read_10x_mtx with different prefix
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Description
Hi scanpy team,
I am not sure if I just missed it, but there does not seem to be a way to specify a different filename for .mtx files. For instance, assuming I have multiple .mtx files in a folder sample1.matrix.mtx, sample2.matrix.mtx ... with corresponding sample1.genes.tsv and sample1.barcodes.tsv. It would be useful to be able either specify matrix/genes/barcodes filename, etc. and/or a suffix for the files.
Thanks in advance, Alex
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 read_10x_mtx entry point and inspect how it derives the matrix, genes, and barcodes filenames. Reproduce the request with files such as sample1.matrix.mtx and sample1.genes.tsv. Done means the reader can accept explicit filenames or a suffix and load the corresponding files together.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 42/100