2strong.slim

initialize() {
	defineConstant("L", 25e6);
	initializeTreeSeq();
	initializeMutationRate(0);
	initializeMutationType("m1", 0.5, "f", 0.075);
	initializeGenomicElementType("g1", m1, 1.0);
	initializeGenomicElement(g1, 0, L-1);
	initializeRecombinationRate(1e-8);
}


1 late() {
	num_variants = 2;
	print(num_variants);
	
	sim.addSubpop("p1", 1);
	sim.addSubpop("p2", 1);
	sim.treeSeqRememberIndividuals(sim.subpopulations.individuals);
	num1 = asInteger(num_variants/2);
	half = asInteger(((L-1)/2));
	p1_loci = sample(0:half, num1);
	p1.genomes.addNewDrawnMutation(m1, p1_loci);
	p1_loci = sample(half:(L-1), num_variants-num1);
	p1.genomes.addNewDrawnMutation(m1, p1_loci);
	p1_pos = p1.genomes[0].positionsOfMutationsOfType(m1);
	p1_s = p1.genomes[0].mutationsOfType(m1).selectionCoeff;
	
	lines=NULL;
	for (i in 0:(num_variants-1)) {
		mutLine = paste(c(p1_pos[i], "\t", p1_s[i], "\n"), "");
		lines= c(lines, mutLine);
	}
	file = paste(lines, "");
	file="p1_pos\tp1_s\n" + file;
	
	outname = "" + out + "_variants.txt";
	//outname="/Users/iman/Desktop/strong_mut_out.txt";
	
	if (!writeFile(outname, file))
		stop("Error writing file.");
	
	sim.addSubpop("p3", 10000);
	p3.setMigrationRates(c(p1, p2), c(0.5, 0.5));
}

2 late() {
	p3.setMigrationRates(c(p1, p2), c(0.0, 0.0));
	p1.setSubpopulationSize(0);
	p2.setSubpopulationSize(0);
}

50 late() {
	outtrees = "" + out + ".trees";
	//outtrees = "/Users/iman/Desktop/strong_mut.trees";
	sim.treeSeqOutput(outtrees);
	
	sim.simulationFinished();
}