func main() {
flag.BoolVar(&Mul, "c", false, "number of sequence to average")
flag.Parse()
if flag.NArg() != 1 {
fmt.Println("Usage: executable [-c] filename\n")
return
}
file, err := os.Open(flag.Arg(0))
if err != nil {
fmt.Println(err)
return
}
defer file.Close()
seq, err := aln.Read(file)
if err != nil {
fmt.Println(err)
return
}
if len(seq) == 0 {
fmt.Println("File is empty")
return
}
if Mul {
l, r := 0, len(seq[0].Seq)-1
for i, _ := range seq {
for seq[i].Seq[l] == '-' && l < r {
l++
}
for seq[i].Seq[r] == '-' && l < r {
r--
}
}
for i, _ := range seq {
seq[i].Seq = seq[i].Seq[l : r+1]
}
}
n := strings.LastIndexByte(os.Args[1], '.')
if n > 0 {
os.Args[1] = os.Args[1][:n]
}
file, err = os.Create(os.Args[1] + ".phy")
if err != nil {
fmt.Println(err)
return
}
defer file.Close()
err = phy.Write(file, seq)
if err != nil {
fmt.Println("Can't create output file\n")
return
}
}
func main() {
if len(os.Args) != 2 {
fmt.Println("Usage: executable filename\n")
return
}
file, err := os.Open(os.Args[1])
if err != nil {
fmt.Println(err)
return
}
defer file.Close()
seq, err := aln.Read(file)
if err != nil {
fmt.Println(err)
return
}
if len(seq) == 0 {
fmt.Println("File is empty")
return
}
l, r := 0, len(seq[0].Seq)-1
for i, _ := range seq {
for seq[i].Seq[l] == '-' && l < r {
l++
}
for seq[i].Seq[r] == '-' && l < r {
r--
}
}
for i, _ := range seq {
seq[i].Seq = seq[i].Seq[l : r+1]
}
n := strings.LastIndexByte(os.Args[1], '.')
if n > 0 {
os.Args[1] = os.Args[1][:n]
}
file, err = os.Create(os.Args[1] + ".fas")
if err != nil {
fmt.Println(err)
return
}
defer file.Close()
err = fas.Write(file, seq)
if err != nil {
fmt.Println("Can't create output file\n")
return
}
}
func main() {
switch len(os.Args) {
case 1:
fmt.Println("usage: executable aln-name [spl-name]")
return
case 2, 3:
chest = os.Args[1]
piece := strings.Split(chest, ".")
if l := len(piece); l > 1 && piece[l-1] == "aln" {
align = chest
chest = strings.Join(piece[:l-1], ".")
} else if l > 1 && piece[l-1] == "spl" {
chest = strings.Join(piece[:l-1], ".")
align = chest + ".aln"
} else {
align = chest + ".aln"
}
if len(os.Args) == 2 {
split = chest + ".spl"
} else {
split = os.Args[2]
}
default:
fmt.Println("too many arguments")
return
}
file, err := os.Open(align)
if err != nil {
fmt.Println(err)
return
}
defer file.Close()
cds, err := aln.Read(file)
if err != nil {
fmt.Println(err)
return
}
file, err = os.Open(split)
if err != nil {
fmt.Println(err)
return
}
defer file.Close()
seq, err := spl.Read(file)
if err != nil {
fmt.Println(err)
return
}
l := len(cds)
w := len(cds[0].Seq)
img := paint.Image{Image: image.NewRGBA(image.Rect(0, 0, w+240, l*40+50)), FR: image.Black}
draw.Draw(img, img.Bounds(), image.White, image.Point{0, 0}, draw.Src)
con.SetSrc(image.Black)
con.SetDst(img)
con.SetClip(img.Bounds())
std := make([]byte, w)
for i := 0; i < w; i++ {
s := map[byte]int{'-': 0, 'A': 0, 'G': 0, 'C': 0, 'T': 0}
for j := 0; j < l; j++ {
c := cds[j].Seq[i]
if _, ok := s[c]; ok {
s[c]++
} else {
s['-']++
}
}
std[i] = '-'
M := 0
for k, v := range s {
if M < v {
std[i], M = k, v
}
}
}
for j := 0; j < l; j++ {
pt := freetype.Pt(w+15, j*40+70)
con.DrawString(cds[j].Name, pt)
img.Line(10, j*40+49, 9+w, j*40+49)
img.Line(10, j*40+80, 9+w, j*40+80)
}
pt := freetype.Pt(w+15, 25)
con.DrawString("Average", pt)
img.Line(10, 9, 9+w, 9)
img.Line(10, 30, 9+w, 30)
for i := 0; i < w; i++ {
img.FR = image.Black
if n, ok := gene.Dna[std[i]]; ok {
img.FR = color.RGBA{uint8(n[0]*64) + 191, uint8(n[1]*64) + 191, uint8(n[2]*64) + 191, 255}
}
img.Line(i+10, 10, i+10, 29)
for j := 0; j < l; j++ {
img.FR = image.Black
if c := cds[j].Seq[i]; c == std[i] && c != '-' {
img.FR = image.White
} else if n, ok := gene.Dna[c]; ok {
img.FR = color.RGBA{uint8(n[0]*64) + 191, uint8(n[1]*64) + 191, uint8(n[2]*64) + 191, 255}
}
img.Line(i+10, j*40+50, i+10, j*40+69)
}
}
for j := 0; j < l; j++ {
t := 0
for ; t < len(seq); t++ {
if strings.Contains(seq[t].Name, cds[j].Name) {
break
}
}
if t >= len(seq) {
continue
}
a, b := 0, seq[t].Seg[0][0]
for i := 0; i < w; i++ {
if cds[j].Seq[i] != '-' {
if a%2 == 0 {
img.FR = color.RGBA{60, 60, 60, 255}
img.Line(i+10, j*40+70, i+10, j*40+79)
} else {
img.FR = color.RGBA{180, 180, 180, 255}
img.Line(i+10, j*40+70, i+10, j*40+79)
}
b++
if b == seq[t].Seg[a][1] {
a++
if a < len(seq[t].Seg) {
b = seq[t].Seg[a][0]
}
}
} else if a < len(seq[t].Seg) && b < seq[t].Seg[a][1] && b > seq[t].Seg[a][0] {
if a%2 == 0 {
img.FR = color.RGBA{60, 60, 60, 255}
img.Line(i+10, j*40+70, i+10, j*40+79)
} else {
img.FR = color.RGBA{180, 180, 180, 255}
img.Line(i+10, j*40+70, i+10, j*40+79)
}
}
}
}
file, err = os.Create(chest + ".png")
if err != nil {
fmt.Println(err)
return
}
defer file.Close()
png.Encode(file, img)
}