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| """Publication audit: independent randomized checks for sequence utilities. | |
| These tests deliberately use independent Biopython implementations as the | |
| reference rather than reusing BioNexus helper functions. The pseudo-random | |
| inputs are deterministic so a failure can be reproduced exactly. | |
| """ | |
| from __future__ import annotations | |
| import random | |
| import pytest | |
| from Bio.Seq import Seq | |
| from Bio.SeqUtils import gc_fraction, molecular_weight | |
| from app.services.sequence_utils import detect_sequence_type | |
| from app.tools.sequence_utilities import analyze_sequence, clean_sequence | |
| SEED = 20260916 | |
| def _dna_cases(n: int = 100): | |
| rng = random.Random(SEED) | |
| for _ in range(n): | |
| length = rng.randint(1, 300) | |
| yield "".join(rng.choice("ACGT") for _ in range(length)) | |
| def _rna_cases(n: int = 100): | |
| rng = random.Random(SEED + 1) | |
| for _ in range(n): | |
| length = rng.randint(1, 300) | |
| yield "".join(rng.choice("ACGU") for _ in range(length)) | |
| def test_random_dna_metrics_match_independent_biopython_reference(): | |
| for sequence in _dna_cases(): | |
| observed = analyze_sequence(sequence, "dna") | |
| assert observed["length"] == len(sequence) | |
| assert observed["gc_content"] == pytest.approx(gc_fraction(sequence) * 100.0, abs=0.05) | |
| assert observed["reverse_complement"] == str(Seq(sequence).reverse_complement()) | |
| assert observed["molecular_weight"] == pytest.approx( | |
| molecular_weight(sequence, seq_type="DNA", double_stranded=False, circular=False), | |
| abs=0.05, | |
| ) | |
| def test_random_rna_metrics_match_independent_biopython_reference(): | |
| for sequence in _rna_cases(): | |
| observed = analyze_sequence(sequence, "rna") | |
| assert observed["length"] == len(sequence) | |
| assert observed["gc_content"] == pytest.approx(gc_fraction(sequence) * 100.0, abs=0.05) | |
| assert observed["reverse_complement"] == str(Seq(sequence).reverse_complement_rna()) | |
| assert observed["molecular_weight"] == pytest.approx( | |
| molecular_weight(sequence, seq_type="RNA", double_stranded=False, circular=False), | |
| abs=0.05, | |
| ) | |
| def test_rna_cleaning_does_not_silently_convert_u_to_t(): | |
| assert clean_sequence("AUGCUU", "rna") == "AUGCUU" | |
| def test_iupac_dna_reverse_complement_is_iupac_aware_and_mass_is_not_fabricated(): | |
| sequence = "ACGTRYSWKMBDHVN" | |
| observed = analyze_sequence(sequence, "dna") | |
| assert observed["reverse_complement"] == str(Seq(sequence).reverse_complement()) | |
| assert observed["molecular_weight"] is None | |
| assert any("molecular weight" in issue.lower() and "ambiguous" in issue.lower() for issue in observed["issues"]) | |
| def test_iupac_rna_reverse_complement_is_iupac_aware_and_mass_is_not_fabricated(): | |
| sequence = "ACGURYSWKMBDHVN" | |
| observed = analyze_sequence(sequence, "rna") | |
| assert observed["reverse_complement"] == str(Seq(sequence).reverse_complement_rna()) | |
| assert observed["molecular_weight"] is None | |
| assert any("molecular weight" in issue.lower() and "ambiguous" in issue.lower() for issue in observed["issues"]) | |
| def test_auto_detection_handles_iupac_when_nucleotide_identity_is_explicit(): | |
| assert detect_sequence_type("ACGTRY") == "dna" | |
| assert detect_sequence_type("ACGURY") == "rna" | |
| def test_mixed_thymine_and_uracil_is_not_silently_classified_as_protein(): | |
| assert detect_sequence_type("ACGTUACG") == "unknown" | |