Esempio n. 1
0
File: gff.go Progetto: frogs/biogo
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
}
Esempio n. 2
0
File: gff.go Progetto: frogs/biogo
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
}