func main() {
// use all cpus
runtime.GOMAXPROCS(runtime.NumCPU())
// population paramters
length := 1000 // genome length = 1000
mutation := 0.00001 // mutation rate = 1e-5
transfer := 0.0 // transfer rate = 0
fragment := 0 // transferred length = 0
// simulation parameters
samplesize := 100
numofgen := 100000
// population size array
sizearray := []int{100, 1000, 10000}
for _, size := range sizearray {
// population
pop := fwd.NewSeqPop(size, length, mutation, transfer, fragment)
// result files
ksname := fmt.Sprintf("ks_size_%d.csv", size)
ksfile, err := os.Create(ksname)
if err != nil {
panic(err)
}
vdname := fmt.Sprintf("vd_size_%d.csv", size)
vdfile, err := os.Create(vdname)
if err != nil {
panic(err)
}
// info file
infoname := fmt.Sprintf("ks_size_%d.txt", size)
infofile, err := os.Create(infoname)
if err != nil {
panic(err)
}
infofile.WriteString(fmt.Sprintf("Size = %d\n", pop.Size))
infofile.WriteString(fmt.Sprintf("Length = %d\n", pop.Length))
infofile.WriteString(fmt.Sprintf("Mutation = %g\n", pop.Mutation))
// population evolve
for i := 0; i < numofgen; i++ {
pop.Evolve()
sample := fwd.Sample(pop.Genomes, samplesize)
dmatrix := fwd.GenerateDistanceMatrix(sample)
cmatrix := covs.NewCMatrix(samplesize, length, dmatrix)
ks, vd := cmatrix.D()
ksfile.WriteString(fmt.Sprintf("%g\n", ks))
vdfile.WriteString(fmt.Sprintf("%g\n", vd))
}
// close files
ksfile.Close()
vdfile.Close()
infofile.Close()
}
}
func init() {
//assign flags
flag.IntVar(&size, "size", 1000, "usage: -size 1000")
flag.IntVar(&length, "length", 1000, "usage: -length 1000")
flag.IntVar(&ngen, "ngen", 1000, "usage: -ngen 1000")
flag.IntVar(&sampleSize, "samplesize", 100, "usage: -samplesize 1000")
flag.IntVar(&sampleTime, "sampletime", 1, "usage: -sampletime 10")
flag.IntVar(&fragment, "fragment", 100, "usage: -fragment 1000")
flag.Float64Var(&mutation, "mutation", 1e-5, "usage: -mutation 1e-5")
flag.Float64Var(&transfer, "transfer", 0.0, "usage: -transfer 1e-9")
flag.StringVar(&fname, "fname", "ks", "usage: -fname ks")
// parse flags
flag.Parse()
// construct a population
pop = fwd.NewSeqPop(size, length, mutation, transfer, fragment)
// use all the available CPUs
runtime.GOMAXPROCS(runtime.NumCPU())
}
