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Improve mapping to ensembl ids with pyensembl package #50

Merged
merged 12 commits into from
Jul 15, 2024
Merged

Improve mapping to ensembl ids with pyensembl package #50

merged 12 commits into from
Jul 15, 2024

Commits on Jul 10, 2024

  1. Search and replace gene_col_name -> gene_names

    @bputzeys
    bputzeys committed Jul 10, 2024
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Commits on Jul 11, 2024

  1. Provide more granularity when passing configs to benchmarking

    @bputzeys
    bputzeys committed Jul 11, 2024
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  2. Replace the mapping to ensembl ids with a better 

    one from the pyensembl package. Also include
a mapping from ensembl ids to gene names.
    @bputzeys
    bputzeys committed Jul 11, 2024
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  3. Change the default gene_names var to index with the better mapping no… 

    …w available
    @bputzeys
    bputzeys committed Jul 11, 2024
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  4. Merge branch 'main' into fix-gene-col-name

    @bputzeys
    bputzeys committed Jul 11, 2024
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  5. Fix failing unit test

    @bputzeys
    bputzeys committed Jul 11, 2024
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  6. Merge branch 'improve-ensembl-id-mapping' into fix-gene-col-name

    @bputzeys
    bputzeys committed Jul 11, 2024
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  7. Add pyensembl requirement

    @bputzeys
    bputzeys committed Jul 11, 2024
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Commits on Jul 12, 2024

  1. Make the ensemblID mapping more generalizable to 

    more species.
    @bputzeys
    bputzeys committed Jul 12, 2024
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  2. Add unit tests to check the mapping is done correctly with the pyense… 

    …mbl package
    @bputzeys
    bputzeys committed Jul 12, 2024
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  3. Add comment about downloading dataset for first execution

    @bputzeys
    bputzeys committed Jul 12, 2024
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  4. Skip pytest because it takes long to run and because it would exceed … 

    …the limit of memory available on GitHub Actions
    @bputzeys
    bputzeys committed Jul 12, 2024
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