fasta

Documentation

Overview

Package to read and write FASTA format files

Index

• Variables
• func Format(s *seq.Seq, width int) (sequence string)
• type Reader
  • func NewReader(f io.ReadCloser) *Reader
  • func NewReaderName(name string) (r *Reader, err error)
  • func (self *Reader) Close() (err error)
  • func (self *Reader) Read() (sequence *seq.Seq, err error)
  • func (self *Reader) Rewind() (err error)
• type Writer
  • func NewWriter(f io.WriteCloser, width int) *Writer
  • func NewWriterName(name string, width int) (w *Writer, err error)
  • func (self *Writer) Close() (err error)
  • func (self *Writer) Flush() error
  • func (self *Writer) Write(s *seq.Seq) (n int, err error)

Variables

var (
	IDPrefix  = []byte(">") // default delimiters
	SeqPrefix = []byte("")  // default delimiters
)

Functions

func Format

func Format(s *seq.Seq, width int) (sequence string)

Format a single sequence into fasta string

Types

type Reader

type Reader struct {
	IDPrefix  []byte
	SeqPrefix []byte
	// contains filtered or unexported fields
}

Fasta sequence format reader type.

func NewReader

func NewReader(f io.ReadCloser) *Reader

Returns a new fasta format reader using f.

func NewReaderName

func NewReaderName(name string) (r *Reader, err error)

Returns a new fasta format reader using a filename.

func (*Reader) Close

func (self *Reader) Close() (err error)

Close the reader.

func (*Reader) Read

func (self *Reader) Read() (sequence *seq.Seq, err error)

Read a single sequence and return it or an error.

func (*Reader) Rewind

func (self *Reader) Rewind() (err error)

Rewind the reader.

type Writer

type Writer struct {
	IDPrefix  string
	SeqPrefix string
	Width     int
	// contains filtered or unexported fields
}

Fasta sequence format writer type.

func NewWriter

func NewWriter(f io.WriteCloser, width int) *Writer

Returns a new fasta format writer using f.

func NewWriterName

func NewWriterName(name string, width int) (w *Writer, err error)

Returns a new fasta format writer using a filename, truncating any existing file. If appending is required use NewWriter and os.OpenFile.

func (*Writer) Close

func (self *Writer) Close() (err error)

Close the writer, flushing any unwritten sequence.

func (*Writer) Flush

func (self *Writer) Flush() error

Flush the writer.

func (*Writer) Write

func (self *Writer) Write(s *seq.Seq) (n int, err error)

Write a single sequence and return the number of bytes written and any error.