Beispiel #1
0
func initBufferedReader(file string, bufferSize int, chunkSize int, fn func(line string) (interface{}, bool, error)) (*BufferedReader, error) {
	if bufferSize < 1 {
		bufferSize = 1
	}
	if chunkSize < 1 {
		chunkSize = 1
	}

	reader := new(BufferedReader)
	fh, err := xopen.Ropen(file)
	if err != nil {
		return nil, err
	}
	reader.reader = fh

	reader.BufferSize = bufferSize
	reader.ChunkSize = chunkSize
	reader.ProcessFunc = fn
	reader.Ch = make(chan Chunk, bufferSize)
	reader.done = make(chan struct{})

	reader.finished = false
	reader.cancelled = false
	return reader, nil
}
Beispiel #2
0
// NewReader is constructor of FASTX Reader.
//
// Parameters:
//
//        t            sequence alphabet
//                     if nil is given, it will guess alphabet by the first record
//        file         file name, "-" for stdin
//        idRegexp     id parsing regular expression string, must contains "(" and ")" to capture matched ID
//                     "" for default value: `^([^\s]+)\s?`
//                     if record head does not match the idRegxp, whole name will be the id
//
func NewReader(t *seq.Alphabet, file string, idRegexp string) (*Reader, error) {
	var r *regexp.Regexp
	if idRegexp == "" {
		r = regexp.MustCompile(DefaultIDRegexp)
		isUsingDefaultIDRegexp = true
	} else {
		if !reCheckIDregexpStr.MatchString(idRegexp) {
			return nil, fmt.Errorf(`fastx: regular expression must contain "(" and ")" to capture matched ID. default: %s`, DefaultIDRegexp)
		}
		var err error
		r, err = regexp.Compile(idRegexp)
		if err != nil {
			return nil, fmt.Errorf("fastx: fail to compile regexp: %s", idRegexp)
		}
		if idRegexp == DefaultIDRegexp {
			isUsingDefaultIDRegexp = true
		}
	}

	fh, err := xopen.Ropen(file)
	if err != nil {
		return nil, fmt.Errorf("fastx: %s", err)
	}

	fastxReader := &Reader{
		fh:           fh,
		buf:          make([]byte, pageSize),
		t:            t,
		IDRegexp:     r,
		firstseq:     true,
		checkSeqType: true,
	}
	fastxReader.buffer = bytes.NewBuffer(make([]byte, 0, defaultBytesBufferSize))
	fastxReader.seqBuffer = bytes.NewBuffer(make([]byte, 0, defaultBytesBufferSize))
	fastxReader.qualBuffer = bytes.NewBuffer(make([]byte, 0, defaultBytesBufferSize))

	return fastxReader, nil
}