fasta

Documentation

Overview

Package fasta is a library for parsing and representing FASTA files, and creating and reading elfasta files.

Index

• Variables
• func ParseFai(filename string) (fai map[string]FaiReference)
• func ParseFasta(filename string, fai map[string]FaiReference, toUpper, toN bool) (fasta map[string][]byte)
• func ToElfasta(fasta map[string][]byte, filename string)
• func ToN(base byte) byte
• func ToUpperAndN(base byte) byte
• type FaiReference
• type MappedFasta
  • func OpenElfasta(filename string) (result *MappedFasta)
  • func (fasta *MappedFasta) Close()
  • func (fasta *MappedFasta) Seq(contig string) []byte

Variables

var ElfastaMagic = []byte{0x31, 0xFA, 0x57, 0xA1} // 31FA57A1 => ELFASTA1

ElfastaMagic is the magic byte sequence that every .elfasta file starts with.

Functions

func ParseFai

func ParseFai(filename string) (fai map[string]FaiReference)

ParseFai parses an FAI file.

func ParseFasta

func ParseFasta(filename string, fai map[string]FaiReference, toUpper, toN bool) (fasta map[string][]byte)

ParseFasta sequentially parses a FASTA file.

If fai is given, the sequences can be pre-allocated to reduce pressure on the garbage collector. If toUpper is true, the contents are converetd to upper case. If toN is true, ambiguity codes are normalized.

func ToElfasta

func ToElfasta(fasta map[string][]byte, filename string)

ToElfasta stores fasta data into an elprep-defined mmappable .elfasta file.

func ToN

func ToN(base byte) byte

ToN can be used to normalize ambiguity codes in FASTA references.

func ToUpperAndN

func ToUpperAndN(base byte) byte

ToUpperAndN can be used to normalize ambiguity codes in FASTA references, and convert all codes to upper case.

Types

type FaiReference

type FaiReference struct {
	Length    int32
	Offset    int64
	LineBases int32
	LineWidth int32
}

FaiReference represents an entry in an FAI file.

type MappedFasta

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

MappedFasta represents the contents of an .elfasta file.

func OpenElfasta

func OpenElfasta(filename string) (result *MappedFasta)

OpenElfasta opens a .elfasta file.

func (*MappedFasta) Close

func (fasta *MappedFasta) Close()

Close closes the .elfasta file.

func (*MappedFasta) Seq

func (fasta *MappedFasta) Seq(contig string) []byte

Seq fetches a sequence for the given contig from the .elfasta file.