sc.tl.rank_genes_groups truncates gene ids to 50 bytes/char
Open
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 2.6k
- Forks
- 779
- Avg merge
- 1d 4h
- Merged PRs (30d)
- 27
Description
Ran in to this problem becouse I have gene names longer than U50
as found in this line
https://github.com/theislab/scanpy/blob/master/scanpy/tools/_rank_genes_groups.py#L433
This silently truncates rank genes to 50 characters and the gene groups can't be used to plot or otherwise search indices of my data.
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 in scanpy/tools/_rank_genes_groups.py around line 433 and reproduce the issue with gene identifiers longer than 50 characters. Trace how the truncated identifiers are stored and used for plotting or index lookup; done means rank_genes_groups preserves the original identifiers so downstream searches and plots work.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Activity status
- Stale
- Clarity
- Clearly specified
- Newbie friendliness
- 45/100