Non-unique gene names on AnnData affects some usages

[pcm32]

Sometimes the use of some annotations yields non-unique gene names in our AnnData files. It should be easy to add an option in https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/blob/develop/tools/tertiary-analysis/scanpy/anndata_operations.xml that makes the gene names unique in the specified field (either in the same column where they are or in a new column) in the var object. This allows our AnnData file to be used more nicely with viewers like cellxgene, which ask for a unique index for genes (and that is what they show as symbols).

[pcm32]

This could be done with:

adata.var.set_index("gene_symbols")
adata.var_names_make_unique()

[pcm32]

or, if we don't want to mess with the index:

def rn(df, field, suffix = '-duplicate-'):
     appendents = (suffix + df.groupby(field).cumcount().astype(str).replace('0','')).replace(suffix, '')
     df[f"{field}_u"] = df[field].astype(str) + appendents.astype(str)
     return df

g_symbols_field = "gene_symbols"
adata.var = rn(adata.var, g_symbols_field, suffix = "_d")

[pcm32]

This is going to be resolved as part of #266