anhima.util - Miscellaneous utilities

In [1]:

    

from __future__ import print_function, division
import sys
import numpy as np
import random
# import anhima
# dev imports
sys.path.insert(0, '..')
%reload_ext autoreload
%autoreload 1
%aimport anhima.util


    

In [2]:

    

n_variants = 100000
n_samples = 1000
genotypes = np.random.randint(0, 2, size=(n_variants, n_samples, 2)).astype('i1')
genotypes.shape, genotypes.nbytes / 1e6


    

    
Out[2]:





((100000, 1000, 2), 200.0)

In [3]:

    

gn = anhima.gt.as_n_alt(genotypes)


    

In [4]:

    

gn2 = anhima.util.block_apply(anhima.gt.as_n_alt, genotypes, block_size=1000)


    

In [5]:

    

assert np.array_equal(gn, gn2)


    

In [6]:

    

ac = anhima.af.allele_counts(genotypes)


    

In [7]:

    

ac2 = anhima.util.block_apply(anhima.af.allele_counts, genotypes, block_size=1000)


    

In [8]:

    

assert np.array_equal(ac, ac2)


    

In [9]:

    

packed = anhima.gt.pack_diploid(genotypes)


    

In [10]:

    

packed2 = anhima.util.block_apply(anhima.gt.pack_diploid, genotypes, block_size=1000)


    

In [11]:

    

assert np.array_equal(packed, packed2)


    

In [12]:

    

row_indices = sorted(random.sample(range(n_variants), n_variants//10))
col_indices = sorted(random.sample(range(n_samples), n_samples//10))


    

In [13]:

    

g = genotypes.take(row_indices, axis=0).take(col_indices, axis=1)


    

In [14]:

    

g2 = anhima.util.block_take2d(genotypes, row_indices, col_indices, block_size=1000)


    

In [15]:

    

assert np.array_equal(g, g2)


    

In [16]: