Bioinformatics with Python Cookbook: Use modern Python libraries and applications to solve real-world computational biology problems, 3rd Edition.
Our rebelScience articles and videos are dedicated to engineering primarily. We are learning how to create bioinformatics tools in Python from scratch. Some bioinformaticians are interested in using existing tools, and analyzing the data. This book is amazing for that.
I found this book very useful, as it covers a whole range of topics. From functional programming in Python to Machine Learning for bioinformatics. As the title of the book states, it does indeed cover real-world bioinformatics problems, and not just random algorithms and Python libraries.
While reading some of the chapters of this book, I found them so useful, I really wanted to recreate some of the tools, used in those chapters, from scratch, in Python. Even though this book is primarily about “how to use tools” and not “how to create tools” for bioinformatics, it provides a very good overview of the available tools one could attempt to reproduce (write from scratch) with the goal of learning how the underlying algorithms work. We will be adding a few of those things to our Genome Toolkit. Chapter on PyMOL module, that lets you generate 3D protein structures, was especially interesting.
I would say this is not a very beginner-friendly book. You are expected to know Python on a very good level.
Overall, a very good book. If you are coming from biology, it will help you to set up, and get up-to-speed with all the latest (as it is the new, 3rd Edition) bioinformatics tools. If you are coming from the engineering/programming, you can use it as a reference on available libraries, modules and other tools, you can integrate into your software.
I encourage you to review chapters of this book, to see how comprehensive the coverage is: