Initial commit

src/genomic_consultant/orchestration/workflows.py

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+from __future__ import annotations
+
+from dataclasses import dataclass
+from typing import List
+
+from genomic_consultant.acmg.tagger import ACMGConfig, tag_variant
+from genomic_consultant.panels.panels import GenePanel
+from genomic_consultant.store.query import GenomicStore
+from genomic_consultant.utils.models import FilterConfig, SuggestedClassification, Variant
+
+
+@dataclass
+class PanelVariantResult:
+    variant: Variant
+    acmg: SuggestedClassification
+
+
+@dataclass
+class PanelAnalysisResult:
+    individual_id: str
+    panel: GenePanel
+    variants: List[PanelVariantResult]
+
+
+def run_panel_variant_review(
+    individual_id: str,
+    panel: GenePanel,
+    store: GenomicStore,
+    acmg_config: ACMGConfig,
+    filters: FilterConfig | None = None,
+) -> PanelAnalysisResult:
+    """Query variants for a panel and attach ACMG evidence suggestions."""
+    variants = store.get_variants_by_gene(individual_id=individual_id, genes=panel.genes, filters=filters)
+    enriched = [PanelVariantResult(variant=v, acmg=tag_variant(v, acmg_config)) for v in variants]
+    return PanelAnalysisResult(individual_id=individual_id, panel=panel, variants=enriched)