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Fetch Uniprot entries for a list of organisms - #49

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nanglo123 wants to merge 4 commits into
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fetch_unreviewed_uniprot
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nanglo123 wants to merge 4 commits into
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fetch_unreviewed_uniprot

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@nanglo123

@nanglo123 nanglo123 commented Aug 26, 2026

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This PR adds a method to retrieve Uniprot entries (download_uniprot_entries_for_organisms) for a list of organisms

  • The method was implemented primarily to retrieve unreviewed + reviewed Uniprot entries; however, users can also fetch only reviewed entries
  • Users specify the column names they want retrieved, the valid fields are listed here and the list of organism ids (NCBITaxon IDs) they want to extract entries for
  • This was added as a separate method rather than to existing functionality because download_uniprot_entries has a fixed output format that a parameterised version would break
  • The downloaded file is stored at a user supplied path.

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