sourmash

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useful python API functions

3

**1. A function that reads a sourmash signature file/database and raises exceptions if it runs into issues** ``` db = load_file_as_index(filename) ``` returns `None` if the file cannot be loaded....

bluegenes

Bump pypa/cibuildwheel from 2.10.2 to 2.11.1

1

Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 2.10.2 to 2.11.1. Release notes Sourced from pypa/cibuildwheel's releases. v2.11.1 🛠 Updates to the latest manylinux images, and updates CPython 3.10 to 3.10.8. v2.11.0 🌟 Adds support...

dependabot[bot]

Bump counter from 0.5.6 to 0.5.7

1

Bumps [counter](https://github.com/coriolinus/counter-rs) from 0.5.6 to 0.5.7. Release notes Sourced from counter's releases. v0.5.7: Counters are Multisets What's Changed Implement is_subset and is_superset tests by @​mjpieters in coriolinus/counter-rs#27 Implement bitwise and...

dependabot[bot]

Add documentation to `sourmash signature describe` for source file origin

1

I calculated signatures like this: ``` sourmash compute -o {output} --merge {wildcards.sample}_mgx --scaled 2000 -k 21,31,51 --track-abundance {input.r1} {input.r2} ``` and used `sourmash signature describe` to describe one signature and...

taylorreiter

[WIP] Bring mastiff into core

1

This is likely going to pick some bits from #1943, probably focusing on exposing mastiff as the `RevIndex` for the Python API. Also removes `BIGSI` and `SBT` implementations in Rust,...

luizirber

update sourmash sig export to export to CSV

3

https://github.com/dib-lab/2020-ibd/blob/master/scripts/sig_to_csv.py perhaps do this for import too?

ctb

This came up on microbial bioinformatics slack, thought I'd share - topic was selecting from many viral genomes. > it should be possible to use large-scale ANI-style analyses to select...

ctb

`sourmash tax prepare` fails with `No taxonomic identifiers found.`

9

Command and output pasted below. Lineages csv attached and reproduced! ``` sourmash tax prepare --taxonomy-csv inputs/sourmash_databases/cheesegenomes.lineages.csv -o tmp.sqldb == This is sourmash version 4.5.0. == == Please cite Brown and...

taylorreiter

[WIP] add `tax summarize`

1

This PR adds a `tax summarize` command per #2212. It also: * tackles native loading of with-lineages files produced by `tax annotate` as taxonomy spreadsheets (not yet implemented) * improves...

ctb

what are the various MAGsearch-related repos?

1

these have accumulated over time with recent wild proliferation... which ones am I missing? 😭 ## actual core repos - https://github.com/sourmash-bio/sra_search - actual `searcher` code in Rust - https://github.com/sourmash-bio/wort -...

ctb