Saving output

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Nkrumah Grant

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Aug 29, 2021, 1:57:24 PM8/29/21
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Hi all:

I am trying to save run data every 500 generations for the script below. Currently, the data I want prints to the window. I want the same data to be printed to a txt or csv file.

I know about LogFile, but can't get that to work. Can someone help me with this?


Reproducible example below:

initialize()

{

initializeSLiMOptions(mutationRuns=1);

setSeed(737);

defineConstant("Ne", 10000);

defineConstant("Mu", 1e-8);

defineConstant("genomeSize", 1e6);

defineConstant("N_generations", 1000);

initializeMutationRate(Mu);


initializeMutationType("m1", 1.0, "f", 0.0); //neutral mutation

initializeMutationType("m2", 1.0, "f", 0.005); //beneficial mutation

initializeMutationType("m3", 1.0, "g", -0.03, 0.2); //deleterious mutation

m1.color = "yellow";

m2.color = "green";

m3.color = "red";


m1.colorSubstitution = "grey";

m2.colorSubstitution = "green";

m3.colorSubstitution = "red";


initializeGenomicElementType("g1", c(m1), c(1)); //neutral mutations

initializeGenomicElementType("g2", c(m1,m3), c(0.95,0.05)); // purifying selection

initializeGenomicElementType("g3", c(m1,m2), c(0.5,0.5)); // positive selection

initializeGenomicElementType("g4", c(m1,m3), c(0.5,0.5)); // non-essential genes

g1.color = "yellow";

g2.color = "blue";

g3.color = "green";

g4.color = "red";


for (index in 0:9)

initializeGenomicElement(g1, index*1000, index*1000 + 499);

for (index in 10:19)

initializeGenomicElement(g2, index*1000, index*1000 + 499);

for (index in 20:29)

initializeGenomicElement(g3, index*1000, index*1000 + 499);

for (index in 30:39)

initializeGenomicElement(g4, index*1000, index*1000 + 499);

initializeRecombinationRate(0); // In SLiM recombination is between sister chromatids

}


// At the first generation:

// - create a subpopulation (or many)


1 early ()

{

sim.chromosome.colorSubstitution = ""; //keeps the color I defined for mutation events above in the initialize callback.

sim.addSubpop("p1", asInteger(Ne));

p1.setCloningRate(1.0); // Essential for bacteria.

sim.rescheduleScriptBlock(s1, start=N_generations, end=N_generations);

}


fitness(m3)

{

// convert fecundity-based selection to survival-based selection

if (runif(1) < relFitness)

return 1.0;

else

return 0.0;

}


//Remove mutations from second chromosome

modifyChild()

{

if (size(childGenome2.mutations))

childGenome2.removeMutations();

return T;

}


// At each generation:

// - Remove fixed mutations

late()

{

// Remove fixed mutation

// (SLiM does it automatically for diploid,

// but for haploid, mutations are fixed at 0.5)

//This must be done for each mutation class (m1-m3 in this model).

muts_m1 = sim.mutationsOfType(m1);

freqs = sim.mutationFrequencies(NULL, muts_m1);

fixed_muts_m1 = muts_m1[freqs == 0.5];

if (size(fixed_muts_m1) > 0)

sim.subpopulations.genomes.removeMutations(fixed_muts_m1, T);

muts_m2 = sim.mutationsOfType(m2);

freqs = sim.mutationFrequencies(NULL, muts_m2);

fixed_muts_m2 = muts_m2[freqs == 0.5];

if (size(fixed_muts_m2) > 0)

sim.subpopulations.genomes.removeMutations(fixed_muts_m2, T);

muts_m3 = sim.mutationsOfType(m3);

freqs = sim.mutationFrequencies(NULL, muts_m3);

fixed_muts_m3 = muts_m3[freqs == 0.5];

if (size(fixed_muts_m3) > 0)

sim.subpopulations.genomes.removeMutations(fixed_muts_m3, F); //pg 254

}


// Create custom output of segregating sites and those being fixed in the population.

// I would also like to know what type of mutation it is.

// pg 463


//Create output showing mutations segregating and fixing in the population at 500 generation intervals. Code works, but prints to GUI.

//TODO: figure out how to print to a file.



1:2000 late ()

{

if (sim.generation % 500 == 0)

{

sim.outputMutations(sim.mutationsOfType(m1));

sim.outputMutations(sim.mutationsOfType(m2));

sim.outputMutations(sim.mutationsOfType(m3));

sim.outputFixedMutations();

}

}




// End simulation

s1 1000 late ()

{

}


Ben Haller

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Aug 29, 2021, 2:07:34 PM8/29/21
to slim-discuss
Hi!  You're referring to the output from outputMutations() and outputFixedMutations(), I take it?  Both of those methods can take a file path as a parameter, and can either create a new file or append to an existing file.  See the SLiM manual for documentation of this.

Cheers,
-B.

Benjamin C. Haller
Messer Lab
Cornell University

Nkrumah Grant

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Aug 29, 2021, 2:09:23 PM8/29/21
to Ben Haller, slim-discuss
Wow, thank you so much. Easy fix. 

--
SLiM forward genetic simulation: http://messerlab.org/slim/
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Nkrumah A.Grant, Ph.D.
Postdoctoral Research Fellow
Department of Biological Sciences
University of Idaho
875 Perimeter MS 3051
Moscow, ID 83844

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