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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 80 81 82 83 84 85 86 87 88 | """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"
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