FA-12501 / Biological sequence representation / Open access

Reverse complement leaves ambiguity symbols untranslated · case 01

Reverse complement leaves ambiguity symbols untranslated.

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

ROOT CAUSE

The reversal omits complementation.

THE FAILURE

The reversal omits complementation.

Unsuccessful approach: Complementing only canonical letters leaves the paired ambiguity markers unchanged.

Case contract

Reverse the string then substitute A:T,T:A,C:G,G:C,R:Y,Y:R,N:N,-:-. Inputs use only this explicit uppercase alphabet.

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):
    return s[::-1]
def check(label, actual, expected):
    observations.append({"check": label, "actual": actual, "expected": expected, "passed": actual == expected})
check('variable', solve('A'*N+'R'), 'Y'+'T'*N)
check('gap', solve('A-C'), 'G-T')
check('unknown', solve('N'), 'N')
check('empty', solve(''), '')
check('paired', solve('RY'), 'RY')
check('asymmetric', solve('YCA'), 'TGR')
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	`RA`	`YT`	Failed
gap	`C-A`	`G-T`	Failed
unknown	`N`	`N`	Passed
empty			Passed
paired	`YR`	`RY`	Failed
asymmetric	`ACY`	`TGR`	Failed

SHA-256 / 728b7a2b1c4012169ac6a0558cb083ea745090bf7b01d7aad974ae5c1beef9af

2 / The unsuccessful fix

Exit 1

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

N = 1
observations = []
def solve(s):
    return s[::-1].translate(str.maketrans('ACGT','TGCA'))
def check(label, actual, expected):
    observations.append({"check": label, "actual": actual, "expected": expected, "passed": actual == expected})
check('variable', solve('A'*N+'R'), 'Y'+'T'*N)
check('gap', solve('A-C'), 'G-T')
check('unknown', solve('N'), 'N')
check('empty', solve(''), '')
check('paired', solve('RY'), 'RY')
check('asymmetric', solve('YCA'), 'TGR')
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	`RT`	`YT`	Failed
gap	`G-T`	`G-T`	Passed
unknown	`N`	`N`	Passed
empty			Passed
paired	`YR`	`RY`	Failed
asymmetric	`TGY`	`TGR`	Failed

SHA-256 / 5c3f16514458c172f50202842bdcc7fe83793a44c8fb0b890f28e3276997e6ee

HELD IN THE MEMBER ARCHIVE

The verified repair and its recorded checks are member-only.

This mechanism has 6 recorded checks per implementation. The open-access tier publishes the failure and the unsuccessful fix; the repaired source that passes every check, and the observations that prove it, are available to members.

Every case sharing this mechanism uses the same contract and the same repair, so this one record is held back for all of them.

Member access is invitation-based. Sign in with your invited account to inspect the repair.

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 2026-09-29T14:38:57.485308+00:00.

Case digest / 81778af913fcd3198f9c7abf4e29a0b13dbaa40c4d77542a2f33ba4c432874de