Set gene_symbol as a index if provided

[anilthanki]

Description

Often in AnnData files the index is the gene_id and the gene symbols are in another field of the var. However, gene set tools will often rely on the gene symbol, so this PR is to indicate where the gene symbol is in anndata and make use of this information so that the tool runs against those gene symbols.

Fixes # (Issue 327)

Type of change

• [ ] Bug fix (non-breaking change which fixes an issue)
• [ ] New feature (non-breaking change which adds functionality)
• [x] Breaking change (fix or feature that would cause existing functionality to not work as expected)
• [x] This change requires a documentation update

Checklist

• [ ] I have made any required changes to upstream dependencies for a tool wrapper, and they are available in distribution channels (e.g. Pip, Conda).
• [ ] If I have updated the underlying software for a tool wrapper (e.g. scanpy-scripts by changing the value of @TOOL_VERSION@), then I have reset all 'build' values to 0 (e.g. @TOOL_VERSION@+galaxy0)
• [ ] If I have updated a tool wrapper without a software change, then I have bumped the associated 'build' values (e.g. @TOOL_VERSION@+galaxy0 @TOOL_VERSION@+galaxy1). It is acceptable to do this as well when the cli version changed but not the underlying tool (to avoid issues in the coming point).
• [ ] If I changed the version, the @TOOL_VERSION@ part of the version does not contain any + symbols within, otherwise this will break tool ordering on the interface and the default tool being picked. Tool version should always conform to PEP440 to avoid this issue. The only + should be the one preceding galaxy<build> (unless that all the versions from that tool previously followed a different pattern).

[pcm32]

@anilthanki this looks good, I only wonder whether there is any license issue to redistribute the whole mouse progeny network (or is this a subset?).

[pcm32]

Ok, apparently this is fine as long as we include the LICENSE file from https://github.com/saezlab/progeny/. Maybe you can add it in the test-data folder as PROGENy_LICENSE?

[anilthanki]

@anilthanki this looks good, I only wonder whether there is any license issue to redistribute the whole mouse progeny network (or is this a subset?).

Apologies for late reply..

its subset of the mouse progeny supplied by decoupleR same as we had human ones.