genetest - A Python module for statistical genetics

The genetest module includes a script that will perform various statistical analysis on genetics data (e.g. hard calls, imputed data, etc.).

Dependencies

The tool requires a standard Python installation (3.4 or higher are supported) with the following modules:

1. numpy version 1.12 or latest
2. pandas version 0.19 or latest
3. stasmodels version 0.8 or latest
4. grako version 3.10 or latest
5. geneparse version 0.1 or latest

The tool has been tested on Linux only, but should work on MacOS operating systems as well.

Documentation

Documentation is available at http://pgxcentre.github.io/genetest/.

Installation

Using pip:

pip install genetest

Updating

To update the module using pip:

pip install -U genetest

Testing

To test the module, just perform the following command:

$ python -m genetest.tests
...
----------------------------------------------------------------------
Ran 104 tests in 1.684s

OK (skipped=41, expected failures=1)