OpenCloning / OpenCloning/OpenCloning_backend
permutate_trace: improve discriminating between Sanger and full-plasmid sequence
Open
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 8
- Forks
- 11
- Avg merge
- 14m
- Merged PRs (30d)
- 5
Description
As of now it tests:
if len_diff > 0 and (len(sanger_trace) / len(reference) < 0.8):
padded_trace = sanger_trace + len_diff * 'N'
And adds padding, otherwise it assumes it's a full-plasmid seq
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First steps
- Read the whole issue, then the project's contributing guide.
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- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Locate the permutate_trace function and inspect its current length comparison and padding branch. Trace how it receives Sanger and full-plasmid sequences, then identify observable cases where the current assumption is wrong. Done means the function more reliably distinguishes the two sequence types without relying only on the shown length threshold.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- backend
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100