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GeneProtein synonym conflation #185

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GeneProtein synonym conflation #185

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Commits on Dec 2, 2023

  1. Add object normalization for PubChem IDs in drugchemical conflation.

    @gaurav
    gaurav committed Dec 2, 2023
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  2. Replaced exceptions with warnings.

    @gaurav
    gaurav committed Dec 2, 2023
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  3. Reverted one of the warnings back to an exception.

    @gaurav
    gaurav committed Dec 2, 2023
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  4. Prevent and log KeyError in anatomy.

    @gaurav
    gaurav committed Dec 2, 2023
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  5. Reverted anatomy hiding code.

    @gaurav
    gaurav committed Dec 2, 2023
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  6. Moved UniProtKB downloads into Snakefile as wget commands.

    @gaurav
    gaurav committed Dec 2, 2023
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  7. Improved progress output so it can be mixed with other logs better.

    @gaurav
    gaurav committed Dec 2, 2023
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  8. Deleted redundant output filename from pull_panther_pathways().

    @gaurav
    gaurav committed Dec 2, 2023
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  9. Took out --progress=dot as this somehow makes it even harder to read.

    @gaurav
    gaurav committed Dec 2, 2023
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  10. Added -k to gunzip so we keep the gzip file in case it's needed.

    @gaurav
    gaurav committed Dec 2, 2023
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  11. Removed babel-private.

    @gaurav
    gaurav committed Dec 2, 2023
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  12. Upgraded UMLS and RxNorm versions.

    @gaurav
    gaurav committed Dec 2, 2023
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  13. Switched HGNC to HTTP from FTP. 

    The FTP server seems to be having issues right now.
    @gaurav
    gaurav committed Dec 2, 2023
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  14. Fixed FTP -> HTTP change for HGNC.

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    gaurav committed Dec 2, 2023
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  15. Added code to skip hgfemale_gene_ensembl.

    @gaurav
    gaurav committed Dec 2, 2023
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  16. Improved debugging.

    @gaurav
    gaurav committed Dec 2, 2023
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  17. Removed unnecessary import.

    @gaurav
    gaurav committed Dec 2, 2023
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Commits on Dec 3, 2023

  1. First stab at generating a GeneProtein conflation.

    @gaurav
    gaurav committed Dec 3, 2023
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  2. Improved output variable name.

    @gaurav
    gaurav committed Dec 3, 2023
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  3. Fixed typos.

    @gaurav
    gaurav committed Dec 3, 2023
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  4. Fixed requirement for conflations to be a list.

    @gaurav
    gaurav committed Dec 3, 2023
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