support gzip and/or zipped taxonomy CSVs?

[ctb]

we should support .gz for our input CSVs.

we could also support .zip files that contain a SOURMASH-TAXONOMY.csv file or something. Or even have standard names for genbank, gtdb, and lins taxonomies.

[ctb]

taxonomy csv.gz files implemented in #2178.

[ctb]

so #2195 is implementing CSV loading from zipfiles, and it currently uses SOURMASH-TAXONOMY.csv as the filename inside the zip from which it will load taxonomy information. Is this a good name?

Separately, note that there is no sourmash tax command that takes in both a zipfile database and a taxonomy so at least for the moment this code doesn't simplify the CLI that much. However, it could simplify sourmash lca index a bit.

[bluegenes]

so #2195 is implementing CSV loading from zipfiles, and it currently uses SOURMASH-TAXONOMY.csv as the filename inside the zip from which it will load taxonomy information. Is this a good name?

Idea to allow multiple taxonomies per db here: #2195 (comment)

Separately, note that there is no sourmash tax command that takes in both a zipfile database and a taxonomy so at least for the moment this code doesn't simplify the CLI that much. However, it could simplify sourmash lca index a bit.

Right... I guess I'm thinking tax commands could take in a database and just read the taxonomy file(s) from it. That way folks can just use a single file, rather than needing to mess with two separate ones.

[ctb]

Right... I guess I'm thinking tax commands could take in a database and just read the taxonomy file(s) from it. That way folks can just use a single file, rather than needing to mess with two separate ones.

ok - so it doesn't simplify the CLI, but does remove the need to deal with an extra file. Got it!

[ctb]

note, removed the SOURMASH-TAXONOMY name from #2195; will address over in #2154.

[ctb]

Trying to figure out how distributing multiple taxonomies in a zip file would work at the command line.

The most obvious idea is:

sourmash tax classify -g gather.csv -t gtdb-xyz.zip --gtdb

which would load GTDB-TAXONOMY.csv from gtdb-xyz.zip, vs

sourmash tax classify -g gather.csv -t gtdb-xyz.zip --ncbi

which would load NCBI-TAXONOMY.csv from gtdb-xyz.zip.

Then we could potentially add --lins later on for #1813.

Alternative command-line switches would be --tax-type ncbi or something but I feel like --ncbi and --gtdb are probably simplest and easiest to remember.

[ctb]

@bluegenes thoughts ^^^ ?

[bluegenes]

I like --gtdb and --ncbi, especially since I can't see us integrating so many taxonomies that having an argument per tax type would be unwieldy.

--lins definitely useful when we get there!