_profile:
pic_profile[seq_name] = []
pic_profile[seq_name].append((location, pic))
return pic_profile