func (self *Reader) metaSequence(moltype, id string) (sequence *seq.Seq, err error) {
var line, body []byte
for {
line, err = self.r.ReadBytes('\n')
if err != nil {
return nil, err
}
if len(line) > 0 && line[len(line)-1] == '\r' {
line = line[:len(line)-1]
}
if len(line) == 0 {
continue
}
if len(line) < 2 || !bytes.HasPrefix(line, []byte("##")) {
return nil, bio.NewError("Corrupt metasequence", 0, line)
}
line = bytes.TrimSpace(line[2:])
if string(line) == "end-"+moltype {
break
} else {
line = bytes.Join(bytes.Fields(line), nil)
body = append(body, line...)
}
}
sequence = seq.New(id, body, nil)
sequence.Moltype = bio.ParseMoltype(moltype)
return
}
func (self *Reader) commentMetaline(line string) (f *feat.Feature, err error) {
// Load these into a slice in a MetaField of the Feature
fields := strings.Split(string(line), " ")
switch fields[0] {
case "gff-version":
self.Version, err = strconv.Atoi(fields[1])
if err != nil {
self.Version = DefaultVersion
}
return self.Read()
case "source-version":
if len(fields) > 1 {
self.SourceVersion = strings.Join(fields[1:], " ")
return self.Read()
} else {
return nil, bio.NewError("Incomplete source-version metaline", 0, fields)
}
case "date":
if len(fields) > 1 {
self.Date, err = time.Parse(self.TimeFormat, strings.Join(fields[1:], " "))
return self.Read()
} else {
return nil, bio.NewError("Incomplete date metaline", 0, fields)
}
case "Type":
if len(fields) > 1 {
self.Type = bio.ParseMoltype(fields[1])
return self.Read()
} else {
return nil, bio.NewError("Incomplete Type metaline", 0, fields)
}
case "sequence-region":
if len(fields) > 3 {
var start, end int
start, err = strconv.Atoi(fields[2])
if err != nil {
return nil, err
} else {
if self.OneBased {
start = bio.OneToZero(start)
}
}
end, err = strconv.Atoi(fields[3])
if err != nil {
return nil, err
}
f = &feat.Feature{
Meta: &feat.Feature{
ID: fields[1],
Start: start,
End: end,
},
}
} else {
return nil, bio.NewError("Incomplete sequence-region metaline", 0, fields)
}
case "DNA", "RNA", "Protein":
if len(fields) > 1 {
var s *seq.Seq
s, err = self.metaSequence(fields[0], fields[1])
if err != nil {
return
} else {
f = &feat.Feature{Meta: s}
}
} else {
return nil, bio.NewError("Incomplete sequence metaline", 0, fields)
}
default:
f = &feat.Feature{Meta: line}
}
return
}