example of simulating single genotype matrix

singleGeno.py

import keras
import msprime
import matplotlib
import numpy as np

# generate tree sequence
ts=msprime.simulate(
                Ne=0.5,
                population_configurations=[
                    msprime.PopulationConfiguration(sample_size=1000)],
                mutation_rate=100, recombination_rate=100)
# get genotype matrix from tree sequence
x=ts.genotype_matrix()