Initial commit

tests/test_store_tsv.py

@@ -0,0 +1,33 @@
+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