scverse / scverse/spatialdata-io
Handling of case-variant column names in CosMx data
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 103
- Forks
- 65
- Avg merge
- 1h 8m
- Merged PRs (30d)
- 3
Description
When reading in CosMx data, the metadata file read in to create the obs attribute of the anndata object that becomes the table of the SpatialData object can include both a "cell_id" column and a "cell_ID" column (with different values). This causes the column name sanitization routine in validation to throw an error during SpatialData object creation in the CosMx reader. One way of handling this is to rename the "cell_id" column, which allows the table to validate and the SpatialData object to instantiate.
I have a branch of a fork of this repo that has this behavior implemented and can submit a pull request unless another solution is preferred.
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 with the CosMx reader and the validation column-name sanitization routine described in the issue. Reproduce a read using metadata containing both "cell_id" and "cell_ID", then verify that the resulting SpatialData object instantiates successfully without a validation error.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100