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
}
// Read a single sequence and return it or an error.
// TODO: Does not read interleaved fastq.
func (self *Reader) Read() (sequence *seq.Seq, err error) {
var line, label, seqBody, qualBody []byte
sequence = &seq.Seq{}
inQual := false
READ:
for {
line, err = self.r.ReadBytes('\n')
if err == nil {
if len(line) > 0 && line[len(line)-1] == '\r' {
line = line[:len(line)-1]
}
line = bytes.TrimSpace(line)
if len(line) == 0 {
continue
}
switch {
case !inQual && line[0] == '@':
label = line[1:]
case !inQual && line[0] == '+':
if len(label) == 0 {
return nil, bio.NewError("No ID line parsed at +line in fastq format", 0)
}
if len(line) > 1 && bytes.Compare(label, line[1:]) != 0 {
return nil, bio.NewError("Quality ID does not match sequence ID", 0)
}
inQual = true
case !inQual:
line = bytes.Join(bytes.Fields(line), nil)
seqBody = append(seqBody, line...)
case inQual:
line = bytes.Join(bytes.Fields(line), nil)
qualBody = append(qualBody, line...)
if len(qualBody) >= len(seqBody) {
break READ
}
}
} else {
return
}
}
if len(seqBody) != len(qualBody) {
return nil, bio.NewError("Quality length does not match sequence length", 0)
}
labelString := string(label)
sequence = seq.New(labelString, seqBody, seq.NewQuality(labelString, self.decodeQuality(qualBody)))
return
}
// Read a single sequence and return it or an error.
func (self *Reader) Read() (sequence *seq.Seq, err error) {
var line, label, body []byte
label = self.last
READ:
for {
line, err = self.r.ReadBytes('\n')
if err == nil {
self.line++
if len(line) > 0 && line[len(line)-1] == '\r' {
line = line[:len(line)-1]
}
line = bytes.TrimSpace(line)
if len(line) == 0 {
continue
}
switch {
case bytes.HasPrefix(line, self.IDPrefix):
if self.last == nil {
self.last = line[len(self.IDPrefix):]
} else {
label = self.last
self.last = line[len(self.IDPrefix):] // entering a new sequence so exit read loop
break READ
}
case bytes.HasPrefix(line, self.SeqPrefix):
line = bytes.Join(bytes.Fields(line[len(self.SeqPrefix):]), nil)
body = append(body, line...)
}
} else {
if self.last != nil {
label = self.last
self.last = nil
err = nil
break
} else {
return nil, io.EOF
}
}
}
if len(label) > 0 || len(body) > 0 {
sequence = seq.New(string(label), body, nil)
} else {
err = bio.NewError("fasta: empty sequence", 0, self.line)
}
return
}
