pyJellyfish : Python wrapper around Jellyfish

Introduction

This tool essentially serves as an installer for the k-mer counter Jellyfish for use with Python. A small bundle of utilities is also included. A typical use-case for this package would be km: https://github.com/iric-soft/km.

Citing

• Guillaume Marcais and Carl Kingsford, A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics (2011) 27(6): 764-770; doi: https://doi.org/10.1093/bioinformatics/btr011

Install

With pip

python -m venv $HOME/.virtualenvs/km
source $HOME/.virtualenvs/km/bin/activate
pip install --upgrade pip
pip install .

Options

Note that pyJellyfish has an option to manually specify which Jellyfish version one wishes to build against. This can be done by running pip install with specific arguments:

source $HOME/.virtualenvs/km/bin/activate
pip install . --config-settings="--build-option='--jf-version=2.3.0'"

For building pyJellyfish distributions, use the build command:

source $HOME/.virtualenvs/km/bin/activate
pip install build
python -m build --config-setting="--build-option='--jf-version=2.3.0'"

Requirements

• Python 3.8.0 or later