func main() {
fasta, err := gene.ReadAllFasta(os.Stdin)
if err != nil {
log.Fatal(err)
}
s := fasta[0].Data
t := fasta[1].Data
indices := []int{}
j := 0
for i := range s {
if j >= len(t) {
break
}
if s[i] == t[j] {
indices = append(indices, i)
j++
}
}
if j < len(t) {
log.Fatal("Subsequence not found")
}
for _, i := range indices {
fmt.Printf("%v ", i+1)
}
fmt.Println()
}
func main() {
flag.Parse()
var m, n int
m, _ = strconv.Atoi(flag.Arg(0))
if flag.NArg() == 1 {
n = m
} else {
n, _ = strconv.Atoi(flag.Arg(1))
}
fasta, err := gene.ReadAllFasta(os.Stdin)
if err != nil {
log.Fatal(err)
}
s := fasta[0]
t := fasta[1]
if len(s.Data) > m {
s.Data = s.Data[:m]
}
if len(t.Data) > n {
t.Data = t.Data[:n]
}
gene.WriteFasta(os.Stdout, s)
gene.WriteFasta(os.Stdout, t)
}
func main() {
debug := flag.Bool("debug", false, "Show debug output")
flag.Parse()
strings.DebugEditDistance = *debug
fasta, err := gene.ReadAllFasta(os.Stdin)
if err != nil {
log.Fatal(err)
}
s := []string{}
for _, f := range fasta {
s = append(s, f.Data)
}
scoreFunc := func(c, d int16) int32 {
if c == d {
return 0
}
return -1
}
score, a := strings.MultipleAlignment(s, scoreFunc, '-')
fmt.Println(score)
for _, t := range a {
fmt.Println(t)
}
}
func main() {
fasta, err := gene.ReadAllFasta(os.Stdin)
if err != nil {
log.Fatal(err)
}
s := fasta[0].Data
t := fasta[1].Data
lcs := strings.LongestCommonSubsequence(s, t)
fmt.Println(lcs)
}
func main() {
fasta, err := gene.ReadAllFasta(os.Stdin)
if err != nil {
log.Fatal(err)
}
s := fasta[0].Data
t := fasta[1].Data
m := (1 << 27) - 1
n := strings.NumOptimalAlignments(s, t, m)
fmt.Println(n)
}
func main() {
debug := flag.Bool("debug", false, "Show debug output")
flag.Parse()
strings.DebugEditDistance = *debug
fasta, err := gene.ReadAllFasta(os.Stdin)
if err != nil {
log.Fatal(err)
}
s := fasta[0].Data
t := fasta[1].Data
x := strings.MaxAlignmentScore(s, t, gene.Blosum62Scores, -5)
fmt.Println(x)
}
func main() {
debug := flag.Bool("debug", false, "Show debug output")
flag.Parse()
strings.DebugEditDistance = *debug
fasta, err := gene.ReadAllFasta(os.Stdin)
if err != nil {
log.Fatal(err)
}
s := fasta[0].Data
t := fasta[1].Data
d := strings.EditDistance(s, t)
fmt.Println(d)
}
func main() {
debug := flag.Bool("debug", false, "Show debug output")
flag.Parse()
strings.DebugEditDistance = *debug
fasta, err := gene.ReadAllFasta(os.Stdin)
if err != nil {
log.Fatal(err)
}
s := fasta[0].Data
t := fasta[1].Data
sa, ta := strings.Alignment(s, t, '-')
fmt.Println(strings.HammingDistance(sa, ta))
fmt.Println(sa)
fmt.Println(ta)
}
func main() {
fasta, err := gene.ReadAllFasta(os.Stdin)
if err != nil {
log.Fatal(err)
}
a := make([]string, len(fasta))
for i, f := range fasta {
a[i] = f.Data
}
d := strings.DistanceMatrix(a, strings.PDistance)
for _, row := range d {
for _, x := range row {
fmt.Printf("%7.5f ", x)
}
fmt.Println()
}
}
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() {
fasta, err := gene.ReadAllFasta(os.Stdin)
if err != nil {
log.Fatal(err)
}
s := fasta[0]
t := fasta[1]
if len(s.Data) != len(t.Data) {
log.Fatalf("Length mismatch: %d vs. %d", len(s.Data), len(t.Data))
}
nTransit := float64(0)
nTransver := float64(0)
for i := range s.Data {
switch pair(s.Data[i], t.Data[i]) {
case pair('A', 'G'),
pair('G', 'A'),
pair('C', 'T'),
pair('T', 'C'):
nTransit += 1
case pair('A', 'C'),
pair('C', 'A'),
pair('A', 'T'),
pair('T', 'A'),
pair('C', 'G'),
pair('G', 'C'),
pair('G', 'T'),
pair('T', 'G'):
nTransver += 1
}
}
r := nTransit / nTransver
fmt.Println(r)
}