Exemplo n.º 1
0
Arquivo: fastq.go Projeto: frogs/biogo
// Read a single sequence and return it or an error.
// TODO: Does not read multi-line fastq.
func (self *Reader) Read() (s seq.Sequence, err error) {
	var (
		buff, line, label []byte
		isPrefix          bool
		seqBuff           []alphabet.QLetter
		t                 seqio.SequenceAppender
	)

	inQual := false

	for {
		if buff, isPrefix, err = self.r.ReadLine(); err == nil {
			if isPrefix {
				line = append(line, buff...)
				continue
			} else {
				line = buff
			}

			line = bytes.TrimSpace(line)
			if len(line) == 0 {
				continue
			}
			switch {
			case !inQual && line[0] == '@':
				t = self.readHeader(line)
				label, line = line, nil
			case !inQual && line[0] == '+':
				if len(label) == 0 {
					return nil, bio.NewError("fastq: no header line parsed before +line in fastq format", 0)
				}
				if len(line) > 1 && bytes.Compare(label[1:], line[1:]) != 0 {
					return nil, bio.NewError("fastq: quality header does not match sequence header", 0)
				}
				inQual = true
			case !inQual:
				line = bytes.Join(bytes.Fields(line), nil)
				seqBuff = make([]alphabet.QLetter, len(line))
				for i := range line {
					seqBuff[i].L = alphabet.Letter(line[i])
				}
			case inQual:
				line = bytes.Join(bytes.Fields(line), nil)
				if len(line) != len(seqBuff) {
					return nil, bio.NewError("fastq: sequence/quality length mismatch", 0)
				}
				for i := range line {
					seqBuff[i].Q = alphabet.DecodeToQphred(line[i], self.enc)
				}
				t.AppendQLetters(seqBuff...)

				return t, nil
			}
		} else {
			return
		}
	}

	panic("cannot reach")
}
Exemplo n.º 2
0
Arquivo: qseq.go Projeto: frogs/biogo
// Decode a quality letter to a phred score based on the sequence encoding setting.
func (self *QSeq) QDecode(l byte) alphabet.Qphred { return alphabet.DecodeToQphred(l, self.encoding) }