func ToFasta(in, out string) {
if len(in) == 0 {
log.Fatalln("Please provide an input file (.2bit)")
}
if len(out) == 0 {
log.Fatalln("Please provide an output file (.fa)")
}
inFile, err := os.Open(in)
if err != nil {
log.Fatal(err)
}
defer inFile.Close()
tb, err := twobit.NewReader(inFile)
if err != nil {
log.Fatal(err)
}
outFile, err := os.Create(out)
if err != nil {
log.Fatal(err)
}
defer outFile.Close()
w := bufio.NewWriter(outFile)
for _, n := range tb.Names() {
w.WriteString(">")
w.WriteString(n)
w.WriteString("\n")
seq, err := tb.Read(n)
if err != nil {
log.Fatal(err)
}
n := len(seq)
cols := 50
rows := n / cols
if n%cols > 0 {
rows++
}
for r := 0; r < rows; r++ {
end := (r * cols) + cols
if end > n {
end = n
}
w.Write(seq[(r * cols):end])
w.Write([]byte("\n"))
}
}
w.Flush()
}
func IndexInfo(in, out string) {
if len(in) == 0 {
log.Fatalln("Please provide an input file (.2bit)")
}
if len(out) == 0 {
log.Fatalln("Please provide an output file (.fa)")
}
inFile, err := os.Open(in)
if err != nil {
log.Fatal(err)
}
defer inFile.Close()
tb, err := twobit.NewReader(inFile)
if err != nil {
log.Fatal(err)
}
outFile, err := os.Create(out)
if err != nil {
log.Fatal(err)
}
defer outFile.Close()
w := bufio.NewWriter(outFile)
for name, index := range tb.Indexes() {
w.WriteString(name)
w.WriteString("\t")
idx_str := fmt.Sprintf("%d", index)
w.WriteString(idx_str)
w.WriteString("\n")
}
w.Flush()
}
