Improve mapping to ensembl ids with pyensembl package #50
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bputzeys
commented
Jul 10, 2024
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bputzeys
commented
- Search and replace gene_col_name -> gene_names
- Improve mapping to ensembl id with pyensembl package: https://github.com/openvax/pyensembl
one from the pyensembl package. Also include a mapping from ensembl ids to gene names.
bputzeys
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maxiallard
reviewed
Jul 12, 2024
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@bputzeys This will not work anymore if we want to do this for other species. The UCE model for example needs macacus genes.
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Previously, we had only the mapping from pbmc which is human right? So the previous code would not work with UCE in the first place no?
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I can add the species as input argument?
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Yes add it please. I don't want different methods for different models. This way we can use UCE across more species. Thanks.
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Ok I made the changes and included a unittest where I show how to do it with Macaque. d176049
more species.
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