Bioinformatics with Python Cookbook - Second Edition

How to do it...

Take a look at the following steps:

1. Let's load the metadata, as follows:

f = open('relationships_w_pops_121708.txt')ind_pop = {}f.readline() # headerfor l in f:    toks = l.rstrip().split('\t')    fam_id = toks[0]    ind_id = toks[1]    pop = toks[-1]    ind_pop['/'.join([fam_id, ind_id])] = popf.close()ind_pop['2469/NA20281'] = ind_pop['2805/NA20281']

In this case, we will add an entry that is consistent with what is available in the PLINK file.

2. Let's convert the PLINK file into the EIGENSOFT format:

from genomics.popgen.plink.convert import to_eigento_eigen('hapmap10_auto_noofs_ld_12', 'hapmap10_auto_noofs_ld_12')

This uses a function that I have written to convert from PLINK to the EIGENSOFT format. This is mostly text manipulation—not ...