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Arcadia-Science / sourmashconsumr

Working with the outputs of sourmash in R
https://arcadia-science.github.io/sourmashconsumr/
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Add functions to transform from sourmash taxonomy annotate outputs to phyloseq object #27

Closed taylorreiter closed 2 years ago

taylorreiter commented 2 years ago

As annotated here: https://taylorreiter.github.io/2022-07-28-From-raw-metagenome-reads-to-phyloseq-taxonomy-table-using-sourmash-gather-and-sourmash-taxonomy/

This function works for both GTDB and GenBank data base runs.

Imports the outputs of sourmash taxonomy annotate to a phyloseq object. Once in a phyloseq object, the object can be used for any sort of phyloseq analysis.

taylorreiter commented 2 years ago

LGTM! I have a general question/comment that I just now noticed - for functions related to a package such as metacoder/phyloseq the script is just named the package name such as phyloseq.R - is this fine in terms of clarity?

I'll change them! I'll go with from_taxonomy_annotate_to_metacoder.R and from_taxonomy_annotate_to_phyloseq.R