Recipe 17.3 - Simulation conditional upon fixation of a sweep, preserving ancestry II.txt

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

initialize() {
	initializeTreeSeq();
	initializeMutationRate(1e-8);
	initializeMutationType("m2", 0.5, "g", -0.01, 1.0);  // deleterious
	initializeMutationType("m3", 1.0, "f", 0.05);        // introduced
	initializeGenomicElementType("g1", m2, 1.0);
	initializeGenomicElement(g1, 0, 99999);
	initializeRecombinationRate(1e-8);
}
1 early() {
	defineConstant("simID", getSeed());
	sim.addSubpop("p1", 500);
}
1000 late() {
	target = sample(p1.genomes, 1);
	target.addNewDrawnMutation(m3, 10000);
	sim.treeSeqOutput("/tmp/slim_" + simID + ".trees");
}
1000:100000 late() {
	if (sim.countOfMutationsOfType(m3) == 0) {
		if (sum(sim.substitutions.mutationType == m3) == 1) {
			cat(simID + ": FIXED\n");
			sim.treeSeqOutput("slim_" + simID + "_FIXED.trees");
			sim.simulationFinished();
		} else {
			cat(simID + ": LOST - RESTARTING\n");
			
			sim.readFromPopulationFile("/tmp/slim_" + simID + ".trees");
			setSeed(rdunif(1, 0, asInteger(2^62) - 1));
		}
	}
}