from typing import Optional
from ..effect import EffectFactory
from .effect_checker import AnnotationEffect, AnnotationRequest, EffectChecker
[docs]class ProteinChangeEffectChecker(EffectChecker):
"""Protein change effect checker."""
[docs] def mutation_type(
self, aaref: list[Optional[str]],
aaalt: list[Optional[str]]) -> str:
"""Check the mutation type."""
assert len(aaref) == len(aaalt)
if "End" in aaalt and "End" not in aaref:
return "nonsense"
for ref, alt in zip(aaref, aaalt):
if ref == "?" or alt == "?":
return "coding_unknown"
if ref != alt:
return "missense"
return "synonymous"
[docs] def get_effect(
self, request: AnnotationRequest,
) -> Optional[AnnotationEffect]:
coding_regions = request.cds_regions()
assert request.variant.reference is not None
assert request.variant.alternate is not None
ref_length = len(request.variant.reference)
alt_length = len(request.variant.alternate)
length = abs(alt_length - ref_length)
if length != 0:
return None
for j in coding_regions:
if j.start <= request.variant.position <= j.stop:
if length == 0:
ref_aa, alt_aa = request.get_amino_acids()
return EffectFactory.create_effect_with_aa_change(
self.mutation_type(ref_aa, alt_aa), request,
)
return None