OpenCloning / OpenCloning/OpenCloning_frontend
Handle assembly edge case
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- JavaScript
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- Avg merge
- 11d 9h
- Merged PRs (30d)
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Description
Documented in examples/example_insertion_vs_circle.py
In an insertion assembly, when the two homology regions overlap, the same assembly could be interpreted as a circular one.
In the picture below, we could have:
- An insertion where the bottom sequence gets inserted into the top
- A circularisation of the bottom one, with the top acting as a "bridge"
This bridge thing could be not supported, but I suppose it can actually be quite useful for something like a gibson assembly.
Supporting this two cases makes it necessary to have the parameter is_insertion in assemble. Passing the same fragment twice for the insertion assembly would solve the problem and turned into a pydantic object, since the fragment representation would start with None and end with None locations, if the ids are the same it could be inferred that it's an insertion.
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with examples/example_insertion_vs_circle.py and the assemble entry point described in the issue. Compare the insertion and circularisation cases when homology regions overlap, then determine how is_insertion, repeated fragments, and the proposed pydantic representation should distinguish them; done means both interpretations are supported or the bridge case is explicitly rejected.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- backend
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100