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Bioinformatics with Python Cookbook

You're reading from   Bioinformatics with Python Cookbook Learn how to use modern Python bioinformatics libraries and applications to do cutting-edge research in computational biology

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Product type Paperback
Published in Nov 2018
Publisher Packt
ISBN-13 9781789344691
Length 360 pages
Edition 2nd Edition
Languages
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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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Table of Contents (12) Chapters Close

Preface 1. Python and the Surrounding Software Ecology FREE CHAPTER 2. Next-Generation Sequencing 3. Working with Genomes 4. Population Genetics 5. Population Genetics Simulation 6. Phylogenetics 7. Using the Protein Data Bank 8. Bioinformatics Pipelines 9. Python for Big Genomics Datasets 10. Other Topics in Bioinformatics 11. Advanced NGS Processing

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...
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