Bioinformatics with Python Cookbook - Second Edition

How to do it...

Take a look at the following steps:

1. First, let's compute F-statistics (F_ST, F_IS, and F_IT ) for our dataset with all 11 populations, as follows:

from Bio.PopGen.GenePop import Controller as gpcmy_pops = [l.rstrip() for l in open('hapmap10_auto_noofs_2.pops')]num_pops = len(my_pops)ctrl = gpc.GenePopController()(multi_fis, multi_fst, multi_fit), f_iter = ctrl.calc_fst_all('hapmap10_auto_noofs_2.gp')print(multi_fis, multi_fst, multi_fit)

As with the previous recipe, we will first load population names and initialize a controller to interact with the Genepop application. Then, we will calculate various F-statistics.

The function will return a loci iterator that returns several F-statistics per loci as the last parameter. You ...