Speed up aln2counts.py
Open
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enhancement
- Dominant language
- Python
- Stars
- 21
- Forks
- 11
- Avg merge
- 12h 5m
- Merged PRs (30d)
- 24
Description
It would be nice to use multiple processes to handle very large result files, but this is not trivial because all of the functionality in this script is tucked into classes and Python Pool objects don't like to share class methods.
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 reading aln2counts.py and profiling it on a very large result file. Examine how its classes process data and where Python Pool objects would need process-safe entry points. Done means large result files can be handled with multiple processes while preserving the script’s existing results.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Refactor
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100