twobit

package module

v0.0.0-...-05260b0 Latest Latest Go to latest Published: Jul 23, 2021 License: BSD-3-Clause Imports: 9 Imported by: 0

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Repository

github.com/mendelics/twobit

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Open Source Insights

README ¶

mendelics/twobit

twobit is a 2bit file reader

twobit is pure Go library for reading 2bit files [1]. The 2bit file format stores DNA sequences in a compact randomly-accessible format.

Modified from github.com/aebruno/twobit.

References

[1] http://genome.ucsc.edu/FAQ/FAQformat#format7

Documentation ¶

Overview ¶

Package twobit implements the 2bit compact randomly-accessible file format for storing DNA sequence data.

Index ¶

Constants
Variables
func Unpack(raw []byte, sz int) string
type Block
type Reader
- func NewReader(r io.ReadSeeker) (*Reader, error)
type Service
- func NewDataService(twobitFile string) (Service, error)
type Writer

Constants ¶

View Source

const BASE_A = 'A'

BASE_A -

View Source

const BASE_C = 'C'

BASE_C -

View Source

const BASE_G = 'G'

BASE_G -

View Source

const BASE_N = 'N'

BASE_N -

View Source

const BASE_T = 'T'

BASE_T -

View Source

const SIG = 0x1A412743

SIG -

Variables ¶

View Source

var BYTES2NT = []byte{
	BASE_T,
	BASE_C,
	BASE_A,
	BASE_G,
}

BYTES2NT -

View Source

var NT2BYTES = []byte{}

NT2BYTES -

Functions ¶

func Unpack ¶

func Unpack(raw []byte, sz int) string

Unpack array of bytes to DNA string of length sz

Types ¶

type Block ¶

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

Block represents either blocks of Ns or masked (lower-case) blocks

func (*Block) Count ¶

func (b *Block) Count() int

Count - Return count of block

func (*Block) Length ¶

func (b *Block) Length() int

Length - Return length of block

func (*Block) Start ¶

func (b *Block) Start() int

Start - Return start of block

type Reader ¶

type Reader twoBit

Reader reads twobits

func NewReader ¶

func NewReader(r io.ReadSeeker) (*Reader, error)

NewReader returns a new TwoBit file reader which reads from r

func (*Reader) Count ¶

func (r *Reader) Count() int

Count - Returns the count of sequences in the 2bit file

func (*Reader) Length ¶

func (r *Reader) Length(name string) (int, error)

Length - Returns the length for sequence with name

func (*Reader) LengthNoN ¶

func (r *Reader) LengthNoN(name string) (int, error)

LengthNoN - Returns the length for sequence with name but does not count Ns

func (*Reader) NBlocks ¶

func (r *Reader) NBlocks(name string) ([]*Block, error)

NBlocks - Return blocks of Ns in sequence with name

func (*Reader) Names ¶

func (r *Reader) Names() []string

Names - Returns the names of sequences in the 2bit file

func (*Reader) Read ¶

func (r *Reader) Read(name string) ([]byte, error)

Read entire sequence.

func (*Reader) ReadRange ¶

func (r *Reader) ReadRange(name string, start, end int) ([]byte, error)

ReadRange - Read sequence from start to end.

func (*Reader) Version ¶

func (r *Reader) Version() int

Version - Returns the version of the 2bit file

type Service ¶

type Service interface {
	// Genomic Interval-based services
	GenomicInterval(chr string, start, end int) (string, error)                                                                                      // returns genomic sequence using 2-bit (from memory)
	GetGenomicIntervalWindow(chr string, start, end int, ref, alt string, windowL, windowR int) (seqRef, seqAlt string, err error)                   // returns ref and alt with window to left and right
	GetGenomicIntervalBound(chr string, start, end int, ref, alt string, intervalStart, intervalEnd int) (seqRef, seqAlt string, err error)          // returns ref and alt bound by interval (ex. interval = exon, will return exonRef and exonAlt sequences)
	GetGenomicIntervalStrand(chr string, start, end int, ref, alt string, windowL, windowR int, isPosStrand bool) (seqRef, seqAlt string, err error) // returns ref and alt with window to left and right, correct strand
}

Service includes all services

func NewDataService ¶

func NewDataService(twobitFile string) (Service, error)

NewDataService - Open 2-bit genome reference

type Writer ¶

type Writer twoBit

Writer writes twobits

Source Files ¶

View all Source files

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