func simusome(begin, end int, ch chan Results) {
for i := begin; i < end; i++ {
w := coals.NewWFPopulation(size, sample, length, mutation, transfer, fragment)
w.Seed(i)
w.Backtrace()
seqs := w.Fortrace()
diffmatrix := [][]int{}
sample := w.SampleSize
for j := 0; j < sample; j++ {
for k := j + 1; k < sample; k++ {
diff := []int{}
for h := 0; h < length; h++ {
if seqs[j][h] != seqs[k][h] {
diff = append(diff, h)
}
}
diffmatrix = append(diffmatrix, diff)
}
}
cmatrix := covs.NewCMatrix(len(diffmatrix), length, diffmatrix)
ks, vd := cmatrix.D()
scovs, rcovs, xyPL, xsysPL, smXYPL := cmatrix.CovCircle(maxl)
results := Results{
ks: ks,
vd: vd,
scovs: scovs,
rcovs: rcovs,
xyPL: xyPL,
xsysPL: xsysPL,
smXYPL: smXYPL,
}
ch <- results
}
}
func main() {
means := make([][]*desc.Mean, 5)
sds := make([][]*desc.StandardDeviation, 5)
for i := 0; i < 5; i++ {
means[i] = make([]*desc.Mean, maxl)
sds[i] = make([]*desc.StandardDeviation, maxl)
for j := 0; j < maxl; j++ {
means[i][j] = desc.NewMean()
sds[i][j] = desc.NewStandardDeviationWithBiasCorrection()
}
}
dfile, err := os.Create(prefix + "_d.csv")
if err != nil {
panic(err)
}
defer dfile.Close()
dfile.WriteString(fmt.Sprintf("#size: %d\n", size))
dfile.WriteString(fmt.Sprintf("#sample: %d\n", sample))
dfile.WriteString(fmt.Sprintf("#length: %d\n", length))
dfile.WriteString(fmt.Sprintf("#fragment: %d\n", fragment))
dfile.WriteString(fmt.Sprintf("#repeats: %d\n", repeats))
dfile.WriteString(fmt.Sprintf("#maxl: %d\n", maxl))
dfile.WriteString(fmt.Sprintf("#mutation: %g\n", mutation))
dfile.WriteString(fmt.Sprintf("#transfer: %g\n", transfer))
dfile.WriteString("#ks, vd\n")
runtime.GOMAXPROCS(runtime.NumCPU())
t0 := time.Now()
for c := 0; c < repeats; c++ {
w := coals.NewWFPopulation(size, sample, length, mutation, transfer, fragment)
w.Seed(c)
w.Backtrace()
seqs := w.Fortrace()
diffmatrix := [][]int{}
for i := 0; i < sample; i++ {
for j := i + 1; j < sample; j++ {
diff := []int{}
for k := 0; k < length; k++ {
if seqs[i][k] != seqs[j][k] {
diff = append(diff, k)
}
}
diffmatrix = append(diffmatrix, diff)
}
}
cmatrix := covs.NewCMatrix(len(diffmatrix), length, diffmatrix)
ks, vd := cmatrix.D()
dfile.WriteString(fmt.Sprintf("%g,%g\n", ks, vd))
scovs, rcovs, xyPL, xsysPL, smXYPL := cmatrix.CovCircle(maxl)
for l := 0; l < maxl; l++ {
means[0][l].Increment(scovs[l])
means[1][l].Increment(rcovs[l])
means[2][l].Increment(xyPL[l])
means[3][l].Increment(xsysPL[l])
means[4][l].Increment(smXYPL[l])
sds[0][l].Increment(scovs[l])
sds[1][l].Increment(rcovs[l])
sds[2][l].Increment(xyPL[l])
sds[3][l].Increment(xsysPL[l])
sds[4][l].Increment(smXYPL[l])
}
if (c+1)%(repeats/100) == 0 {
t1 := time.Now()
fmt.Printf("%d%%,%v\n", (c+1)/(repeats/100), t1.Sub(t0))
covfile, err := os.Create(prefix + "_covs.csv")
if err != nil {
fmt.Println(err)
}
covfile.WriteString(fmt.Sprintf("#size: %d\n", size))
covfile.WriteString(fmt.Sprintf("#sample: %d\n", sample))
covfile.WriteString(fmt.Sprintf("#length: %d\n", length))
covfile.WriteString(fmt.Sprintf("#fragment: %d\n", fragment))
covfile.WriteString(fmt.Sprintf("#repeats: %d\n", repeats))
covfile.WriteString(fmt.Sprintf("#maxl: %d\n", maxl))
covfile.WriteString(fmt.Sprintf("#mutation: %g\n", mutation))
covfile.WriteString(fmt.Sprintf("#transfer: %g\n", transfer))
covfile.WriteString("#dist, scov, rcov, xy, xsys, smxy, scov_sd, rcov_sd, xy_sd, xsys_sd, smxy_sd\n")
for i := 0; i < maxl; i++ {
covfile.WriteString(fmt.Sprintf("%d,%g,%g,%g,%g,%g,%g,%g,%g,%g,%g\n",
i,
means[0][i].GetResult(),
means[1][i].GetResult(),
means[2][i].GetResult(),
means[3][i].GetResult(),
means[4][i].GetResult(),
sds[0][i].GetResult()/math.Sqrt(float64(repeats)),
sds[1][i].GetResult()/math.Sqrt(float64(repeats)),
sds[2][i].GetResult()/math.Sqrt(float64(repeats)),
sds[3][i].GetResult()/math.Sqrt(float64(repeats)),
sds[4][i].GetResult()/math.Sqrt(float64(repeats)),
))
}
covfile.Close()
}
}
covfile, err := os.Create(prefix + "_covs.csv")
if err != nil {
fmt.Println(err)
}
defer covfile.Close()
covfile.WriteString(fmt.Sprintf("#size: %d\n", size))
covfile.WriteString(fmt.Sprintf("#sample: %d\n", sample))
covfile.WriteString(fmt.Sprintf("#length: %d\n", length))
covfile.WriteString(fmt.Sprintf("#fragment: %d\n", fragment))
covfile.WriteString(fmt.Sprintf("#repeats: %d\n", repeats))
covfile.WriteString(fmt.Sprintf("#maxl: %d\n", maxl))
covfile.WriteString(fmt.Sprintf("#mutation: %g\n", mutation))
covfile.WriteString(fmt.Sprintf("#transfer: %g\n", transfer))
covfile.WriteString("#dist, scov, rcov, xy, xsys, smxy, scov_sd, rcov_sd, xy_sd, xsys_sd, smxy_sd\n")
for i := 0; i < maxl; i++ {
covfile.WriteString(fmt.Sprintf("%d,%g,%g,%g,%g,%g,%g,%g,%g,%g,%g\n",
i,
means[0][i].GetResult(),
means[1][i].GetResult(),
means[2][i].GetResult(),
means[3][i].GetResult(),
means[4][i].GetResult(),
sds[0][i].GetResult()/math.Sqrt(float64(repeats)),
sds[1][i].GetResult()/math.Sqrt(float64(repeats)),
sds[2][i].GetResult()/math.Sqrt(float64(repeats)),
sds[3][i].GetResult()/math.Sqrt(float64(repeats)),
sds[4][i].GetResult()/math.Sqrt(float64(repeats)),
))
}
}