FA-12531 / Biological sequence representation / Open access

DNA and RNA normalization silently changes molecule type · case 01

DNA and RNA normalization silently changes molecule type.

Verified by executionVariant 1 · 6 checks per implementationDownload source bundle ↓JSON ↗

ROOT CAUSE

Unconditional U-to-T substitution accepts RNA symbols in DNA input.

VERIFIED REPAIR

Implement the stated sequence contract while preserving its positional and symbol semantics.

Unsuccessful approach: Uppercasing without validating allows mixed alphabets.

Case contract

Return uppercase input if every symbol belongs to ACGTN for type DNA or ACGUN for type RNA; otherwise None. Type is DNA or RNA. No cross-type conversion.

Why this case matters

An offline abstract sequence-data model; useful for testing representation invariants without biological inference.

1 / The failure

Exit 1

"""Failure Map reference implementation. Python standard library only."""
import json

N = 1
observations = []
def solve(s,kind):
    return s.upper().replace('U','T')
def check(label, actual, expected):
    observations.append({"check": label, "actual": actual, "expected": expected, "passed": actual == expected})
check('variable mixed DNA', solve('a'*N+'u','DNA'), None)
check('RNA U', solve('acu','RNA'), 'ACU')
check('RNA T rejected', solve('ACT','RNA'), None)
check('DNA valid', solve('actn','DNA'), 'ACTN')
check('empty', solve('','DNA'), '')
check('invalid', solve('AX','RNA'), None)
print(json.dumps({"observations": observations, "passed": all(x["passed"] for x in observations)}, ensure_ascii=False))
raise SystemExit(0 if all(x["passed"] for x in observations) else 1)

Boundary fixture	Actual	Expected	Outcome
variable mixed DNA	`AT`	`None`	Failed
RNA U	`ACT`	`ACU`	Failed
RNA T rejected	`ACT`	`None`	Failed
DNA valid	`ACTN`	`ACTN`	Passed
empty			Passed
invalid	`AX`	`None`	Failed

SHA-256 / 11644dc5fc20d675bf193ddb3c3c537293e60ec1cb293f1526e2afb6f66a7efc

2 / The unsuccessful fix

Exit 1

"""Failure Map reference implementation. Python standard library only."""
import json

N = 1
observations = []
def solve(s,kind):
    return s.upper()
def check(label, actual, expected):
    observations.append({"check": label, "actual": actual, "expected": expected, "passed": actual == expected})
check('variable mixed DNA', solve('a'*N+'u','DNA'), None)
check('RNA U', solve('acu','RNA'), 'ACU')
check('RNA T rejected', solve('ACT','RNA'), None)
check('DNA valid', solve('actn','DNA'), 'ACTN')
check('empty', solve('','DNA'), '')
check('invalid', solve('AX','RNA'), None)
print(json.dumps({"observations": observations, "passed": all(x["passed"] for x in observations)}, ensure_ascii=False))
raise SystemExit(0 if all(x["passed"] for x in observations) else 1)

Boundary fixture	Actual	Expected	Outcome
variable mixed DNA	`AU`	`None`	Failed
RNA U	`ACU`	`ACU`	Passed
RNA T rejected	`ACT`	`None`	Failed
DNA valid	`ACTN`	`ACTN`	Passed
empty			Passed
invalid	`AX`	`None`	Failed

SHA-256 / 4938b782963449f83160f2267f200179b646a5e7dff8770f47311974739fc98c

3 / The verified repair

Exit 0

"""Failure Map reference implementation. Python standard library only."""
import json

N = 1
observations = []
def solve(s,kind):
    s=s.upper()
    allowed='ACGTN' if kind=='DNA' else 'ACGUN'
    return s if all(c in allowed for c in s) else None
def check(label, actual, expected):
    observations.append({"check": label, "actual": actual, "expected": expected, "passed": actual == expected})
check('variable mixed DNA', solve('a'*N+'u','DNA'), None)
check('RNA U', solve('acu','RNA'), 'ACU')
check('RNA T rejected', solve('ACT','RNA'), None)
check('DNA valid', solve('actn','DNA'), 'ACTN')
check('empty', solve('','DNA'), '')
check('invalid', solve('AX','RNA'), None)
print(json.dumps({"observations": observations, "passed": all(x["passed"] for x in observations)}, ensure_ascii=False))
raise SystemExit(0 if all(x["passed"] for x in observations) else 1)

Boundary fixture	Actual	Expected	Outcome
variable mixed DNA	`None`	`None`	Passed
RNA U	`ACU`	`ACU`	Passed
RNA T rejected	`None`	`None`	Passed
DNA valid	`ACTN`	`ACTN`	Passed
empty			Passed
invalid	`None`	`None`	Passed

SHA-256 / 3c4ab799dfd09f6476734d403bbacfd4ed4d8186024dca744655fa877be7d0e2

Verification & scope

Synthetic strings and explicit policies only; no biological interpretation or laboratory workflow. This reproducer isolates one failure mechanism. Results cover the supplied fixtures. Variants within a family share a test contract and should remain grouped when constructing evaluation splits. Related mechanisms with a shared evaluation_group must also remain together; these controlled models are not independent production incidents.

Observations recorded using Python 3.12.14 at 2026-09-29T14:38:57.752152+00:00.

Case digest / dc2c74846ff719ca9613cd95a658e0cf8cab3848798cc239e8bf2548f2052f95