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Uploaded script for Uniprot to ncbi function addresses issue #109#139

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SunSummoner wants to merge 5 commits intoJRaviLab:mainfrom
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Uploaded script for Uniprot to ncbi function addresses issue #109#139
SunSummoner wants to merge 5 commits intoJRaviLab:mainfrom
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@SunSummoner SunSummoner commented Sep 23, 2025

Description

What kind of change(s) are included?

  • Feature (adds or updates new capabilities)
  • Bug fix (fixes an issue).
  • Enhancement (adds functionality).
  • Breaking change (these changes would cause existing functionality to not work as expected).

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Please ensure that all boxes are checked before indicating that this pull request is ready for review.

  • I have read and followed the CONTRIBUTING.md guidelines.
  • I have searched for existing content to ensure this is not a duplicate.
  • I have performed a self-review of these additions (including spelling, grammar, and related).
  • I have added comments to my code to help provide understanding.
  • I have added a test which covers the code changes found within this PR.
  • I have deleted all non-relevant text in this pull request template.
  • Reviewer assignment: Tag a relevant team member to review and approve the changes.

@SunSummoner SunSummoner changed the title Uploaded script for Uniprot to ncbi function addresses #109 Uploaded script for Uniprot to ncbi function addresses issue #109 Sep 23, 2025
@SunSummoner SunSummoner mentioned this pull request Sep 23, 2025
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Added functions to map NCBI RefSeq Protein IDs to UniProt Accessions and NCBI Protein Accessions to IPG IDs.
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Great start! Everything works as described!

A couple of suggestions before approving/merging:

  • Let's avoid using library() and requireNamespace() in user facing functions. Instead, we should rely on roxygen import tags to handle package dependencies.
  • MolEvolvR already has quite a few dependencies, it might be worth refactoring acc2ipg() to use httr2. That would let us drop httr and simplify the dependencies for the package

Thanks for putting this together and apologies for the delay in getting the review back to you!

@SunSummoner
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Great start! Everything works as described!

A couple of suggestions before approving/merging:

  • Let's avoid using library() and requireNamespace() in user facing functions. Instead, we should rely on roxygen import tags to handle package dependencies.
  • MolEvolvR already has quite a few dependencies, it might be worth refactoring acc2ipg() to use httr2. That would let us drop httr and simplify the dependencies for the package

Thanks for putting this together and apologies for the delay in getting the review back to you!

Thanks for the suggestions. I will keep them in mind miving forward.

Renamed functions and updated documentation for consistency. Used @importFrom for sourcing and changed function and variable names to match the convention. Removed other inconsistencies
Removed commented-out example usage from documentation.
@jananiravi
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have these been tested on example accessions -- assuming local checks are now working? If so, I'd be happy to merge this right away. thank you, @SunSummoner!

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SunSummoner commented Jan 24, 2026

@jananiravi the example accessions are working! Thank you!

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3 participants