pyJellyfish : Python wrapper around Jellyfish (k-mer counter)

NOTE

This install script is not yet PEP517 compliant, which means the wheel and setuptools packages need to be in your environment.

Do not forget this line when setting up your environment (see below):

pip install --upgrade setuptools wheel pip

Introduction

This tool essentially serves as an installer for Jellyfish for use with Python. A small bundle of utilities is also included.

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 setuptools wheel pip
pip install .

Options

Additionally, pyJellyfish contains an option to manually specify which Jellyfish version one wishes to build against. This can be done by running setup.py with the custom build command jellyfish.

source $HOME/.virtualenvs/km/bin/activate
python setup.py jellyfish --version 2.2.10

Note that the setup script will automatically detect if jellyfish has already been built and use that instead of re-running the jellyfish step. After running the previous command, installation will proceed as usual.

pip install .

Requirements

• Python 3.6.0 or later