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support taxonomy format-loading plugins #2694

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ctb opened this issue Jul 31, 2023 · 0 comments
Open

support taxonomy format-loading plugins #2694

ctb opened this issue Jul 31, 2023 · 0 comments

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@ctb
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ctb commented Jul 31, 2023

(discussion points moved here from #1353)

it would be nice to be able to load taxonomies in different formats (e.g. greengenes) 'natively' within sourmash. I think a good way to do this would be to generalize the loading code under tax/ in the same way that we generalized the loading code for sketches from files/etc in https://github.com/sourmash-bio/sourmash/pull/2428/files (see save_load.py).

There is code in #2538 for parsing greengenes.

also we could load taxonomies via URL (with fsspec).

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