fasta

package
v0.2.7 Latest Latest
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Published: Mar 30, 2018 License: GPL-2.0 Imports: 7 Imported by: 3

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Constants

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

Variables

This section is empty.

Functions

func WriteAlignment

func WriteAlignment(al align.Alignment) string

func WriteSequences added in v0.1.1

func WriteSequences(al align.Alignment) string
This function writes the 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() (align.Alignment, error)

Parse parses a FASTA alignment

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
)

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