import matplotlib.pyplot as plt import numpy as np from numpy import array from moments import Misc, Spectrum, Numerics, Manips, Integration, Demographics1D, Demographics2D import sys, os import argparse os.chdir("/home/cbattey2/speciation_cyclical_migration/") parser = argparse.ArgumentParser() parser.add_argument("--infile") args = parser.parse_args() #args=argparse.Namespace(infile="simulations/msprime/constant/constant_sim_10441991.trees.vcf") # import data print(args.infile) dd = Misc.make_data_dict_vcf(vcf_filename=args.infile, popinfo_filename="id_pop_moments.txt") pop_ids = ["1", "2"] projections = [40, 40] data = Spectrum.from_data_dict(dd, pop_ids, projections, polarized=False) ns = data.sample_sizes np.set_printoptions(precision=3) # print info about sfs print("projection", projections) print("sample sizes", data.sample_sizes) sfs_sum = np.around(data.S(), 2) print("Sum of SFS = ", sfs_sum, '\n', '\n') # define model def IM(params, ns):