func main() {
flag.Parse()
// Now really print out the connected components
seqtype := alphabet.DNA
f1, err := os.Open(*in)
if err != nil {
fmt.Fprintf(os.Stderr, "Error: %v.\n", err)
os.Exit(1)
}
defer f1.Close()
f2, err := os.Create(*out)
if err != nil {
fmt.Fprintf(os.Stderr, "Error: %v.\n", err)
os.Exit(1)
}
defer f2.Close()
fastaSeqs := fasta.NewReader(f1, linear.NewSeq("", nil, seqtype))
fastaOut := fasta.NewWriter(f2, 80)
rand.Seed(time.Now().UnixNano())
list := rand.Perm(*total)
keep := make(map[int]bool)
for i := 0; i < *numkeep; i++ {
keep[list[i]] = true
}
counter := 0
for true {
seq, e := fastaSeqs.Read()
if e != nil {
break
}
if keep[counter] {
fastaOut.Write(seq)
}
counter++
}
fmt.Fprintf(os.Stderr, "Done.\n")
}
// Write meta data to a GFF file.
func (self *Writer) WriteMetaData(d interface{}) (n int, err error) {
switch d.(type) {
case []byte, string:
n, err = self.w.WriteString("##" + d.(string) + "\n")
case *seq.Seq:
sw := fasta.NewWriter(self.f, self.Width)
sw.IDPrefix = []byte(fmt.Sprintf("##%s ", d.(*seq.Seq).Moltype))
sw.SeqPrefix = []byte("##")
n, err = sw.Write(d.(*seq.Seq))
if err != nil {
return
}
err = sw.Flush()
if err != nil {
return
}
var m int
m, err = self.w.WriteString("##end-" + d.(*seq.Seq).Moltype.String() + "\n")
n += m
if err != nil {
return
}
err = self.w.Flush()
return
case *feat.Feature:
start := d.(*feat.Feature).Start
if self.OneBased && start >= 0 {
start++
}
n, err = self.w.WriteString("##sequence-region " + string(d.(*feat.Feature).ID) + " " +
strconv.Itoa(start) + " " +
strconv.Itoa(d.(*feat.Feature).End) + "\n")
default:
n, err = 0, bio.NewError("Unknown meta data type", 0, d)
}
if err == nil {
err = self.w.Flush()
}
return
}