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fasta.go
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fasta.go
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// Copyright ©2011-2013 The bíogo Authors. All rights reserved.
// Use of this source code is governed by a BSD-style
// license that can be found in the LICENSE file.
// Package fasta provides types to read and write FASTA format files.
package fasta
import (
"github.com/biogo/biogo/alphabet"
"github.com/biogo/biogo/io/seqio"
"github.com/biogo/biogo/seq"
"bufio"
"bytes"
"fmt"
"io"
)
var (
_ seqio.Reader = (*Reader)(nil)
_ seqio.Writer = (*Writer)(nil)
)
// Default delimiters.
const (
DefaultIDPrefix = ">"
DefaultSeqPrefix = ""
)
// Fasta sequence format reader type.
type Reader struct {
r *bufio.Reader
t seqio.SequenceAppender
IDPrefix []byte
SeqPrefix []byte
working seqio.SequenceAppender
err error
}
// Returns a new fasta format reader using f. Sequences returned by the Reader are copied
// from the provided template.
func NewReader(f io.Reader, template seqio.SequenceAppender) *Reader {
return &Reader{
r: bufio.NewReader(f),
t: template,
IDPrefix: []byte(DefaultIDPrefix),
SeqPrefix: []byte(DefaultSeqPrefix),
}
}
// Read a single sequence and return it and potentially an error. Note that
// a non-nil returned error may be associated with a valid sequence, so it is
// the responsibility of the caller to examine the error to determine whether
// the read was successful.
// Note that if the Reader's template type returns different non-nil error
// values from calls to SetName and SetDescription, a new error string will be
// returned on each call to Read. So to allow direct error comparison these
// methods should return the same error.
func (r *Reader) Read() (seq.Sequence, error) {
var (
buff, line []byte
isPrefix bool
s seq.Sequence
)
defer func() {
if r.working == nil {
r.err = nil
}
}()
for {
var err error
if buff, isPrefix, err = r.r.ReadLine(); err != nil {
if err != io.EOF || r.working == nil {
return nil, err
}
s, err = r.working, r.err
r.working = nil
return s, err
}
line = append(line, buff...)
if isPrefix {
continue
}
line = bytes.TrimSpace(line)
if len(line) == 0 {
continue
}
if bytes.HasPrefix(line, r.IDPrefix) {
if r.working == nil {
r.working, r.err = r.header(line)
line = nil
} else {
s, err = r.working, r.err
r.working, r.err = r.header(line)
return s, err
}
} else if bytes.HasPrefix(line, r.SeqPrefix) {
if r.working == nil {
return nil, fmt.Errorf("fasta: badly formed line %q", line)
}
line = bytes.Join(bytes.Fields(line[len(r.SeqPrefix):]), nil)
r.working.AppendLetters(alphabet.BytesToLetters(line)...)
line = nil
} else {
return nil, fmt.Errorf("fasta: badly formed line %q", line)
}
}
}
func (r *Reader) header(line []byte) (seqio.SequenceAppender, error) {
s := r.t.Clone().(seqio.SequenceAppender)
fieldMark := bytes.IndexAny(line, " \t")
var err error
if fieldMark < 0 {
err = s.SetName(string(line[len(r.IDPrefix):]))
return s, err
} else {
err = s.SetName(string(line[len(r.IDPrefix):fieldMark]))
_err := s.SetDescription(string(line[fieldMark+1:]))
if err != nil || _err != nil {
switch {
case err == _err:
return s, err
case err != nil && _err != nil:
return s, fmt.Errorf("fasta: multiple errors: name: %s, desc:%s", err, _err)
case err != nil:
return s, err
case _err != nil:
return s, _err
}
}
}
return s, nil
}
// Fasta sequence format writer type.
type Writer struct {
w io.Writer
IDPrefix []byte
SeqPrefix []byte
Width int
}
// Returns a new fasta format writer using f.
func NewWriter(w io.Writer, width int) *Writer {
return &Writer{
w: w,
IDPrefix: []byte(DefaultIDPrefix),
SeqPrefix: []byte(DefaultSeqPrefix),
Width: width,
}
}
// Write a single sequence and return the number of bytes written and any error.
func (w *Writer) Write(s seq.Sequence) (n int, err error) {
var (
_n int
prefix = append([]byte{'\n'}, w.SeqPrefix...)
)
id, desc := s.Name(), s.Description()
header := make([]byte, 0, len(w.IDPrefix)+len(id)+len(desc)+1)
header = append(header, w.IDPrefix...)
header = append(header, id...)
if len(desc) > 0 {
header = append(header, ' ')
header = append(header, desc...)
}
n, err = w.w.Write(header)
if err != nil {
return n, err
}
for i := 0; i < s.Len(); i++ {
if i%w.Width == 0 {
_n, err = w.w.Write(prefix)
if n += _n; err != nil {
return n, err
}
}
_n, err = w.w.Write([]byte{byte(s.At(i).L)})
if n += _n; err != nil {
return n, err
}
}
_n, err = w.w.Write([]byte{'\n'})
if n += _n; err != nil {
return n, err
}
return n, nil
}