Feature Request: Custom Codon Tables
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- Dominant language
- Jupyter Notebook
- Stars
- 17
- Forks
- 15
- PR merge metrics
- No merged PRs in 30d
Description
Great work folks!
I was using dnachisel for non-model organisms, and wondered if it would be reasonable to allow the substitution of a custom codon frequency table from an uploaded JSON or CSV.
I think I can volunteer a snippet to convert a pandas df to the nested dictionary format that dnachisel wants.
potential impact: this might cause interface logic problems with your new codon-pair additions.
Contributor guide
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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 by tracing how the project currently supplies codon frequency tables and how uploaded data is handled. Review the potential interface impact of the codon-pair additions mentioned in the issue. Done means custom tables can be supplied from JSON or CSV without breaking those additions, with the expected nested dictionary format defined.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook, pandas
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100