Source code for dae.enrichment_tool.tool

from typing import Iterable, Any

from dae.effect_annotation.effect import expand_effect_types

from dae.enrichment_tool.genotype_helper import children_stats, VariantEvent
from dae.enrichment_tool.base_enrichment_background import \
    BaseEnrichmentBackground
from dae.enrichment_tool.event_counters import CounterBase, \
    EnrichmentResult


class EnrichmentTool:
    """Construct and run enrichment tool test."""

    def __init__(
        self, config: dict[str, Any],
        background: BaseEnrichmentBackground,
        event_counter: CounterBase
    ):
        self.config = config

        self.background = background
        self.event_counter = event_counter

    def calc(
        self,
        gene_syms: Iterable[str],
        variant_events: list[VariantEvent],
        effect_types: Iterable[str],
        children_by_sex: dict[str, set[tuple[str, str]]]
    ) -> dict[str, EnrichmentResult]:
        """Perform the enrichment tool test."""
        requested_effect_types = expand_effect_types(effect_types)
        enrichment_events = self.event_counter.events(
            variant_events, children_by_sex, requested_effect_types
        )
        if not self.background.is_loaded():
            self.background.load()

        return self.background.calc_enrichment_test(
            enrichment_events, gene_syms,
            effect_types=effect_types,
            children_stats=children_stats(children_by_sex)
        )