def de_variants_clean(variants, sequences=None):
"""
Apply the 3' rule to delins variants, get rid of equals, and substitute
any slices relative to the observed sequence.
"""
new_variants = []
for variant in variants:
if variant.get("type") == "inversion":
new_variants.append(copy.deepcopy(variant))
elif variant.get("type") == "deletion_insertion":
variant["inserted"] = update_inserted_with_sequences(
variant["inserted"], sequences)
inserted_sequence = get_inserted_sequence(variant, sequences)
new_variant = copy.deepcopy(variant)
shift3 = 0
shift5 = 0
if get_location_length(
variant["location"]) and not inserted_sequence:
shift5, shift3 = roll(
sequences["reference"],
variant["location"]["start"]["position"] + 1,
variant["location"]["end"]["position"],
)
elif not get_location_length(
variant["location"]) and inserted_sequence:
rolled_sequence = (
sequences["reference"][:get_start(variant)] +
inserted_sequence +
sequences["reference"][get_end(variant):])
shift5, shift3 = roll(
rolled_sequence,
get_start(variant) + 1,
get_end(variant) + len(inserted_sequence),
)
if shift3:
inserted_rolled_sequence = rolled_sequence[
get_start(variant) + shift3:get_end(variant) + shift3 +
len(inserted_sequence)]
new_variant["inserted"] = [{
"sequence": inserted_rolled_sequence,
"source": "description"
}]
shift = shift3 + shift5
new_variant["location"]["start"]["position"] += shift3
new_variant["location"]["start"]["shift"] = shift
new_variant["location"]["end"]["position"] += shift3
new_variant["location"]["end"]["shift"] = shift
new_variants.append(new_variant)
return new_variants
def de_to_hgvs(variants, sequences=None):
"""
Convert the description extractor variants to an HGVS format (e.g., a
deletion insertion of one nucleotide is converted to a substitution).
"""
if len(variants) == 1 and variants[0].get("type") == "equal":
new_variant = copy.deepcopy(variants[0])
new_variant.pop("location")
return [new_variant]
new_variants = []
for variant in de_variants_clean(variants, sequences):
if variant.get("type") == "inversion":
new_variants.append(copy.deepcopy(variant))
elif variant.get("type") == "deletion_insertion":
inserted_sequence = get_inserted_sequence(variant, sequences)
if len(inserted_sequence) == 0:
new_variants.append(delins_to_del(variant))
elif (get_location_length(variant["location"]) ==
len(inserted_sequence) == 1):
new_variants.append(delins_to_substitution(variant, sequences))
elif is_repeat(variant, sequences):
new_variants.append(delins_to_repeat(variant, sequences))
elif is_duplication(variant, sequences):
new_variants.append(delins_to_duplication(variant, sequences))
elif get_start(variant["location"]) == get_end(
variant["location"]):
new_variants.append(delins_to_insertion(variant))
else:
new_variants.append(delins_to_delins(variant))
return new_variants
def _location_in_same_intron(location, exons):
start_i = bisect.bisect_right(exons, get_start(location))
end_i = bisect.bisect_left(exons, get_end(location))
if start_i == end_i and start_i % 2 == 0:
return True
else:
return False
def delins_to_repeat(variant, sequences):
new_variant = copy.deepcopy(variant)
inserted_sequence = get_inserted_sequence(variant, sequences)
repeat_seq, repeat_number = seq_present_before(
sequences["reference"],
inserted_sequence,
get_start(variant["location"]),
get_end(variant["location"]),
)
shift_left = len(repeat_seq)
while True:
if (get_start(variant) - len(repeat_seq) > 0
and sequences["reference"][get_start(variant) - shift_left -
len(repeat_seq):get_start(variant) -
shift_left] == repeat_seq):
shift_left += len(repeat_seq)
else:
break
repeat_number += shift_left // len(repeat_seq)
new_variant["location"]["start"]["position"] -= shift_left
new_variant["type"] = "repeat"
new_variant["inserted"] = [{
"sequence": repeat_seq,
"source": "description",
"repeat_number": {
"value": repeat_number
},
}]
if new_variant["location"]["start"].get("shift"):
new_variant["location"]["start"]["shift"] -= shift_left
if new_variant["location"]["end"].get("shift"):
new_variant["location"]["end"]["shift"] -= shift_left
return new_variant
def duplication_to_delins(variant):
new_variant = copy.deepcopy(variant)
new_variant["type"] = "deletion_insertion"
new_variant["inserted"] = [
{"source": "reference", "location": copy.deepcopy(new_variant["location"])}
]
set_start(new_variant["location"], get_end(new_variant["location"]))
return new_variant
def update_inserted_with_sequences(inserted, sequences):
new_inserted = []
for insert in inserted:
if insert["source"] == "observed":
seq = sequences["observed"][
get_start(insert["location"]):get_end(insert["location"])]
if seq:
new_inserted.append({"sequence": seq, "source": "description"})
else:
new_inserted.append(insert)
return new_inserted
def to_exon_positions(variants, exons, cds):
exons = _get_cds_into_exons(exons, cds)
new_variants = []
for variant in variants:
if (
variant.get("type") == "deletion_insertion"
and variant.get("location")
and not _location_in_same_intron(variant["location"], exons)
and not (get_start(variant) <= exons[0] and get_end(variant) <= exons[0])
):
n_v = copy.deepcopy(variant)
exon_s = bisect.bisect(exons, get_start(n_v))
if exon_s % 2 == 0 and exon_s < len(exons):
n_v["location"]["start"]["position"] = exons[exon_s]
exon_e = bisect.bisect(exons, get_end(n_v))
if exon_e % 2 == 0 and exon_e < len(exons):
n_v["location"]["end"]["position"] = exons[exon_e]
new_variants.append(n_v)
return new_variants
def is_repeat(variant, sequences):
"""
Note that it works only in the context of the `de_to_hgvs` function flow.
"""
inserted_sequence = get_inserted_sequence(variant, sequences)
repeat_seq, repeat_number = seq_present_before(
sequences["reference"],
inserted_sequence,
get_start(variant["location"]),
get_end(variant["location"]),
)
if repeat_number > 1:
return True
return False
def _splice_site_removal(location, exons):
start_i = bisect.bisect_right(exons, get_start(location))
end_i = bisect.bisect_left(exons, get_end(location))
if end_i - start_i == 1:
return True
def get_inserted_sequence(insertion, sequences):
return sequences[insertion["source"]][
get_start(insertion["location"]) : get_end(insertion["location"])
]