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Upgrade sourmash categorize to take LCA databases as well as SBT. #829

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ctb opened this issue Jan 7, 2020 · 5 comments · Fixed by #1392
Closed

Upgrade sourmash categorize to take LCA databases as well as SBT. #829

ctb opened this issue Jan 7, 2020 · 5 comments · Fixed by #1392

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@ctb
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ctb commented Jan 7, 2020

sourmash categorize should be able to take an LCA database as well as an SBT.

There are a lot of other things we could do upgrade categorize as well; could brainstorm a little about what it is doing, should be doing, and could be doing.

@ctb
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ctb commented Jan 8, 2020

Two idle thoughts --

  • we could move categorize to the --db and --query command line UX used in sourmash lca classify, to permit multiple db.
  • this is an opportunity to add a generic sourmash.load function that would load any kind of database.

@ctb
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ctb commented May 3, 2020

ref #978

@ctb
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ctb commented Jun 29, 2020

whups, turns out that categorize ignores self, and cannot be used efficiently on LCA databases.

@ctb
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ctb commented Jun 29, 2020

also, here we probably want to remove LoadSingleSignature in favor of new load_file_as_signatures function.

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ctb commented Mar 28, 2021

This might be fixed in #1406.

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