add scanpy score_genes and score_genes_cell_cycle components

[dorien-er]

Changelog

add scanpy score_genes and score_genes_cell_cycle components

Issue ticket number and link

Closes #xxxx (Replace xxxx with the GitHub issue number)

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• I have performed a self-review of my code

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• Check the correct box. Does this PR contain:

  • Breaking changes
  • New functionality
  • Major changes
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  • Documentation
  • Bug fixes

• Proposed changes are described in the CHANGELOG.md

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[DriesSchaumont]

I'm not sure, but I think this also works and uses the intended pandas methods. Could you test it?

Suggested change

	gene_list_index = input_adata.var.index[[gene in gene_list for gene in gene_names]]
	gene_pool_index = input_adata.var_names.intersection(gene_names.reindex(gene_list)[0])

[DriesSchaumont]

My previous comment will not work when gene_names contains duplicate entries

What I would do is change starting from line 38:

gene_names_index = input_adata.var[par["var_gene_names"]] if par["var_gene_names"] else input_adata.var_names
gene_names = pd.Series(input_adata.var_names, index=gene_names_index)

Make sure that read_gene_list works with the Series object or just pass gene_names.index as the second argument

And then use:

gene_list_index = gene_names.loc[gene_list].tolist()

But perhaps tbd with @rcannood

[dorien-er]

@rcannood i commited those changes in e87c9bd, so can be merged/reverted back

[DriesSchaumont]

My previous comment will not work when gene_names contains duplicate entries

What I would do is change starting from line 38:

gene_names_index = input_adata.var[par["var_gene_names"]] if par["var_gene_names"] else input_adata.var_names
gene_names = pd.Series(input_adata.var_names, index=gene_names_index)

Make sure that read_gene_list works with the Series object or just pass gene_names.index as the second argument

And then use:

gene_list_index = gene_names.loc[gene_list].tolist()

But perhaps tbd with @rcannood

[DriesSchaumont]

LGTM! Thank you @dorien-er