import logging
from typing import Optional
from ..effect import EffectFactory
from .effect_checker import AnnotationEffect, AnnotationRequest, EffectChecker
logger = logging.getLogger(__name__)
[docs]class IntronicEffectChecker(EffectChecker):
"""Intonic effect checker class."""
def __init__(self, splice_site_length: int = 2):
self.splice_site_length = splice_site_length
[docs] def get_effect(
self, request: AnnotationRequest,
) -> Optional[AnnotationEffect]:
coding_regions = request.cds_regions()
prev = coding_regions[0].stop
last_position = request.variant.corrected_ref_position_last
intron_regions_before_coding = 0
for exon in request.transcript_model.exons:
logger.debug(
"reg %d-%d cds:%d",
exon.start,
exon.stop,
request.transcript_model.cds[0],
)
if request.transcript_model.cds[0] <= exon.stop:
break
intron_regions_before_coding += 1
for i, j in enumerate(coding_regions):
logger.debug(
"pos: %d-%d checking intronic region %d-%d",
request.variant.position,
last_position,
prev,
j.start,
)
if prev < request.variant.position and last_position < j.start:
return EffectFactory.create_intronic_effect(
"intron",
request,
prev,
j.start,
intron_regions_before_coding + i,
)
prev = j.stop
return None