fasta

Documentation

Index

• Constants
• func WriteAlignment(sb align.SeqBag) string
• func WriteSequences(sb align.SeqBag) string
• type Parser
  • func NewParser(r io.Reader) *Parser
  • func (p *Parser) Parse() (al align.Alignment, err error)
  • func (p *Parser) ParseUnalign() (sb align.SeqBag, err error)
• type Scanner
  • func NewScanner(r io.Reader) *Scanner
  • func (s *Scanner) Scan() (tok Token, lit string)
• type Token

Constants

const (
	FASTA_LINE_LEN   = 80 // max line length for fasta output
	FASTA_INITIAL_NB = 2  // max line length for fasta output
)

const (
	FASTA_LINE = 80
)

Functions

func WriteAlignment

func WriteAlignment(sb align.SeqBag) string

func WriteSequences

func WriteSequences(sb align.SeqBag) string

Write input alignment as standard fasta sequences It removes "-" characters.

Types

type Parser

type Parser struct {
	// contains filtered or unexported fields
}

Parser represents a parser.

func NewParser

func NewParser(r io.Reader) *Parser

NewParser returns a new instance of Parser.

func (*Parser) Parse

func (p *Parser) Parse() (al align.Alignment, err error)

Parse parses a FASTA alignment

func (*Parser) ParseUnalign

func (p *Parser) ParseUnalign() (sb align.SeqBag, err error)

ParseUnalign parses an unaligned FASTA file

type Scanner

type Scanner struct {
	// contains filtered or unexported fields
}

Scanner represents a lexical scanner.

func NewScanner

func NewScanner(r io.Reader) *Scanner

NewScanner returns a new instance of Scanner.

func (*Scanner) Scan

func (s *Scanner) Scan() (tok Token, lit string)

Scan returns the next token and literal value.

type Token

type Token int64

const (
	ILLEGAL    Token = iota
	STARTIDENT       // > start of ident line
	IDENTIFIER       // Identifier of sequence or part of sequence
	ENDOFLINE        // End of line token
	EOF              // End of File
)