upgrade `sourmash watch` to take multiple kinds of databases

sourmash-bio / sourmash

Quickly search, compare, and analyze genomic and metagenomic data sets.

http://sourmash.readthedocs.io/en/latest/

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Open ctb opened 4 years ago

ctb commented 4 years ago

similar to #829

probably should use new sourmash_args.load_file_as_signatures function re #1059

ctb commented 3 years ago

(we could also just deprecate it, but it's cool demo functionality even if no one is using it 🤔 )

ctb commented 3 years ago

I think this ends up being reasonably straightforward now?

in the watch(...) function in commands.py, replace tree = load_sbt_index(args.sbt_name) with db = load_file_as_index; note that other than the code in the if ksize is None branch that figures out ksize to use, tree.search(...) is now generic to all Index subclasses so should Just Work with any db;
adjust rest of code accordingly.

There may be reasons this won't work easily, but reading through the code it's worth a try!