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Running on Zero
Running on Zero
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b0f65a7 72aa48b b0f65a7 72aa48b b0f65a7 72aa48b b0f65a7 72aa48b b0f65a7 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | import pytest
from variantllm.inference.scorer import ZeroShotVariantScorer
def test_zero_shot_scorer_esm2():
scorer = ZeroShotVariantScorer(model_name="facebook/esm2_t6_8M_UR50D")
# Test TP53 R175H (known pathogenic mutation)
wt = "MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSD"
mut = "MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTHVRAMAIYKQSQHMTEVVRRCPHHERCSDSD"
res = scorer.score_sequence_pair(wt, mut)
assert "zero_shot_llr_score" in res
assert "pathogenicity_prob" in res
assert "prediction" in res
assert res["gene_position"] > 0
assert res["wildtype_residue"] == "R"
assert res["mutant_residue"] == "H"
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