This repository provides tools for population genomic analyses. It mainly contains python3 libraries and scripts, but also some shell and awk scripts.
You can either just download a .zip and decompress, or clone the respository
git clone https://github.com/feilchenfeldt/pypopgen3.git
In order for the python modules to be found by your system python, you need to add the local path to the repository to your python path. To achieve this permanently, add a .pth file containing this path to your python site-packages folder. For example, you to once:
#locate your python site package folder
python -m site --user-site
#outputs <your_site_package_folder>
cd <your_site_package_folder>
echo <path_to_parent_folder_of_pypopgen3> >> mypackages.pth
Alternatively, you can just add the folder to the python path in each python session in which you want to use pypopgen3.
import sys
sys.path.append('<path_to_parent_folder_of_pypopgen3>')
The python modules depend on some python packages, including numpy, pandas, ete3, matplotlib. You will need to install these packages manually, for example with conda or pip.
Start python(3) and load modules from pypopgen3 like
from pypopgen3.modules import treetools