| # Annotation equivalence fails after construct-orientation normalization |
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|
| A construct-annotation workflow built on the supplied Biopython snapshot |
| normalizes circular DNA records into the opposite display orientation before |
| shipping GenBank files to downstream design and review tools. The input batch |
| is stored in `fixtures/construct_manifest.json` and contains the mixture of |
| feature representations used by the delivery workflow. |
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|
| The normalization and export complete without exceptions, and the generated |
| GenBank records can be parsed again. Nevertheless, the downstream annotation |
| equivalence check rejects part of the batch: the nucleotide sequence and |
| basic file structure remain usable, but the transformed annotations do not all |
| describe the same biological content. |
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|
| Run `python reproduce.py` from the task directory. It executes the user |
| workflow and reports only record-level structural observations. The public |
| workflow is intended to show useful delivery behavior without embedding a |
| second annotation oracle. |
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|
| Use the supplied scientific references, complete source snapshot, input |
| records, and any diagnostic experiments you design yourself to determine why |
| the library produces inconsistent annotations. Repair the scientific |
| implementation for general valid records without hard-coding the public |
| batch or its stored outputs. Existing behavior for unaffected annotation |
| representations and ordinary sequence operations must remain compatible. |
|
|
| Do not use the network or add external data files. Keep the repair inside the |
| supplied source snapshot. |
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|
