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