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grst avatar grst commented on August 17, 2024

Thanks for reporting this, I will add a better error message to define_clonotypes.

from scirpy.

grst avatar grst commented on August 17, 2024

I tried to reproduce this and I'm already getting "Obs names need to be unique" as error message in the new v0.13.0rc1.

In the updated tutorials there are also better instructions for concatenating AnnData objects that don't lead to duplicated obs_names in the first place.

The trick is to store AnnData objects as a dictionary rather than a list:

adatas = {
   'sample1': adata_sample1, 
   'sample2': adata_sample2
}

and then use anndata.concat with the index_unique option:

adata = anndata.concat(adatas, index_unique="_")

The obs names will then be a combination of the cell barcode and the sample id.

from scirpy.

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