Code to run simple ALF simulation from R

ALF.R

## Generate ALF simulations
library(whisker)
ALF_template <- function() {
  "  webRequest := false;
  uuid := '4e4937bd-70e5-4caf-8521-f4340a4b7e09';
  
  # name of simulation - you may want to change this
  mname := {{{simname}}};
  
  # directories for file storage - you may want to change these
  wdir := '{{{dir}}}';
  dbdir := 'DB/';
  dbAncdir := 'DBancestral/';
  
  # time scale for simulation (PAM is default)
  unitIsPam := true:
    
  # parameters concerning the root genome
  realseed := false;
  protStart := {{ngenes}};
  minGeneLength := {{mingenelen}};
  gammaLengthDist := [2.4019, 133.8063];
  blocksize := 3:
    
  # parameters concerning the species tree
  treeType := 'BDTree';
  birthRate := {{brate}};
  deathRate := {{drate}};
  NSpecies := {{nspec}};
  ultrametric := true;
  mutRate := {{PAMunits}};
  scaleTree := false;
  
  # parameters concerning the substitution models
  substModels := [SubstitutionModel('CPAM')];
  indelModels := [IndelModel({{indelrate}}, ZIPF, [1.821], 50)];
  rateVarModels := [RateVarModel(Gamma, 5, 0.01, 1)];
  modelAssignments := [1]:
  modelSwitchS := [[1]]:
  modelSwitchD := [[1]]:
    
  # parameters concerning gene duplication
  geneDuplRate := 0;
  numberDupl := 0;
  transDupl := 0;
  fissionDupl := 0;
  fusionDupl := 0;
  P_pseudogene := 0;
  P_neofunc := 0;
  P_subfunc := 0;
  
  # parameters concerning gene loss
  geneLossRate := 0;
  
  # parameters concerning LGT
  lgtRate := 0;
  lgtGRate := 0;
  lgtGSize := 0;
  
  # parameters concerning rate heterogeneity among genes
  amongGeneDistr := 'Gamma';
  aGAlpha := 1;"
  
}

gen_ALF_drw <- function(simname, nspec, ngenes, mingenelen, PAMunits, brate, drate, indelrate, dir) {
  parms <- list(simname = simname, nspec = nspec, ngenes = ngenes, mingenelen = mingenelen,
                PAMunits = PAMunits, brate = brate, drate = drate, indelrate = indelrate,
                dir = dir)
  whisker.render(ALF_template(), parms) 
}

run_ALF <- function(simname, nspec, ngenes, mingenelen, PAMunits, brate, drate, indelrate, dir, ALF_dir) {
  filename <- paste0(dir, "/", simname, ".drw")
  cat(gen_ALF_drw(simname, nspec, ngenes, mingenelen, PAMunits, brate, drate, indelrate, dir), file = filename)
  system(paste0(ALF_dir, "/alfsim ", filename))
  return(paste0(dir, "/", simname))
}

## example
dir <- "/home/din02g/Testing"
run_ALF("test", 15, 20, 400, 100, 0.04, 0.025, 0.0001, dir, "/home/din02g/ALF_standalone/bin")