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IMP: Allow the ability to download SILVA alignment. - #266

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mikerobeson merged 13 commits into
bokulich-lab:masterfrom
mikerobeson:dl_silva_alignment
Sep 23, 2026
Merged

mikerobeson merged 13 commits into
bokulich-lab:masterfrom
mikerobeson:dl_silva_alignment

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@mikerobeson mikerobeson commented Sep 11, 2026 •

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Description

Addresses #265.

  • Adds the flag --p-seq-format. This will allow the user to download :
    • Aligned sequence data
    • Unaligned sequence data
    • Both the aligned and unaligned sequence data
    • None of the sequence data, just the taxonomy
  • Deprecates --p-download-sequences flag.
    • This will be handled by --p-seq-format moving forward.

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mikerobeson marked this pull request as ready for review September 14, 2026 18:37

@VinzentRisch VinzentRisch left a comment

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Hey @mikerobeson
It would be better if the download_sequences parameter is not directly removed but rather deprecated. See below for changes.

Comment thread rescript/get_data.py Resolved
Comment thread rescript/plugin_setup.py Resolved
@VinzentRisch VinzentRisch changed the title ENH: Allow the ability to download SILVA alignment. IMP: Allow the ability to download SILVA alignment. Sep 23, 2026
@mikerobeson
mikerobeson merged commit af29a4f into bokulich-lab:master Sep 23, 2026
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mikerobeson deleted the dl_silva_alignment branch September 23, 2026 23:04
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2 participants