biokit 0.4.1

BioKit

Bioinformatics tools in Python

note:	BioKit is tested with Travis for the following Python version: 2.7.9 3.4.2 and 3.5.0
contributions:	Please join https://github.com/biokit/biokit and share your notebooks https://github.com/biokit/biobooks/
issues:	Please use https://github.com/biokit/biokit/issues

Contents

BioKit is a set of tools gathered from several other Python packages. The goal is to gather tools that should be useful to develop computational biology software. Biokit contains a few plotting tools (viz module), some statistical analysis (mixture model), some tools to access to Taxon and GO identifier, some basic tools to manipulate sequences and so on. It is linked to BioServices package to provide access to biological resources. Lots of biological software are developed in R. We have also added a module to ease the installation and usage of R tools within BioKit.

Installation

pip install biokit

Note about testing

From travis, coverage is about 50% at the moment, which is low because some tests are ignored. Tests ignored are those that are slow or required R dependencies. To be ignored, we filled the setup.cfg with an option called attr. IF you comment that attribute in the setup.cfg and run

python setup.py nosetests

You should reach a higher coverage (about 70%)