3.10 Code from Week 2

Here is the final simulation developed in class:
initialize(){
    initializeMutationRate(1e-7);
    
    // Create mutation types
    initializeMutationType("m1", 0.5, "f", 0.0); // neutral mutation 
    initializeMutationType("m2", 1, "f", 0.03);
    m2.convertToSubstitution = F; // Continue tracking m2 after it reaches fixation
    m2.mutationStackPolicy="l"; // If multiple mutations at m2 in a single genome, only care about the last one

    
    // Create Types of DNA 
    initializeGenomicElementType("g1", m1, 1);   
    
    // Arrange DNA into a genome
    initializeGenomicElement(g1, 0, 3000);

    initializeRecombinationRate(1e-8);
    
    defineConstant('trialNumber', 1); // Used for construction of file name and in the trial column
    initializeSex("A"); // Track sexes of individuals and allow random mating
}

1 early(){
    sim.addSubpop("p1", 500);
}

400 late(){
    sim.setValue("counter", 0); // initialize counter to keep track of generations
    
    // Manually introduce mutations 
    // Find how many genomes to add m2 to
    p1_size = size(p1.genomes); 
    starting_allele_freq = 0.05;
    initial_freq = asInteger(p1_size * starting_allele_freq);
    // sample genomes 
    target = sample(p1.genomes, initial_freq);
    // add m2 
    target.addNewDrawnMutation(m2, 1000);   
    
    // Start writing to file
    line = "Generation, Allele.Frequency, Trial";
    defineConstant("fname", paste("~/AF_trial", trialNumber, ".csv", sep ="")); // File path will be different for Windows users
    writeFile(fname, line, append=F); 
}

400:2000 late(){
    gen = sim.getValue("counter"); // get current generation 
    m2_count = sum(p1.genomes.countOfMutationsOfType(m2)); // count number of occurences of m2
    // write line to end of file
    line = paste(gen, m2_count, trialNumber, sep = ","); 
    writeFile(fname, line, append=T);
    
    // increment counter bt 1
    sim.setValue("counter", gen + 1);
}


2000 late() { 
    // End simulation
    print('Number of fixed mutations:');
    print(length(sim.substitutions));
    sim.simulationFinished();
}