drosophila_debug_mwe.py

import msprime


import stdpopsim
from stdpopsim import drosophila_melanogaster

chr_str = "chr2L"
genetic_map = stdpopsim.drosophila_melanogaster.Comeron2012_dm6()
genetic_map.download()
chrom = drosophila_melanogaster.genome.chromosomes[chr_str]
recomb_map = chrom.recombination_map()

print(f"Testing Li and Stephan (2006) model- with on {chr_str} map")
model = drosophila_melanogaster.LiStephanTwoPopulation()
model.debug()

samples = [msprime.Sample(population=0, time=0)] * 10 + [msprime.Sample(population=1, time=0)] * 10


ts = msprime.simulate(
    samples=samples,
    recombination_map=chrom.recombination_map(),
    mutation_rate=chrom.default_mutation_rate,
    **model.asdict())
print("simulated:", ts.num_trees, ts.num_sites)