from collections.abc import Iterable
from dataclasses import dataclass
from typing import Optional, cast
from dae.person_sets import PersonSetCollection
from dae.studies.study import GenotypeData
from dae.variants.attributes import Inheritance
from dae.variants.family_variant import FamilyAllele, FamilyVariant
[docs]@dataclass(frozen=True)
class GeneEffect:
gene: str
effect: str
[docs]@dataclass(frozen=True)
class AlleleEvent:
persons: set[tuple[str, str]]
# person_sets: set[str]
effect_genes: set[GeneEffect]
[docs]@dataclass(frozen=True)
class VariantEvent:
family_id: str
fvuid: str
allele_events: list[AlleleEvent]
[docs]class GenotypeHelper:
"""Genotype helper for enrichment tools."""
def __init__(
self, genotype_data: GenotypeData,
person_set_collection: PersonSetCollection,
effect_types: Optional[list[str]] = None,
genes: Optional[list[str]] = None,
):
self.genotype_data = genotype_data
self.person_set_collection = person_set_collection
denovo_variants = self.genotype_data.query_variants(
effect_types=effect_types,
genes=genes,
inheritance=str(Inheritance.denovo.name))
self._denovo_events = self.collect_denovo_events(denovo_variants)
[docs] @staticmethod
def collect_denovo_events(
denovo_variants: Iterable[FamilyVariant],
) -> list[VariantEvent]:
"""Collect denovo events."""
result = []
for fv in denovo_variants:
allele_events = []
for aa in fv.alt_alleles:
fa = cast(FamilyAllele, aa)
gene_effects = set()
if fa.effects is None or fa.effects.genes is None:
continue
for ge in fa.effects.genes:
if ge.symbol is None or ge.effect is None:
continue
gene_effects.add(GeneEffect(ge.symbol.upper(), ge.effect))
persons = set(fa.variant_in_members_fpid)
allele_events.append(
AlleleEvent(
persons,
gene_effects,
))
result.append(
VariantEvent(
fv.family_id,
fv.fvuid,
allele_events,
),
)
return result
[docs] def get_denovo_events(self) -> list[VariantEvent]:
return self._denovo_events