@gmod/twobit

Read .2bit sequence files using pure JavaScript, works in node or in the browser.

Install

$ npm install --save @gmod/twobit

Usage

const { TwoBitFile } = require('@gmod/twobit')
const t = new TwoBitFile({
  path: require.resolve('./data/foo.2bit'),
})

// get the first 10 bases of a sequence from the file.
// coordinates are UCSC standard 0-based half-open
const chr1Region = await t.getSequence('chr1', 0, 10)
// chr1Region is now a string of bases, 'ACTG...'

// get a whole sequence from the file
const chr1Bases = await t.getSequence('chr1')

// get object with all seq lengths as { seqName => length, ... }
const allSequenceSizes = await t.getSequenceSizes()

// get the size of a single sequence
const chr1Size = await t.getSequenceSize('chr1')

// get an array of all sequence names in the file
const seqNames = await t.getSequenceNames()

API

TwoBitFile

Table of Contents

• constructor
  • Parameters
• getHeader
• getIndex
• getSequenceNames
• getSequenceSizes
• getSequenceSize
  • Parameters
• getSequence
  • Parameters

constructor

Parameters

• args object

  • args.filehandle Filehandle? node fs.promises-like filehandle for the .2bit file. Only needs to support filehandle.read(buffer, offset, length, position)
  • args.path string? filesystem path for the .2bit file to open

getHeader

Returns Promise for object with the file's header information, like { magic: 0x1a412743, version: 0, sequenceCount: 42, reserved: 0 }

getIndex

Returns Promise for object with the file's index of offsets, like { seqName: fileOffset, ...}

getSequenceNames

Returns Promise for an array of string sequence names that are found in the file

getSequenceSizes

Returns Promise for an object listing the lengths of all sequences like {seqName: length, ...}.note: this is a relatively slow operation especially if there are many refseqs in the file, if you can get this information from a different file e.g. a chrom.sizes file, it will be much faster

getSequenceSize

Parameters

• seqName string name of the sequence

Returns Promise for the sequence's length, or undefined if it is not in the file

getSequence

Parameters

• seqName string name of the sequence you want
• regionStart number? optional 0-based half-open start of the sequence region to fetch. (optional, default 0)
• regionEnd number? optional 0-based half-open end of the sequence region to fetch. defaults to end of the sequence (optional, default Number.POSITIVE_INFINITY)

Returns Promise for a string of sequence bases

Academic Use

This package was written with funding from the NHGRI as part of the JBrowse project. If you use it in an academic project that you publish, please cite the most recent JBrowse paper, which will be linked from jbrowse.org.

License

MIT © Robert Buels