Bioinformatics tools in Python
- note
BioKit is tested with Travis for the following Python version: 2.7.9 3.3.5, 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
BioKit is a set of tools gathered from several other Python packages. So far, it contains a few plotting tools (viz module), some statistical analysis, 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.
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 nosetestsYou should reach a higher coverage (about 70%)