func main() {
file, err := os.Open(flag.Arg(0))
if err != nil {
fmt.Println(err)
return
}
defer file.Close()
seq, err := spl.Read(file)
if err != nil {
fmt.Println(err)
return
}
pic := strings.Split(flag.Arg(0), ".")
if len(pic) > 1 {
if *intron {
pic[len(pic)-2] += "-intron"
} else {
pic[len(pic)-2] += "-cds"
}
pic[len(pic)-1] = "fas"
} else {
if *intron {
pic[0] += "-intron"
} else {
pic[0] += "-cds"
}
pic = append(pic, "fas")
}
file, err = os.Create(strings.Join(pic, "."))
if err != nil {
fmt.Println(err)
return
}
defer file.Close()
if !*intron {
cds := make([]gene.Sequence, len(seq))
for i, s := range seq {
cds[i] = gene.Sequence(s.CDS())
}
fas.Write(file, cds)
} else {
for _, s := range seq {
introns := make([]gene.Sequence, len(s.Seg)-1)
for i, t := range s.Introns() {
introns[i] = gene.Sequence(t)
}
fas.Write(file, introns)
}
}
}
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() {
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 := fas.Read(file)
if err != nil {
fmt.Println(err)
return
}
if len(seq) == 0 {
fmt.Println("File is empty")
return
}
for i, _ := range seq {
seq[i].Seq = gene.Complement(gene.Format(seq[i].Seq, "dna"), "dna")
seq[i].Name += "_cpl"
}
n := strings.LastIndexByte(os.Args[1], '.')
if n > 0 {
os.Args[1] = os.Args[1][:n]
}
file, err = os.Create(os.Args[1] + ".rev-cpl.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
}
}