WIP: minimal adaptations from 0.9.0 release to handle new/unordered ranks

fhcrc / taxtastic

Create and maintain phylogenetic "reference packages" of biological sequences.

GNU General Public License v3.0

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WIP: minimal adaptations from 0.9.0 release to handle new/unordered ranks #141

Closed dhoogest closed 3 years ago

dhoogest commented 3 years ago

only concentrated on taxtable for now, see https://gitlab.labmed.uw.edu/molmicro/airflow/-/issues/22

dhoogest commented 3 years ago

@crosenth @nhoffman turns out that deenurp uses TaxNode.from_taxtable classmethod, which I'm not sure has been updated to accomodate unordered ranks.

I think that basically that method needs treatment similar to subcommands/taxtable.py replace_unordered, but am struggling a little bit with the logic. Can one of you take a look to see if there's a quick fix?

dhoogest commented 3 years ago

Closing this PR in favor of https://github.com/fhcrc/taxtastic/issues/142