Speed up read_airr
Open
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 265
- Forks
- 50
- Avg merge
- 9d 9h
- Merged PRs (30d)
- 4
Description
Description of feature
Loading AIRR data with 1.5M rows takes ~10 minutes. This is not too bad, but could be made less annoying
- Make validation optional (I expect the validation of the
airrimplementation takes a good chunk of that time) - Parallelization (read different parts of the file in parallel - or first read into pandas, parse several chunks of the dataframe in parallel)
- Progress bar (this at least shows that this will eventually finish)
Contributor guide
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 at the read_airr entry point and profile loading and validation for a 1.5M-row AIRR dataset. Compare the potential approaches named in the issue—optional validation, parallel parsing, and a progress bar—then define completion by a measurable reduction in load time or visible progress without changing parsed results.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- pandas, python
- Domain
- data, performance
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100