biojup

A collection of custom jupyter notebook widget extensions for biojs visualization components using the jupyter notebook. Uses biopython for parsing and biojs for visualization.

Install

Setup the environment

To install biojup from git you will need Jupyter notebook and ipywidgets. Install using conda is the simplest

conda create -n venv jupyter ipywidgets numpy biopython
source activate venv

Alternatively, you can setup a virtual environment (using virtualenv) and install requirements from pip.

vitualenv venv
source venv/bin/activate
pip install -r requirements.txt

Now to install biojup, run the following commands.

git clone https://github.com/zsameem/biojup.git
cd biojup

For a normal install do

python setup.py install

For dev install

python setup.py develop

Usage

Render MSA visualizations from clustal files. See examples