Book Image

Bioinformatics with Python Cookbook - Second Edition

By : Tiago Antao
Book Image

Bioinformatics with Python Cookbook - Second 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. This book covers next-generation sequencing, genomics, metagenomics, population genetics, phylogenetics, and proteomics. You'll learn modern programming techniques to analyze large amounts of biological data. With the help of real-world examples, you'll convert, analyze, and visualize datasets using various Python tools and libraries. This book will help you get a better understanding of working with a Galaxy server, which is the most widely used bioinformatics web-based pipeline system. This updated edition also includes advanced next-generation sequencing filtering techniques. You'll also explore topics such as SNP discovery using statistical approaches under high-performance computing frameworks such as Dask and Spark. By the end of this book, you'll be able to use and implement modern programming techniques and frameworks to deal with the ever-increasing deluge of bioinformatics data.
Table of Contents (16 chapters)
Title Page
About Packt
Contributors
Preface
Index

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 look at how to parse and analyze GFF files, using the annotation of the Anopheles gambiae genome as an example.

Getting ready

Use the Chapter03/Annotations.ipynb Notebook file, which is provided in the code bundle of this book.

How to do it...

Let's take a look at the following steps:

  1. Let's start by creating an annotation database with gffutils, based on our GFF file:
import gffutils
import sqlite3
try:
    db = gffutils.create_db('gambiae.gff.gz', 'ag.db')
except sqlite3.OperationalError:
db = gffutils.FeatureDB('ag.db')

The gffutils library creates a SQLite database to store annotations efficiently. Here, we will try to create the database, but if it already exists, we will use the existing...