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e3a2796 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 | """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("-")
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