

In [1]:

    
import numpy as np
np.random.seed(1)
import scipy.stats
import sys
import cProfile
%load_ext memory_profiler
# dev imports
sys.path.insert(0, '../src')
%reload_ext autoreload
%autoreload 1
%aimport anhima.sim
%aimport anhima.gt

Pack/unpack



In [2]:

    
genotypes = np.random.randint(-1, 3, size=(200000, 100, 2)).astype('i1')
genotypes.nbytes / 1e6









    Out[2]:





40.0



In [3]:

    
packed = anhima.gt.pack_diploid(genotypes)



In [4]:

    
packed.nbytes / 1e6









    Out[4]:





20.0



In [5]:

    
%timeit anhima.gt.pack_diploid(genotypes)









    



1 loops, best of 3: 209 ms per loop



In [6]:

    
%memit anhima.gt.pack_diploid(genotypes)









    



peak memory: 215.93 MiB, increment: 91.63 MiB



In [7]:

    
unpacked = anhima.gt.unpack_diploid(packed)



In [8]:

    
unpacked.nbytes / 1e6









    Out[8]:





40.0



In [9]:

    
%timeit anhima.gt.unpack_diploid(packed)









    



10 loops, best of 3: 116 ms per loop



In [10]:

    
%memit anhima.gt.unpack_diploid(packed)









    



peak memory: 274.00 MiB, increment: 111.22 MiB



In [ ]: