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

Georeferencing GBIF datasets


In this recipe, we will work with the geo-referenced data from the GBIF dataset. We will take this opportunity to look at how to interface Python with OpenStreetMap (https://www.openstreetmap.org ), a freely available mapping service. We will also use a Python image processing library called Pillow (http://python-pillow.github.io/), which is based on PIL. You may want to read a little bit about both before starting. Tile Map Services (http://wiki.openstreetmap.org/wiki/TMS) is quite an important concept to get a basic grasp of. The GBIF and OpenStreetMap tiles are available behind REST services.

In our example, we will try to extract information from GBIF using the geographic coordinates of the Galápagos archipelago.

Getting ready

You will need to install Pillow by using conda install pillow or pip install pillow.

You can find this content in the Chapter10/GBIF_extra.ipynb Notebook.

How to do it...

Let's take a look at the following steps:

  1. First, let's define a function...