C. Titus Brown

tax in zip files; supporting multiple taxonomies with command-line switches

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In https://github.com/sourmash-bio/sourmash/issues/2154, we've been talking about how to include taxonomic information in zipfiles, and I've been trying to figure out how that would work at the command line. But all...

In https://github.com/sourmash-bio/sourmash/pull/2195, we added generic support for gzipped CSVs. In most of the codebase, we use `FileInputCSV` which will auto-detect gzipped files, but this is not yet usable by the...

In https://github.com/sourmash-bio/sourmash/pull/2204, we added `--fail-on-empty-database/--no-fail-on-empty-database`, with the default being `--fail`. For v5, we should consider changing this to `--no-fail`.

[EXP] support taxonomies in zipfiles

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This PR supports automatic detection/loading of taxonomies from zip files (including zip databases), when the taxonomy file is named `SOURMASH-TAXONOMY.csv`. Fixes https://github.com/sourmash-bio/sourmash/issues/2012

translating between taxonomies - maybe a `sourmash tax translate`?

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there is some interest in translating between taxonomies (GTDB, NCBI, and maybe LINS), and this is something that we should be able to do somewhat straightforwardly in sourmash. relevant issues...

dynamically adapt `scaled` for gather

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conversation with @bluegenes - >for sourmash gather, we could (a) set scaled automatically based on the threshold-bp (whether default or specified by user). This would be a move towards “automatic”...

tutorial: k-mer-based analysis of metagenomes with sourmash

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from STAMPS 2022 - https://hackmd.io/vYaK2UngTWSkKmcpQMP6NA associated presentations and tutorials - [taylor on assembly and binning](https://github.com/mblstamps/stamps2022/blob/main/assembly_and_binning/20220725_stamps2022_assembly_and_binning_full.pdf) [tutorial on assembly and binning with ATLAS](https://github.com/mblstamps/stamps2022/blob/main/assembly_and_binning/tutorial_assembly_and_binning.md) [titus on assembly free analysis with k-mers](https://github.com/mblstamps/stamps2022/blob/main/kmers_and_sourmash/2022-stamps-assembly-free%20class.pdf) [titus...

consider further optimization/exploitation of `FrozenMinHash`

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Over in https://github.com/sourmash-bio/sourmash/issues/2128, I wrote >>Also while I am at it, any speed/memory advantage using FrozenHashes? >Not a big one. The main goal of FrozenMinHash is to enable future optimizations...

consider eliminating all of the identifier version removal in `lca` and `tax`

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when I first implemented the LCA stuff, I was young and foolish and thought there was a point to allowing flexibility in removing identifier versions - e.g. converting `GCF_000422665.1` into...

`lca index` could use some upgrading

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First, it doesn't pick up the k-mer size from the available signatures, so you have to specify it explicitly on the command line (unlike `sourmash index`, where you only need...