Bioinformatics with Python Cookbook - Second Edition

Getting ready

You will need to have run the previous two recipes and should have the hapmap10_auto_noofs_2.gp and hapmap10_auto_noofs_2.pops files downloaded. We will also use the metadata file that we downloaded in the first recipe. For this code to work, you will need to install Genepop from either http://kimura.univ-montp2.fr/~rousset/Genepop.htm or, if you're using Anaconda Python, by using conda install -c bioconda genepop. We will use the interface provided by Biopython to execute Genepop and parse its output files.

There is a Notebook file with this recipe, called Chapter04/Exploratory_Analysis.ipynb, but it will still require running the previous two Notebooks in this chapter in order for the required files to be generated.