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Bioinformatics with Python Cookbook

You're reading from   Bioinformatics with Python Cookbook Use modern Python libraries and applications to solve real-world computational biology problems

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Product type Paperback
Published in Sep 2022
Publisher Packt
ISBN-13 9781803236421
Length 360 pages
Edition 3rd Edition
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Author (1):
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Tiago Antao Tiago Antao
Author Profile Icon Tiago Antao
Tiago Antao
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Toc

Table of Contents (15) Chapters Close

Preface 1. Chapter 1: Python and the Surrounding Software Ecology 2. Chapter 2: Getting to Know NumPy, pandas, Arrow, and Matplotlib FREE CHAPTER 3. Chapter 3: Next-Generation Sequencing 4. Chapter 4: Advanced NGS Data Processing 5. Chapter 5: Working with Genomes 6. Chapter 6: Population Genetics 7. Chapter 7: Phylogenetics 8. Chapter 8: Using the Protein Data Bank 9. Chapter 9: Bioinformatics Pipelines 10. Chapter 10: Machine Learning for Bioinformatics 11. Chapter 11: Parallel Processing with Dask and Zarr 12. Chapter 12: Functional Programming for Bioinformatics 13. Index 14. Other Books You May Enjoy

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/Annotations.py 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
    try:
        db = gffutils.create_db('gambiae...
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