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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 Jun 2015
Publisher
ISBN-13 9781782175117
Length 306 pages
Edition 1st Edition
Languages
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Toc

Table of Contents (11) Chapters Close

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

Geo-referencing GBIF datasets


Here, we will work with the geo-referenced data from the GBIF dataset. We will take this opportunity to see how to interface 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 on both before starting. Tile Map Services (http://wiki.openstreetmap.org/wiki/TMS) will be quite an important concept to get a basic grasp of. 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 using conda install pillow or pip install pillow. You can find this content in the 07_Other/GBIF_extra.ipynb notebook.

How to do it...

Take a look at the following steps:

  1. First, let's define a function to get a map tile (a PNG image...

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