import logging
from typing import Optional
from ..effect import EffectFactory
from .effect_checker import AnnotationEffect, AnnotationRequest, EffectChecker
logger = logging.getLogger(__name__)
[docs]class StopLossEffectChecker(EffectChecker):
"""Stop loss effect checker class."""
[docs] def get_effect(
self, request: AnnotationRequest,
) -> Optional[AnnotationEffect]:
assert request.variant.reference is not None
last_position = request.variant.position + len(
request.variant.reference,
)
logger.debug(
"position check %d <= %d-%d <= %d",
request.transcript_model.cds[1] - 2,
request.variant.position,
last_position,
request.transcript_model.cds[0],
)
if request.is_stop_codon_affected():
try:
ref_aa, alt_aa = request.get_amino_acids()
if len(ref_aa) == len(alt_aa):
if alt_aa[ref_aa.index("End")] == "End":
return None
logger.debug("ref aa=%s, alt aa=%s", ref_aa, alt_aa)
except IndexError:
pass
except ValueError:
pass
return EffectFactory.create_effect_with_prot_pos("noEnd", request)
return None