Integration with Loompy

[pranzatelli]

@edg1983 mentioned here that anndata fails to read in the loom files generated by loompy (necessary to link loompy and scvelo). I've fixed this locally by changing some code in io_/read.py's _fmt_loom_axis_attrs() from

        if v.ndim > 1 and v.shape[1] > 1:
            axis_mapping[k] = v
        else:
            axis_df[k] = v

to

        try:
            if v.ndim > 1 and v.shape[1] > 1:
                axis_mapping[k] = v
            else:
                axis_df[k] = v
        except:
            warn('Failed to import item '+k+' from loom file.')

However, I'm sure there's a more elegant (and professional) solution.

[ivirshup]

Hi @pranzatelli, thanks for reporting this.

From the linked issue:

The problem is that the loom file produced by loompy using their reference file for hg38 has a row attribute Aliases which contains None object and thus crash the code.

AFAICT, this is a bug in loompy, since the spec says:

There MUST be a group /row_attrs There can OPTIONALLY be one or more datasets at /row_attrs/{name} whose first dimension has length N

I've opened an issue on loompy about this: https://github.com/linnarsson-lab/loompy/issues/175

[github-actions[bot]]

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