Save / load `DeseqDataSet` states and write anndata to disk as h5ad
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 761
- Forks
- 90
- Avg merge
- 25m
- Merged PRs (30d)
- 10
Description
Is your feature request related to a problem? Please describe.
#328 makes the DeseqDataSet class unpicklable due to decorated methods. This makes it harder to save results on disk.
Describe the solution you'd like
As suggested by @grst:
implement a .save() and (static) .load() method that saves the anndata as h5ad and the state of the model as pickle or any other > suited format.
The .load() should be able to restore the full state of the dds object, including the formulaic metadata ideally
Describe alternatives you've considered
Use the to_picklable_anndata() method introduced in #328, but this loses the dds state.
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 at the DeseqDataSet save/load entry points and review the existing to_picklable_anndata() method from #328. Define how the AnnData is written as h5ad and how the model state is serialized; done means load() restores the full dds state, including formulaic metadata.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100