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provide generic way(s) to select taxonomic lineages on sourmash commands #2186

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ctb opened this issue Aug 7, 2022 · 1 comment
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@ctb
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ctb commented Aug 7, 2022

starting from discussion here,

Simple use case: I know the family of my organism and just want to get genbank/gtdb matches to anything in that family.

and here:

When we do this, it would be really neat to allow signature selection on the taxonomy, e.g. --include s__Phaeobacter. Yes, we can currently do this with sig grep or picklists using the taxonomy file, but seamless integration would be great.

I wrote:

This doesn't belong in sourmash tax which is specific to taxonomy manipulations - where this really belongs is somewhere generic to all the other sourmash subcommands,as with picklists and --include/--exclude. We want the rest of sourmash to "understand" taxonomies when they are present.

and this then connects with other metadata ideas e.g. stuff in #2180 and #1916.

@ctb ctb changed the title provide generic way(s) to select taxonomy on sourmash commands provide generic way(s) to select taxonomic lineages on sourmash commands Aug 14, 2022
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ctb commented Aug 15, 2022

this could easily be done with standalone manifests - see #1916.

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