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MRG: modify annotate for flexibility #2518

Merged
merged 102 commits into from
Apr 5, 2023
Merged

MRG: modify annotate for flexibility #2518

merged 102 commits into from
Apr 5, 2023

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bluegenes
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@bluegenes bluegenes commented Mar 8, 2023

tax annotate does not need to require the gather columns that are required for tax metagenome and tax genome.
These got especially strict after the recent taxonomy refactor.

This PR modifies tax annotate so that it is just looking for a column it can match to taxonomy assignments. This will allow annotation of search, prefetch files and any other file with a good column name.

(new) Acceptable column names, in the order annotate will look for them:

  • name (in search, gather output)
  • match_name (in prefetch output)
  • ident
  • accession

Are there any others we should add? We could also let the user specify a column name via cli input, but I don't see the need to enable it unless requested?

Closes #2472

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@ctb ctb left a comment

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nice and clean! LGTM!

src/sourmash/tax/__main__.py Show resolved Hide resolved
Base automatically changed from lins-v2 to latest April 5, 2023 14:00
@bluegenes bluegenes changed the base branch from latest to genome-lins April 5, 2023 15:10
Base automatically changed from genome-lins to latest April 5, 2023 16:42
@bluegenes bluegenes enabled auto-merge (squash) April 5, 2023 17:23
@ctb ctb disabled auto-merge April 5, 2023 18:39
@ctb ctb merged commit 7e90715 into latest Apr 5, 2023
@ctb ctb deleted the flex-annotate branch April 5, 2023 18:39
@ctb ctb mentioned this pull request Apr 6, 2023
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Add lineages column in prefetch csv output
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