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| """Publication audit: randomized and known-answer pairwise-alignment checks.""" | |
| from __future__ import annotations | |
| import random | |
| import pytest | |
| from app.tools.pairwise_alignment import PairwiseAlignError, pairwise_align | |
| SEED = 20260916 | |
| AA = "ACDEFGHIKLMNPQRSTVWY" | |
| def test_random_identical_proteins_are_100_percent_identical_in_global_and_local_modes(): | |
| rng = random.Random(SEED) | |
| for _ in range(75): | |
| n = rng.randint(5, 100) | |
| sequence = "".join(rng.choice(AA) for _ in range(n)) | |
| for mode in ("global", "local"): | |
| result = pairwise_align(sequence, sequence, mode=mode) | |
| assert result["identity"] == n | |
| assert result["alignment_length"] == n | |
| assert result["pct_identity"] == 100.0 | |
| assert result["gaps_total"] == 0 | |
| assert result["query_start"] == 1 | |
| assert result["query_end"] == n | |
| assert result["hit_start"] == 1 | |
| assert result["hit_end"] == n | |
| def test_local_alignment_reports_original_coordinates_for_internal_matches(): | |
| rng = random.Random(SEED + 1) | |
| flank_alphabet = "ACDEFGHIKLMNPQRSTVY" # excludes W | |
| motif = "WWWWWW" | |
| for _ in range(40): | |
| left_len = rng.randint(1, 35) | |
| right_len = rng.randint(1, 35) | |
| left = "".join(rng.choice(flank_alphabet) for _ in range(left_len)) | |
| right = "".join(rng.choice(flank_alphabet) for _ in range(right_len)) | |
| query = left + motif + right | |
| result = pairwise_align(query, motif, mode="local") | |
| assert result["aligned_query"] == motif | |
| assert result["aligned_hit"] == motif | |
| assert result["query_start"] == left_len + 1 | |
| assert result["query_end"] == left_len + len(motif) | |
| assert result["hit_start"] == 1 | |
| assert result["hit_end"] == len(motif) | |
| def test_non_matrix_residues_are_rejected_instead_of_becoming_server_errors(): | |
| for bad in ("MOU", "PEPTJDE", "ABC123O"): | |
| with pytest.raises(PairwiseAlignError): | |
| pairwise_align(bad, "ACDEFG") | |
| def test_positive_gap_rewards_are_rejected_as_invalid_alignment_parameters(): | |
| with pytest.raises(PairwiseAlignError): | |
| pairwise_align("ACDEFG", "ACDEFG", open_gap_score=5) | |
| with pytest.raises(PairwiseAlignError): | |
| pairwise_align("ACDEFG", "ACDEFG", extend_gap_score=1) | |
| def test_random_global_alignment_coordinate_and_count_invariants(): | |
| rng = random.Random(SEED + 2) | |
| for _ in range(75): | |
| a = "".join(rng.choice(AA) for _ in range(rng.randint(5, 80))) | |
| b = "".join(rng.choice(AA) for _ in range(rng.randint(5, 80))) | |
| result = pairwise_align(a, b, mode="global") | |
| assert len(result["aligned_query"]) == len(result["aligned_hit"]) == result["alignment_length"] | |
| assert result["identity"] <= result["alignment_length"] | |
| assert 0.0 <= result["pct_identity"] <= 100.0 | |
| assert result["query_start"] == 1 | |
| assert result["query_end"] == len(a) | |
| assert result["hit_start"] == 1 | |
| assert result["hit_end"] == len(b) | |
| assert result["gaps_total"] == result["aligned_query"].count("-") + result["aligned_hit"].count("-") | |