def integrate_fs(args):
dg = demes.load(args.yaml)
final_demes = get_final_demes(dg)
return moments.Spectrum.from_demes(dg, final_demes,
[2 * args.nsam] * len(final_demes))
def runsim(args, simseed, npseed):
dg = demes.load(args.yaml)
final_demes = get_final_demes(dg)
demog = fwdpy11.discrete_demography.from_demes(dg, burnin=args.burnin)
final_deme_ids = sorted([
i for i in demog.metadata["deme_labels"]
if demog.metadata["deme_labels"][i] in final_demes
])
initial_sizes = [
demog.metadata["initial_sizes"][i]
for i in sorted(demog.metadata["initial_sizes"].keys())
]
recrate = RHO / (4.0 * initial_sizes[0])
pdict = {
"nregions": [],
"sregions": [],
"recregions": [fwdpy11.PoissonInterval(0, 1, recrate)],
"gvalue": fwdpy11.Multiplicative(2.0),
"rates": (0.0, 0.0, None),
"simlen": demog.metadata["total_simulation_length"],
"demography": demog,
}
params = fwdpy11.ModelParams(**pdict)
pop = fwdpy11.DiploidPopulation(initial_sizes, 1.0)
# FIXME: need seed as input argument to this fxn
rng = fwdpy11.GSLrng(simseed)
np.random.seed(npseed)
fwdpy11.evolvets(rng, pop, params, 100)
nmuts = fwdpy11.infinite_sites(rng, pop, THETA / (4.0 * initial_sizes[0]))
md = np.array(pop.diploid_metadata, copy=False)
sample_nodes = []
for i in final_deme_ids:
w = np.where(md["deme"] == i)
s = np.random.choice(w[0], args.nsam, replace=False)
sample_nodes.append(md["nodes"][s].flatten())
fs = pop.tables.fs(sample_nodes)
return fs
def run_ancestry(args):
setup_logging(args)
if args.demography is not None:
graph = demes.load(args.demography)
logger.debug(f"Loaded demes graph from {args.demography}")
demography = msprime.Demography.from_demes(graph)
samples = parse_sample_spec(args.samples)
else:
if len(args.samples) != 1:
raise ValueError("Samples must be a single integer")
demography = None
samples = parse_sample_size(args.samples[0])
tree_sequence = msprime.sim_ancestry(
samples=samples,
demography=demography,
population_size=args.population_size,
sequence_length=args.length,
ploidy=args.ploidy,
recombination_rate=args.recombination_rate,
random_seed=args.random_seed,
)
tree_sequence.dump(args.output)
#!/usr/bin/env python3
import demes
import demesdraw
def size_max(graph):
return max(
max(epoch.start_size, epoch.end_size) for deme in graph.demes
for epoch in deme.epochs)
graph = demes.load("models/IM.yaml")
w = 0.8 * size_max(graph)
positions = dict(A=0, X=-w, Y=w)
fig, ax = demesdraw.utils.get_fig_axes(aspect=1)
ax = demesdraw.tubes(graph, ax=ax, positions=positions, seed=1, inf_ratio=0.4)
ax.figure.savefig(
"fig/IM.pdf",
# Save with a transparent background.
transparent=True,
)
parser = argparse.ArgumentParser(
description="validate demes_schedule_events() against the demes graph")
parser.add_argument(
"-Q",
"--scaling_factor",
type=float,
default=1.0,
help="Scaling factor that was applied to speed up the simulation",
)
parser.add_argument(
"slim_out_filename",
metavar="slim-states.out",
help="Output from test_demes_schedule_events.slim",
)
parser.add_argument(
"yaml_filename",
metavar="model.yaml",
help="The YAML-formatted demes model being simulated.",
)
return parser.parse_args()
if __name__ == "__main__":
args = parse_args()
graph = demes.load(args.yaml_filename)
discrete_graph = graph_to_scaled_discrete(
graph, scaling_factor=args.scaling_factor)
states = parse_slim_states(args.slim_out_filename)
check_states_against_graph(states, discrete_graph)
def size_max(graph):
return max(
max(epoch.start_size, epoch.end_size) for deme in graph.demes
for epoch in deme.epochs)
def get_axes(aspect, scale):
fig_w, fig_h = plt.figaspect(aspect)
fig, ax = plt.subplots(figsize=(scale * fig_w, scale * fig_h))
fig.set_tight_layout(True)
return ax
if __name__ == "__main__":
if len(sys.argv) != 3:
print("usage: {sys.argv[0]} in.yaml out.pdf")
exit(1)
yaml_file, plot_file = sys.argv[1:]
graph = demes.load(yaml_file)
w = 1.5 * size_max(graph)
positions = dict(X=0, A=-w, B=w)
ax = get_axes(aspect=3 / 4, scale=0.5)
ax = demesdraw.tubes(graph,
positions=positions,
ax=ax,
inf_ratio=0.4,
seed=1)
ax.figure.savefig(plot_file)
def draw_model(args):
dg = demes.load(args.yaml)
outfile = os.path.basename(args.yaml).replace(".yml", "_draw.png")
_ = demesdraw.tubes(dg)
plt.savefig(outfile)
return outfile