Exploring a dataset with Bio.PopGen
In this chapter, we will perform an initial exploratory analysis of one of our generated datasets. We will analyze the 10 percent sampling of chromosome 2 without the offspring. We will look for monomorphic loci (in this case, SNPs) across populations along with how to research minimum allele frequencies and expected heterozygosities.
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. We will also use the metadata file downloaded in the first recipe.
For this code to work, you will need to install Genepop from http://kimura.univ-montp2.fr/~rousset/Genepop.htm. We will use the interface provided by Biopython to execute ...
Get Bioinformatics with Python Cookbook now with the O’Reilly learning platform.
O’Reilly members experience books, live events, courses curated by job role, and more from O’Reilly and nearly 200 top publishers.
