Book Image

Bioinformatics with Python Cookbook - Third Edition

By : Tiago Antao
Book Image

Bioinformatics with Python Cookbook - Third Edition

By: Tiago Antao

Overview of this book

Bioinformatics is an active research field that uses a range of simple-to-advanced computations to extract valuable information from biological data, and this book will show you how to manage these tasks using Python. This updated third edition of the Bioinformatics with Python Cookbook begins with a quick overview of the various tools and libraries in the Python ecosystem that will help you convert, analyze, and visualize biological datasets. Next, you'll cover key techniques for next-generation sequencing, single-cell analysis, genomics, metagenomics, population genetics, phylogenetics, and proteomics with the help of real-world examples. You'll learn how to work with important pipeline systems, such as Galaxy servers and Snakemake, and understand the various modules in Python for functional and asynchronous programming. This book will also help you explore topics such as SNP discovery using statistical approaches under high-performance computing frameworks, including Dask and Spark. In addition to this, you’ll explore the application of machine learning algorithms in bioinformatics. By the end of this bioinformatics Python book, you'll be equipped with the knowledge you need to implement the latest programming techniques and frameworks, empowering you to deal with bioinformatics data on every scale.
Table of Contents (15 chapters)

The limits of recursion with Python

Recursion – a function calling itself – is a fundamental concept in functional programming. Many languages that cater to functional programming are able to recurse ad infinitum. Python is not one of those languages. You can use recursion in Python, but you have to be aware of its limits, namely that recursion incurs quite a lot of memory costs and that it cannot be used to replace iteration – a typical case when writing functional programs.

To see the limits of recursion with Python, we are going to implement the Fibonacci sequence in several ways. As a reminder, Fibonacci can be defined as follows:

Fib(0) = 0
Fib(1) = 1
Fib(n) = Fib(n -1) + Fib(n –2)

We are also computing the factorial function, but in this case only in a recursive way:

Fact(1) = 1
Fact(n) = n * Fact(n –1 )

Getting ready

Our code is available in Chapter12/

How to do it...

Follow these steps to get started: