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)