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