pyjellyfish 1.1.1

A python wrapper around DNA k-kmer counter Jellfish

[![Python version][py-image]][py-link] [![PyPi version][pypi-image]][pypi-link]

Introduction

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

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

` {.sourceCode .shell} 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 the custom build command jellyfish.

` {.sourceCode .shell} source $HOME/.virtualenvs/km/bin/activate python setup.py jellyfish --version 2.2.10 `

Note that the setup script will automatically detect if jellyfish is installed on your system and build against it if found. After running the previous commands, installation will proceed as usual, skipping the jellyfish installation step.

` {.sourceCode .shell} pip install . `

#### Requirements

• Python 3.6.0 or later

[py-image]: https://img.shields.io/badge/python-3.6-blue.svg [py-link]: https://www.python.org/download/releases/3.6.0 [pypi-image]: https://img.shields.io/pypi/v/pyjellyfish.svg [pypi-link]: https://pypi.python.org/pypi/pyjellyfish