Type comparison issue when using read_h5ad in backed mode
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- Python
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Description
If I read a file with read_h5ad() and then process with
sc.pp.filter_genes(adata, min_cells=int(foo))
Things work as intended.
But if I change that read line to be read_h5ad(h5_path, backed='r') then when I attempt to filter I get this error instead:
File "/opt/Python-3.7.3/lib/python3.7/site-packages/scanpy/preprocessing/_simple.py", line 228, in filter_genes:
else X > 0, axis=0):
TypeError: '>' not supported between instances of 'SparseDataset' and 'int'
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First steps
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Research direction
Start in scanpy/preprocessing/_simple.py around filter_genes, using the reported line where SparseDataset is compared with an integer. Reproduce the difference between read_h5ad() and read_h5ad(..., backed='r') with sc.pp.filter_genes(adata, min_cells=int(foo)). Done means the backed case no longer raises this TypeError and filtering behavior remains correct.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics, data
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100