Bioinformatics with Python Cookbook - Second Edition

How to do it...

Let's take a look at the following steps:

1. The first thing that we do is select an individual per family at most. This step is not strictly necessary (as opposed to many other recipes where having related individuals will bias the analysis), but we will do it anyway:

from collections import defaultdictimport gzipimport scipyimport scipy.stats as statsgermline_file = 'good.match.gz'sample_file = 'integrated_call_samples.20101123.ped'inds = set()ind_pop = {}selected_inds = {}pop_inds = defaultdict(list)with gzip.open(germline_file, 'rt', encoding='utf-8') as f:    for l in f:        toks = l.rstrip().split()        inds.add(toks[1])        inds.add(toks[3])with open(sample_file, 'rt', encoding='utf-8') as f:    f.readline()  # header    for l in f: toks ...