Initial commit

tests/test_acmg.py

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+from genomic_consultant.acmg.tagger import ACMGConfig, tag_variant
+from genomic_consultant.utils.models import Variant
+
+
+def test_ba1_trumps():
+    cfg = ACMGConfig(ba1_af=0.05, bs1_af=0.01, pm2_af=0.0005, lof_genes=set())
+    v = Variant(chrom="1", pos=1, ref="A", alt="T", allele_frequency=0.2)
+    result = tag_variant(v, cfg)
+    assert result.suggested_class == "Benign"
+    assert any(e.tag == "BA1" for e in result.evidence)
+
+
+def test_pvs1_pm2_likely_pathogenic():
+    cfg = ACMGConfig(lof_genes={"GENE1"}, pm2_af=0.0005, ba1_af=0.05, bs1_af=0.01)
+    v = Variant(
+        chrom="1",
+        pos=1,
+        ref="A",
+        alt="T",
+        gene="GENE1",
+        consequence="stop_gained",
+        allele_frequency=0.0001,
+    )
+    result = tag_variant(v, cfg)
+    assert result.suggested_class == "Likely pathogenic"
+    tags = {e.tag for e in result.evidence}
+    assert {"PVS1", "PM2"} <= tags
+
+
+def test_bp7_supporting():
+    cfg = ACMGConfig(bp7_splice_ai_max=0.1)
+    v = Variant(
+        chrom="1",
+        pos=1,
+        ref="A",
+        alt="T",
+        consequence="synonymous_variant",
+        annotations={"splice_ai_delta_score": 0.05},
+    )
+    result = tag_variant(v, cfg)
+    assert any(e.tag == "BP7" for e in result.evidence)

tests/test_aggregate.py

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+from pathlib import Path
+
+from genomic_consultant.panels.aggregate import merge_mappings
+import json
+
+
+def test_merge_mappings(tmp_path: Path):
+    a = tmp_path / "a.json"
+    b = tmp_path / "b.json"
+    a.write_text('{"source":"A","phenotype_to_genes":{"HP:1":["G1","G2"]}}')
+    b.write_text('{"source":"B","phenotype_to_genes":{"HP:1":["G2","G3"],"HP:2":["G4"]}}')
+    out = tmp_path / "out.json"
+    merge_mappings([a, b], out)
+    data = json.loads(out.read_text())
+    assert sorted(data["phenotype_to_genes"]["HP:1"]) == ["G1", "G2", "G3"]
+    assert data["phenotype_to_genes"]["HP:2"] == ["G4"]

tests/test_phase1_pipeline.py

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+from pathlib import Path
+
+from genomic_consultant.orchestration.phase1_pipeline import run_phase1_pipeline
+
+
+def test_phase1_pipeline_with_existing_tsv():
+    root = Path(__file__).resolve().parents[1]
+    tsv = root / "sample_data/example_annotated.tsv"
+    panel = root / "configs/panel.example.json"
+    acmg = root / "configs/acmg_config.example.yaml"
+    result = run_phase1_pipeline(
+        samples=None,
+        reference_fasta=None,
+        workdir=root / "runtime",
+        output_prefix="demo",
+        acmg_config_path=acmg,
+        max_af=0.05,
+        panel_path=panel,
+        phenotype_id=None,
+        phenotype_mapping=None,
+        report_format="markdown",
+        existing_tsv=tsv,
+        skip_call=True,
+        skip_annotate=True,
+    )
+    assert "Panel Report" in result.panel_report
+    assert result.tsv_path == tsv

tests/test_resolver.py

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+from pathlib import Path
+
+from genomic_consultant.panels.resolver import PhenotypeGeneResolver
+
+
+def test_resolver_build_panel(tmp_path: Path):
+    data = {
+        "version": "test",
+        "source": "example",
+        "phenotype_to_genes": {"HP:0001": ["GENE1", "GENE2"]},
+    }
+    path = tmp_path / "map.json"
+    path.write_text('{"version":"test","source":"example","phenotype_to_genes":{"HP:0001":["GENE1","GENE2"]}}')
+    resolver = PhenotypeGeneResolver.from_json(path)
+    panel = resolver.build_panel("HP:0001")
+    assert panel is not None
+    assert panel.genes == ["GENE1", "GENE2"]
+    assert "phenotype_id" in panel.metadata

tests/test_store.py

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+from genomic_consultant.store.query import GenomicStore
+from genomic_consultant.utils.models import FilterConfig, Variant
+
+
+def test_filter_by_gene_and_af():
+    store = GenomicStore(
+        variants=[
+            Variant(chrom="1", pos=1, ref="A", alt="T", gene="GENE1", allele_frequency=0.02),
+            Variant(chrom="1", pos=2, ref="G", alt="C", gene="GENE2", allele_frequency=0.0001),
+        ]
+    )
+    res = store.get_variants_by_gene("ind", ["GENE2"], filters=FilterConfig(max_af=0.001))
+    assert len(res) == 1
+    assert res[0].gene == "GENE2"
+
+
+def test_consequence_include_exclude():
+    store = GenomicStore(
+        variants=[
+            Variant(chrom="1", pos=1, ref="A", alt="T", gene="GENE1", consequence="missense_variant"),
+            Variant(chrom="1", pos=2, ref="G", alt="C", gene="GENE1", consequence="synonymous_variant"),
+        ]
+    )
+    res = store.get_variants_by_gene(
+        "ind", ["GENE1"], filters=FilterConfig(consequence_includes=["missense"], consequence_excludes=["synonymous"])
+    )
+    assert len(res) == 1
+    assert res[0].consequence == "missense_variant"

tests/test_store_tsv.py

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+from pathlib import Path
+
+from genomic_consultant.store.query import GenomicStore
+
+
+def test_from_tsv_with_extra_columns(tmp_path: Path):
+    content = "\t".join(
+        [
+            "#CHROM",
+            "POS",
+            "REF",
+            "ALT",
+            "SYMBOL",
+            "Consequence",
+            "Protein_position",
+            "PolyPhen",
+            "SIFT",
+            "CLIN_SIG",
+            "AF",
+            "gnomAD_AF",
+            "SpliceAI",
+            "CADD_PHRED",
+        ]
+    ) + "\n"
+    content += "1\t100\tA\tT\tGENE1\tmissense_variant\tp.X\t.\t.\tPathogenic\t0.0001\t0.0002\t0.05\t20.1\n"
+    path = tmp_path / "v.tsv"
+    path.write_text(content)
+
+    store = GenomicStore.from_tsv(path)
+    assert len(store.variants) == 1
+    v = store.variants[0]
+    assert v.annotations["splice_ai_delta_score"] == 0.05
+    assert v.annotations["cadd_phred"] == 20.1