C. Titus Brown

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

1

starting from discussion [here](https://github.com/sourmash-bio/sourmash/pull/2178#issuecomment-1205438578), >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](https://github.com/sourmash-bio/sourmash/issues/2154#issuecomment-1200247625): > When...

add `-n/--num-results` to docs page for sourmash search.

1

per user suggestion via matrix chat. and/or display how to adjust it in search output.

thoughts on `Storage`, manifests, etc.

1

This issue extracts the leftover bits from https://github.com/sourmash-bio/sourmash/issues/1352, mostly to do with evolving the `Storage` class and SBTs to better intersect. From [comment](https://github.com/sourmash-bio/sourmash/issues/1352#issuecomment-797685247) - @luizirber: > Quick comment on supporting...

reimplement wrapping of `Index` classes from command-line for lower memory

1

The `MultiIndex` class is used for four purposes: * loading one or more signatures from JSON via stdin * loading one or more signatures from a JSON file * loading...

should `_load_databases` indicate how many incompatible signatures were filtered out?

4

After https://github.com/dib-lab/sourmash/pull/1420, we run the risk of silently selecting away large numbers of incompatible signatures. Perhaps we should print this out in the `_load_database` code? See for example `test_search_traverse_incompatible` as...

simplify/refactor `load_*` sig/db functions in `sourmash_args.py`

8

There's a confusing mess of loading functions in `sourmash_args.py` that's slowly converging as we simplify and refactor our Index handling code. In no particular order, there's **query loading code**, `load_query_signature`....

should we remove `is_database` from `Index` objects?

2

I don't think it serves a purpose any more; IIRC it was used to indicate that 'number of signatures' was not a useful designation Back When, but that is not...

change `lca` subcommands to use `tax` taxonomy code/handling

1

The CSV parsing code in `src/sourmash/lca/command_index.py` is just terribly complicated and parts of it (`--no-headers`, for example) are not even tested. Given the ongoing maintenance and expansion of `tax` taxonomy...

From https://github.com/sourmash-bio/sourmash/pull/2178, @bluegenes: > More complicated use case that would be _really_ neat to enable: run prefetch against, e.g. genus-level representative database. Then run gather and use the prefetch output...

provide taxonomy operations that work on semicolon-separated lineages

2

when we use `sourmash tax annotate` on gather results, we produce a column with semicolon-separated lineages in it. we don't have many (any?) sourmash subcommands that natively ingest that format,...