scverse / scanpy

Single-cell analysis in Python. Scales to >1M cells.
https://scanpy.readthedocs.io
BSD 3-Clause "New" or "Revised" License
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Can't implicitly convert non-string objects to strings. Bug about tl.filter_rank_genes_groups and tl.rank_genes_groups #2666

Open christophechu opened 1 year ago

christophechu commented 1 year ago

Please make sure these conditions are met

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

kcArtemis commented 12 months ago

Hey @christophechu , can you please elaborate your concerns? Exactly, what were you trying to do ??