pyo3-branchwater 0.6.3

fast search and gather extensions for sourmash

pyo3_branchwater

tl;dr Do fast and low-memory search/gather of many sourmash sketches via a sourmash plugin.

Details

This repo contains a PyO3-based Python wrapper around the core branchwater code. Branchwater is a fast, low-memory and multithreaded application for searching very large collections of FracMinHash sketches as generated by sourmash.

For details, see the Rust code in src/ and Python wrapper in python/.

Uses pyo3 for the Python-to-Rust wrapping.

This functionality can be used from within sourmash as a command-line plugin; see below quickstart.

Documentation

There is a quickstart below, as well as more documentation here.

Quickstart for manysearch.

To try out, you'll need to install a branch of sourmash that contains sourmash#2438.

This quickstart demonstrates manysearch using the 64 genomes from Awad et al., 2017.

First, install this code.

Install this repo in developer mode:

pip install -e .

Second, download sketches.

The following commands will download sourmash sketches for them and unpack them into the directory podar-ref/:

mkdir -p podar-ref
curl -JLO https://osf.io/4t6cq/download
unzip -u podar-reference-genomes-updated-sigs-2017.06.10.zip

Third, create lists of query and subject files.

manysearch takes in lists of signatures to search, so we need to create those files:

ls -1 podar-ref/{2,47,63}.* > query-list.txt
ls -1 podar-ref/* > podar-ref-list.txt

Fourth: Execute!

Now run manysearch:

sourmash scripts manysearch query-list.txt podar-ref-list.txt -o results.csv

You will (hopefully ;) see a set of results in results.csv.

Debugging help

If your file lists are not working properly, try running:

sourmash sig summarize query-list.txt
sourmash sig summarize podar-ref-list.txt

to make sure everything can be loaded.

Future thoughts

The speed and functions of this code will probably be brought into sourmash core in the future, most likely as part of sourmash#2230. However, in the meantime, this is a fun side project that makes use of sourmash plugins and Rust to provide some fast functionality that may be of use to some people, and it can serve as a testbed for future sourmash functionality.

Developer notes

Installing a development environment

You'll need sourmash, rust, and maturin.

A simple way to get up and running is to run:

mamba env create -n branchwatever-dev -f environment.yml

in the top directory of the repo, and then activate the environment and install in editable mode:

mamba activate branchwater-dev
pip install -e .

Running the tests locally

Executing:

make test

will run the Python tests.

Generating a release

1. Bump version number in Cargo.toml and run make to update Cargo.lock. Then commit and push to origin/main.

2. Make a new release on github with a matching version tag.

3. Then pull, and:

make sdist
make upload_sdist

to create a new release on PyPI.

Building wheels

You can build a release wheel for your current platform with:

make wheel

and it will be placed under target/wheels/.

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License

This software is under the AGPL license. Please see LICENSE.txt.

Authors

• Luiz Irber
• C. Titus Brown
• Mohamed Abuelanin
• N. Tessa Pierce-Ward