[BUG] Errors saving `DeseqDataSet` to H5AD
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bug
- Dominant language
- Python
- Stars
- 761
- Forks
- 90
- Avg merge
- 25m
- Merged PRs (30d)
- 10
Description
When I attempt to save my DeseqDataSet AnnData object to H5AD, errors are thrown becuase
dds.varm['replaced']dds.uns['trend_coeffs']
are stored as a pandas.core.series.Series, which cannot be written to H5AD in those positions. Calling
dds.varm['replaced'] = dds.varm['replaced'].valuesdds.uns['trend_coeffs'] = dds.uns['trend_coeffs'].to_dict()
before dds.write_h5ad(<path>) resolved the issue without loss of functionality.
PyDESeq2 version 0.4.7 on CentOS 7.
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 failure with dds.write_h5ad(<path>) using the dds.varm['replaced'] and dds.uns['trend_coeffs'] values described in the report. Inspect the H5AD serialization path for these fields; done means the object saves successfully without manual conversions and retains its functionality.
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
- Mostly clear
- Newbie friendliness
- 45/100