Tessa Pierce Ward

[WIP] fix tax argument parsing

1

Fixes #2213 - [x] add `action= 'extend'` to appropriate args - [ ] add some tests to make sure args are passed in appropriately

[MRG] use stderr for test output printing

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Sets `sys.stdout=sys.stderr`, per https://github.com/sourmash-bio/sourmash/pull/2138#issuecomment-1216779696. Suggested as a solution to `pytest-xdist` not printing test output here: https://github.com/pytest-dev/pytest-xdist/issues/354#issuecomment-430502446 restores test output printing @ctb is this a desired solution? Or did you find...

6-frame translated sketches are useful for searching protein databases, but also come with a few complications. - translated signatures should not be compared to each other (containment, jaccard, ANI will...

specifying multiple lineages for `sourmash tax` commands

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for sourmash `tax`, specify multiple taxonomy files like so: `sourmash tax annotate -g GATHER.csv --taxonomy DB_1.csv DB_2.csv` Here, `DB_1` and `DB_2` taxonomies will be loaded, with `DB_2` overwriting any shared...

check that reported `search` containment ani is using the right containment direction

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for @ctb - If we're running `sourmash search`, are we producing the containment of the query in the reference, or the reference in the query? Thinking about it now I...

add lineages/metadata summarization utility?

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With #2211, I _think_ database preparation is going ok in one of the two scenarios, but we don't have a good `sourmash sig summarize`-style utility to take in a lineages...

`sourmash tax prepare` sometimes fails to create db?

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I'm seeing some odd behavior, but not sure if this is server-related or sourmash related. On a compute node, `tax prepare` will refuse to prepare a new lineages database, saying...

expanding database selection methods: metadata

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Discussion in https://github.com/sourmash-bio/sourmash/pull/2178 reminded me of some things @ctb and I talked around a while back, and that seem like far less of a leap now. With new selection and...

When running large databases (e.g. building a new alphabet or ksize for all of gtdb), it would help to have some progress output from `fromfile`, since we have the whole...

BIOM format would enable direct import as a phyloseq object (ref #2156) and is a standard format folks can use downstream. BIOM version 2.1 spec: https://biom-format.org/documentation/format_versions/biom-2.1.html early examples seem really...