func main() {
flag.Parse()
size, _ := strconv.Atoi(flag.Arg(0))
br := bufio.NewReader(os.Stdin)
line, _ := br.ReadString('\n')
taxa := strings.Fields(line)
taxaToKeep := taxa[:size]
taxaMap := map[string]bool{}
for _, taxon := range taxaToKeep {
taxaMap[taxon] = true
}
line, _ = br.ReadString('\n')
t1, _ := tree.ReadNewick(strings.NewReader(line))
s1 := tree.CollapseUnrootedBinary(t1, taxaMap)
line, _ = br.ReadString('\n')
t2, _ := tree.ReadNewick(strings.NewReader(line))
s2 := tree.CollapseUnrootedBinary(t2, taxaMap)
for _, taxon := range taxaToKeep {
fmt.Printf("%v ", taxon)
}
fmt.Println()
s1.WriteNewick(os.Stdout)
fmt.Println()
s2.WriteNewick(os.Stdout)
fmt.Println()
}
func main() {
br := bufio.NewReader(os.Stdin)
line, _ := br.ReadString('\n')
taxa := strings.Fields(line)
taxaInv := map[string]int{}
for i, taxon := range taxa {
taxaInv[taxon] = i
}
line, _ = br.ReadString('\n')
t1, _ := tree.ReadNewick(strings.NewReader(line))
line, _ = br.ReadString('\n')
t2, _ := tree.ReadNewick(strings.NewReader(line))
splits1 := phylo.Splits(t1, taxaInv)
splits2 := phylo.Splits(t2, taxaInv)
normalize(splits1)
normalize(splits2)
m1 := map[string]bool{}
for _, a := range splits1 {
m1[string(a)] = true
}
shared := 0
for _, a := range splits2 {
if m1[string(a)] {
shared++
}
}
d := 2 * (len(taxa) - 3 - shared)
fmt.Println(d)
}
func main() {
verify := flag.Bool("verify", false, "Check the distance for correctness")
memprof := flag.String("memprof", "", "Write memory profile to this file")
flag.Parse()
br := bufio.NewReader(os.Stdin)
line, _ := br.ReadString('\n')
taxa := strings.Fields(line)
taxaInv := map[string]int{}
for i, taxon := range taxa {
taxaInv[taxon] = i
}
line, _ = br.ReadString('\n')
t1, err := tree.ReadNewick(strings.NewReader(line))
if err != nil {
panic(err)
}
line, _ = br.ReadString('\n')
t2, err := tree.ReadNewick(strings.NewReader(line))
if err != nil {
panic(err)
}
d := phylo.QuartetDistance(t1, t2, len(taxa))
fmt.Println(d)
if *verify {
d2 := distanceFromSplits(t1, t2, taxaInv)
fmt.Println("From splits:", d2)
if d == d2 {
fmt.Println("ok")
} else {
fmt.Println("mismatch")
os.Exit(1)
}
}
if *memprof != "" {
f, err := os.Create(*memprof)
if err != nil {
log.Fatal(err)
}
defer f.Close()
pprof.Lookup("heap").WriteTo(f, 0)
}
}
func main() {
br := bufio.NewReader(os.Stdin)
for {
input, err := br.ReadString(';')
if err == io.EOF {
break
}
if err != nil {
log.Fatal(err)
}
t, err := tree.ReadNewick(strings.NewReader(input))
if err != nil {
log.Fatal(err)
}
_, _ = br.ReadString('\n')
line, err := br.ReadString('\n')
if err != nil {
log.Fatal(err)
}
labels := strings.Fields(line)
fmt.Print(t.Distance(labels[0], labels[1]), " ")
buf, _ := br.Peek(1)
if len(buf) > 0 && buf[0] == '\n' {
_, _ = br.ReadByte()
}
}
fmt.Println()
}
func main() {
br := bufio.NewReader(os.Stdin)
_, _ = br.ReadString('\n')
t, _ := tree.ReadNewick(br)
countLeaves(t)
e := tree.Edge{t, 0}
_, q := countPQ(e, 0, 0)
fmt.Println(q)
}
func main() {
br := bufio.NewReader(os.Stdin)
line, _ := br.ReadString('\n')
t, err := tree.ReadNewick(strings.NewReader(line))
if err != nil {
log.Fatal(err)
}
fasta, err := gene.ReadAllFasta(br)
if err != nil {
log.Fatal(err)
}
for _, f := range fasta {
dna[f.Description] = f.Data
}
n = len(fasta[0].Data)
d := bestDistances(t)
where := make([]int32, n)
total := float32(0)
for i := 0; i < n; i++ {
bestDist := d[i][0]
where[i] = 0
for j := int32(1); j < 5; j++ {
if d[i][j] < bestDist {
bestDist = d[i][j]
where[i] = j
}
}
total += bestDist
}
fmt.Println(total)
collectBestDna(t, where)
}
func main() {
pedigree, _ := tree.ReadNewick(os.Stdin)
fmt.Println(genotypeDistribution(pedigree))
}