func (r *Reader) commentMetaline(line []byte) (f feat.Feature, err error) {
fields := bytes.Split(line, []byte{' '})
if len(fields) < 1 {
return nil, &csv.ParseError{Line: r.line, Err: ErrEmptyMetaLine}
}
switch unsafeString(fields[0]) {
case "gff-version":
v := mustAtoi(fields, 1, r.line)
if v > Version {
return nil, &csv.ParseError{Line: r.line, Err: ErrNotHandled}
}
r.Version = Version
return r.Read()
case "source-version":
if len(fields) <= 1 {
return nil, &csv.ParseError{Line: r.line, Err: ErrBadMetaLine}
}
r.SourceVersion = string(bytes.Join(fields[1:], []byte{' '}))
return r.Read()
case "date":
if len(fields) <= 1 {
return nil, &csv.ParseError{Line: r.line, Err: ErrBadMetaLine}
}
if len(r.TimeFormat) > 0 {
r.Date, err = time.Parse(r.TimeFormat, unsafeString(bytes.Join(fields[1:], []byte{' '})))
if err != nil {
return nil, err
}
}
return r.Read()
case "Type", "type":
if len(fields) <= 1 {
return nil, &csv.ParseError{Line: r.line, Err: ErrBadMetaLine}
}
r.Type = feat.ParseMoltype(unsafeString(fields[1]))
if len(fields) > 2 {
r.Name = string(fields[2])
}
return r.Read()
case "sequence-region":
if len(fields) <= 3 {
return nil, &csv.ParseError{Line: r.line, Err: ErrBadMetaLine}
}
return &Region{
Sequence: Sequence{SeqName: string(fields[1]), Type: r.Type},
RegionStart: feat.OneToZero(mustAtoi(fields, 2, r.line)),
RegionEnd: mustAtoi(fields, 3, r.line),
}, nil
case "DNA", "RNA", "Protein", "dna", "rna", "protein":
if len(fields) <= 1 {
return nil, &csv.ParseError{Line: r.line, Err: ErrBadMetaLine}
}
return r.metaSeq(fields[0], fields[1])
default:
return nil, &csv.ParseError{Line: r.line, Err: ErrNotHandled}
}
}
func (r *Reader) metaSeq(moltype, id []byte) (seq.Sequence, error) {
var line, body []byte
var err error
for {
line, err = r.r.ReadBytes('\n')
if err != nil {
if err == io.EOF {
return nil, err
}
return nil, &csv.ParseError{Line: r.line, Err: err}
}
r.line++
line = bytes.TrimSpace(line)
if len(line) == 0 {
continue
}
if len(line) < 2 || !bytes.HasPrefix(line, []byte("##")) {
return nil, &csv.ParseError{Line: r.line, Err: ErrBadSequence}
}
line = bytes.TrimSpace(line[2:])
if unsafeString(line) == "end-"+unsafeString(moltype) {
break
} else {
line = bytes.Join(bytes.Fields(line), nil)
body = append(body, line...)
}
}
var alpha alphabet.Alphabet
switch feat.ParseMoltype(unsafeString(moltype)) {
case feat.DNA:
alpha = alphabet.DNA
case feat.RNA:
alpha = alphabet.RNA
case feat.Protein:
alpha = alphabet.Protein
default:
return nil, ErrBadMoltype
}
s := linear.NewSeq(string(id), alphabet.BytesToLetters(body), alpha)
return s, err
}