First, we require some prerequisites before getting started with this tutorial. This tutorial assumes that you have some understanding of python, and have it installed on your computer.


  • conda. This is optional, but will make it easier to manage project requirements.
  • python 3.6
  • git
  • a TestPyPI account. This is optional, but is required if you want upload a test package to TestPyPI.

Creating a conda environment

We use conda to manage requirements for different projects. You may be working on multiple python projects that require different packages and versions. To manage this, we can create different conda environments for each project. Although this step is not necessary, it will help you manage your projects so they do not conflict.

Let’s create a conda environment for our project:

conda create -n PlotMAPQ python=3.6 pip
source activate PlotMAPQ

Getting the code

Next, we will want to pull the code for this tutorial. This is a finished project and includes all the code you need. You can use this repository as a reference for future projects.

Clone the repository:

git clone
cd CompBIO_Seminar_2020

You now have everything you need. Let’s get started!