@gmod/twobit
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    1.1.13 • Public • Published

    @gmod/twobit

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    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

    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

    Keywords

    Install

    npm i @gmod/twobit

    DownloadsWeekly Downloads

    374

    Version

    1.1.13

    License

    MIT

    Unpacked Size

    89.2 kB

    Total Files

    23

    Last publish

    Collaborators

    • teresam856
    • nathandunn
    • rbuels
    • enuggetry
    • cmdcolin
    • garrettjstevens