Installation

The genetest module requires a Python version 3.4 or earlier. We recommend using a Python virtual environment specifically for genetest.

Python virtual environment

The following command will create a virtual environment for Python named genetest_venv in your home directory. Note that in order to use the environment, it requires to be activated.

# Creating the environment
python3 -m venv $HOME/genetest_venv

# Activating the environment
source $HOME/genetest_venv/bin/activate

Note

The text (gentest_venv) will be added at the beginning of the terminal prompt.

We recommend upgrading or installing some dependencies first.

pip install -U pip
pip install -U setuptools
pip install -U Cython
pip install -U numpy

Installing the modules

To install genetest module and all its required dependencies, use the following command (making sure the virtual environment is activated).

pip install genetest

The installation process should at least install the following dependencies.

• geneparse: parses multiple genotype file formats.
• pybgen: parses BGEN files (used by geneparse).
• pyplink: parses binary Plink files (used by geneparse).
• cyvcf2: parses VCF files (used by geneparse).

Note

If you intend to parse BGEN files with the 1.3 format specifications (or more recent), you will require the zstandard module.

pip install zstandard

Testing the installation

To test the installation, you can perform the following commands.

python -m genetest.tests
python -m geneparse.tests
python -m pyplink.tests
python -m pybgen.tests