After SeuratDisk the raw.var_names contain the numeric index while raw.var[‘_index’] contain the gene symbols. I need to swap the two but raw data are no mutable, is all locked. Suggestions?
Not sure I understand, but why not simply get a fresh AnnData from .raw, and copy its var over? You could use a layer ('count’?) instead of .raw for downstream analyses to avoid issues like that.
Alternatively, consider not using SeuratDisk. Not sure what’s your exact use case but anndataR can read/write Seurat objects from/to H5AD files that should be compatible with whatever you do on the Python side.
If you provide some more details, I (or someone else) might be able to give you a more helpful response.
found the solution. adata.raw.var.set_index(adata.raw.var[“_index”], inplace=True)