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)

Traversing genome annotations

Having a genome sequence is interesting, but we will want to extract features from it, such as genes, exons, and coding sequences. This type of annotation information is made available in Generic Feature Format (GFF) and General Transfer Format (GTF) files. In this recipe, we will learn how to parse and analyze GFF files while using the annotation of the Anopheles gambiae genome as an example.

Getting ready

Use the Chapter05/ notebook file, which is provided in the code bundle for this book. The up-to-date location of the GFF file that we will be using can be found at the top of the notebook.

You will need to install gffutils:

conda install -c bioconda gffutils

Now, we’re ready to start.

How to do it...

Follow these steps:

  1. Let’s start by creating an annotation database with gffutils, based on our GFF file:
    import gffutils
    import sqlite3
        db = gffutils.create_db('gambiae...