Recipe 17.8 - Starting a hermaphroditic WF model with a coalescent history II.txt

// Keywords: tree-sequence recording, tree sequence recording

// Part I of this recipe, which is a Python script, may be found in
// the Recipes archive downloadable at https://messerlab.org/slim/

initialize() {
	initializeTreeSeq();
	initializeMutationRate(0);
	initializeMutationType("m1", 0.5, "f", 0.0);
	initializeMutationType("m2", 0.5, "f", 0.1);
	initializeGenomicElementType("g1", m2, 1.0);
	initializeGenomicElement(g1, 0, 1e8-1);
	initializeRecombinationRate(1e-8);
}
1 late() {
	sim.readFromPopulationFile("recipe_17.8.trees");
	target = sample(sim.subpopulations.genomes, 1);
	target.addNewDrawnMutation(m2, 10000);
}
1: late() {
	if (sim.mutationsOfType(m2).size() == 0) {
		print(sim.substitutions.size() ? "FIXED" else "LOST");
		sim.treeSeqOutput("recipe_17.8_II.trees");
		sim.simulationFinished();
	}
}
2000 early() { sim.simulationFinished(); }

// Part III of this recipe, which is a Python script, may be found in
// the Recipes archive downloadable at https://messerlab.org/slim/