import logging
from typing import Optional
from ..annotation_request import AnnotationRequest
from ..effect import AnnotationEffect, EffectFactory
from .effect_checker import EffectChecker
[docs]class FrameShiftEffectChecker(EffectChecker):
"""Frame shift effect checker class."""
def __init__(self) -> None:
self.logger = logging.getLogger(__name__)
[docs] def create_effect(
self, request: AnnotationRequest, change_length: int,
) -> Optional[AnnotationEffect]:
"""Create frame-shift annotation effect."""
if change_length > 0:
if change_length % 3 == 0:
if self.check_if_new_stop(request):
effect_name = "no-frame-shift-newStop"
else:
effect_name = "no-frame-shift"
effect = EffectFactory.create_effect_with_aa_change(
effect_name, request,
)
else:
effect_name = "frame-shift"
effect = EffectFactory.create_effect_with_aa_change(
effect_name, request,
)
return effect
return None
[docs] def check_if_new_stop(self, request: AnnotationRequest) -> bool:
"""Check for a new stop codon."""
ref_aa, alt_aa = request.get_amino_acids()
for aa in ref_aa:
if aa == "End":
return False
for aa in alt_aa:
if aa == "End":
return True
return False
[docs] def check_stop_codon(
self, request: AnnotationRequest,
) -> Optional[AnnotationEffect]:
"""Check for stop codon."""
try:
ref_aa, alt_aa = request.get_amino_acids()
if "End" not in ref_aa:
return None
ref_index = ref_aa.index("End")
alt_index = alt_aa.index("End")
if ref_index != alt_index:
diff = abs(ref_index - alt_index) * 3
return self.create_effect(request, diff)
except ValueError:
pass
except IndexError:
pass
return None
[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 request.is_stop_codon_affected():
return self.check_stop_codon(request)
for j in coding_regions:
start = j.start
stop = j.stop
if len(request.variant.reference) == 0:
stop += 1
self.logger.debug(
"frameshift %d<=%d<=%d cds:%d-%d exon:%d-%d",
start,
request.variant.position,
stop,
request.transcript_model.cds[0],
request.transcript_model.cds[1],
j.start,
j.stop,
)
if start <= request.variant.position <= stop:
self.logger.debug(
"fs detected %d<=%d-%d<=%d cds:%d-%d",
start,
request.variant.position,
request.variant.ref_position_last,
stop,
request.transcript_model.cds[0],
request.transcript_model.cds[1],
)
return self.create_effect(request, length)
return None