// 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 = fmt.Sprintf("##%s ", d.(*seq.Seq).Moltype)
sw.SeqPrefix = "##"
if n, err = sw.Write(d.(*seq.Seq)); err != nil {
return
}
if err = sw.Flush(); 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
}
func main() {
var (
in *fasta.Reader
out *fasta.Writer
e error
profile *os.File
)
inName := flag.String("in", "", "Filename for input. Defaults to stdin.")
outName := flag.String("out", "", "Filename for output. Defaults to stdout.")
size := flag.Int("size", 40, "Fragment size.")
width := flag.Int("width", 60, "Fasta output width.")
cpuprofile := flag.String("cpuprofile", "", "write cpu profile to this file.")
help := flag.Bool("help", false, "Print this usage message.")
flag.Parse()
if *help {
flag.Usage()
os.Exit(1)
}
if *cpuprofile != "" {
if profile, e = os.Create(*cpuprofile); e != nil {
fmt.Fprintf(os.Stderr, "Error: %v.", e)
os.Exit(0)
}
fmt.Fprintf(os.Stderr, "Writing CPU profile data to %s\n", *cpuprofile)
pprof.StartCPUProfile(profile)
defer pprof.StopCPUProfile()
}
if *inName == "" {
in = fasta.NewReader(os.Stdin)
} else if in, e = fasta.NewReaderName(*inName); e != nil {
fmt.Fprintf(os.Stderr, "Error: %v.", e)
}
defer in.Close()
if *outName == "" {
out = fasta.NewWriter(os.Stdout, *width)
} else if out, e = fasta.NewWriterName(*outName, *width); e != nil {
fmt.Fprintf(os.Stderr, "Error: %v.", e)
}
defer out.Close()
var (
sequence *seq.Seq
err error
)
t := &seq.Seq{}
for {
if sequence, err = in.Read(); err != nil {
break
}
length := sequence.Len()
t.ID = sequence.ID
switch {
case length >= 20 && length <= 85:
t.Seq = sequence.Seq[5:]
out.Write(t)
case length > 85:
for start := 0; start+*size <= length; start += *size {
t.Seq = sequence.Seq[start : start+*size]
out.Write(t)
}
}
}
}