Can't implicitly convert non-string objects to strings. Bug about tl.filter_rank_genes_groups and tl.rank_genes_groups
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- Dominant language
- Python
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Description
Please make sure these conditions are met
- I have checked that this issue has not already been reported.
- I have confirmed this bug exists on the latest version of scanpy.
- (optional) I have confirmed this bug exists on the master branch of scanpy.
What happened?
When I use sc.tl.filter_rank_genes_groups or sc.tl.filter_rank_genes_groups, I can not write the result file until I delete the output files stored as adata.uns['rank_genes_groups_filtered'] and adata.uns['rank_genes_groups']
Minimal code sample
sc.tl.filter_rank_genes_groups
sc.tl.filter_rank_genes_groups
Both default use
Error output
TypeError: Can't implicitly convert non-string objects to strings
Above error raised while writing key 'names' of <class 'h5py._hl.group.Group'> to /
Versions
anndata: 0.9.2
scanpy version: 1.9.5
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 by reproducing the write failure after using scanpy's tl.filter_rank_genes_groups and tl.rank_genes_groups with the stored adata.uns['rank_genes_groups_filtered'] and adata.uns['rank_genes_groups'] results. Inspect how the names output is written and confirm that the result file can be written without deleting those entries.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100