FA-12511 / Biological sequence representation / Open access

Strand canonicalization compares a word with its reversal · case 01

Strand canonicalization compares a word with its reversal.

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

ROOT CAUSE

Reversal does not represent the specified complementary strand.

VERIFIED REPAIR

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

Unsuccessful approach: Complementing without reversal compares the wrong orientation.

Case contract

Return lexicographic minimum of an ACGT string and its reverse-complement using A:T,C:G. Empty maps to empty.

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 min(s,s[::-1])
def check(label, actual, expected):
    observations.append({"check": label, "actual": actual, "expected": expected, "passed": actual == expected})
check('variable', solve('T'*N+'G'), 'C'+'A'*N)
check('single', solve('T'), 'A')
check('palindrome', solve('AT'), 'AT')
check('empty', solve(''), '')
check('complement reverse', solve('GT'), 'AC')
check('already canonical', solve('AAC'), 'AAC')
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	`GT`	`CA`	Failed
single	`T`	`A`	Failed
palindrome	`AT`	`AT`	Passed
empty			Passed
complement reverse	`GT`	`AC`	Failed
already canonical	`AAC`	`AAC`	Passed

SHA-256 / e6475a9a80e3b41f4012f211cc4aab9548921b7b932377c41efa9412d25fca1e

2 / The unsuccessful fix

Exit 1

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

N = 1
observations = []
def solve(s):
    return min(s,s.translate(str.maketrans('ACGT','TGCA')))
def check(label, actual, expected):
    observations.append({"check": label, "actual": actual, "expected": expected, "passed": actual == expected})
check('variable', solve('T'*N+'G'), 'C'+'A'*N)
check('single', solve('T'), 'A')
check('palindrome', solve('AT'), 'AT')
check('empty', solve(''), '')
check('complement reverse', solve('GT'), 'AC')
check('already canonical', solve('AAC'), 'AAC')
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	`AC`	`CA`	Failed
single	`A`	`A`	Passed
palindrome	`AT`	`AT`	Passed
empty			Passed
complement reverse	`CA`	`AC`	Failed
already canonical	`AAC`	`AAC`	Passed

SHA-256 / 65c42e6b0355cee130c972d20d06a9338f05814a346f4d7435c8892f8c9f748f

3 / The verified repair

Exit 0

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

N = 1
observations = []
def solve(s):
    return min(s,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('T'*N+'G'), 'C'+'A'*N)
check('single', solve('T'), 'A')
check('palindrome', solve('AT'), 'AT')
check('empty', solve(''), '')
check('complement reverse', solve('GT'), 'AC')
check('already canonical', solve('AAC'), 'AAC')
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	`CA`	`CA`	Passed
single	`A`	`A`	Passed
palindrome	`AT`	`AT`	Passed
empty			Passed
complement reverse	`AC`	`AC`	Passed
already canonical	`AAC`	`AAC`	Passed

SHA-256 / a44ffa75c94d7db91686db85bf4a484beaa18247da625a4910244ab12010b392

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 2026-09-29T14:38:57.490957+00:00.

Case digest / 438ff65f4e6d76352ac9747627804130aa2636a7632e35c2354c364c3c6f19d4