import abc
import logging
from collections.abc import Generator
from typing import Any
import numpy as np
from dae.parquet.schema2.variant_serializers import VariantsDataSerializer
from dae.pedigrees.families_data import FamiliesData
from dae.query_variants.query_runners import QueryRunner
from dae.utils.regions import Region
from dae.variants.attributes import Inheritance
from dae.variants.family_variant import FamilyVariant
from dae.variants.variant import SummaryVariant, SummaryVariantFactory
RealAttrFilterType = list[tuple[str, tuple[float | None, float | None]]]
logger = logging.getLogger(__name__)
[docs]
class QueryVariants(abc.ABC):
"""Abstract class for querying variants interface."""
[docs]
@abc.abstractmethod
def has_affected_status_queries(self) -> bool:
"""Return True if the storage supports affected status queries."""
[docs]
@abc.abstractmethod
def build_summary_variants_query_runner(
self, *,
regions: list[Region] | None = None,
genes: list[str] | None = None,
effect_types: list[str] | None = None,
variant_type: str | None = None,
real_attr_filter: RealAttrFilterType | None = None,
ultra_rare: bool | None = None,
frequency_filter: RealAttrFilterType | None = None,
return_reference: bool | None = None,
return_unknown: bool | None = None,
limit: int | None = None,
**kwargs: Any,
) -> QueryRunner | None:
"""Create query runner for searching summary variants."""
[docs]
@abc.abstractmethod
def query_summary_variants(
self, *,
regions: list[Region] | None = None,
genes: list[str] | None = None,
effect_types: list[str] | None = None,
variant_type: str | None = None,
real_attr_filter: RealAttrFilterType | None = None,
ultra_rare: bool | None = None,
frequency_filter: RealAttrFilterType | None = None,
return_reference: bool | None = None,
return_unknown: bool | None = None,
limit: int | None = None,
**kwargs: Any,
) -> Generator[SummaryVariant, None, None]:
"""Execute the summary variants query and yields summary variants."""
[docs]
@abc.abstractmethod
def build_family_variants_query_runner(
self, *,
regions: list[Region] | None = None,
genes: list[str] | None = None,
effect_types: list[str] | None = None,
family_ids: list[str] | None = None,
person_ids: list[str] | None = None,
inheritance: list[str] | None = None,
roles: str | None = None,
sexes: str | None = None,
affected_statuses: str | None = None,
variant_type: str | None = None,
real_attr_filter: RealAttrFilterType | None = None,
ultra_rare: bool | None = None,
frequency_filter: RealAttrFilterType | None = None,
return_reference: bool | None = None,
return_unknown: bool | None = None,
limit: int | None = None,
study_filters: list[str] | None = None,
**kwargs: Any,
) -> QueryRunner | None:
# pylint: disable=too-many-arguments
"""Create a query runner for searching family variants."""
[docs]
@abc.abstractmethod
def query_variants(
self, *,
regions: list[Region] | None = None,
genes: list[str] | None = None,
effect_types: list[str] | None = None,
family_ids: list[str] | None = None,
person_ids: list[str] | None = None,
inheritance: list[str] | None = None,
roles: str | None = None,
sexes: str | None = None,
affected_statuses: str | None = None,
variant_type: str | None = None,
real_attr_filter: RealAttrFilterType | None = None,
ultra_rare: bool | None = None,
frequency_filter: RealAttrFilterType | None = None,
return_reference: bool | None = None,
return_unknown: bool | None = None,
limit: int | None = None,
**kwargs: Any,
) -> Generator[FamilyVariant, None, None]:
# pylint: disable=too-many-arguments
"""Execute the family variants query and yields family variants."""
[docs]
class QueryVariantsBase(QueryVariants):
"""Base class variants for Schema2 query interface."""
RUNNER_CLASS: type[QueryRunner]
def __init__(self, families: FamiliesData) -> None:
self.families = families
self.serializer = VariantsDataSerializer.build_serializer()
[docs]
def has_affected_status_queries(self):
"""Schema2 do support affected status queries."""
return True
[docs]
def deserialize_summary_variant(
self, sv_data: bytes,
) -> SummaryVariant:
"""Deserialize a summary variant from a summary blob."""
sv_record = self.serializer.deserialize_summary_record(sv_data)
return SummaryVariantFactory.summary_variant_from_records(
sv_record,
)
[docs]
def deserialize_family_variant(
self, sv_data: bytes, fv_data: bytes,
) -> FamilyVariant:
"""Deserialize a family variant from a summary and family blobs."""
sv_record = self.serializer.deserialize_summary_record(sv_data)
fv_record = self.serializer.deserialize_family_record(fv_data)
inheritance_in_members = {
int(k): [Inheritance.from_value(inh) for inh in v]
for k, v in fv_record["inheritance_in_members"].items()
}
fattributes = fv_record.get("family_variant_attributes")
fv = FamilyVariant(
SummaryVariantFactory.summary_variant_from_records(
sv_record,
),
self.families[fv_record["family_id"]],
np.array(fv_record["genotype"]),
np.array(fv_record["best_state"]),
inheritance_in_members=inheritance_in_members,
)
if fattributes:
for fa, fattr in zip(
fv.family_alt_alleles, fattributes, strict=True):
fa.update_attributes(fattr)
return fv