@gmod/indexedfasta

    2.0.1 • Public • Published

    NPM version Build Status Coverage Status

    Install

    $ npm install --save @gmod/indexedfasta
    

    Usage

    const { IndexedFasta, BgzipIndexedFasta } = require("@gmod/indexedfasta");
    
    const t = new IndexedFasta({
      path: "test.fa",
      faiPath: "test.fa.fai"
    });
    // or
    const t = new BgzipIndexedFasta({
      path: "test.fa.gz",
      faiPath: "test.fa.gz.fai",
      gziPath: "test.fa.gz.gzi",
      chunkSizeLimit: 500000
    });
    
    // 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();

    If you are using in the browser, you may use the generic-filehandle package and initialize like this

    import { IndexedFasta, BgzipIndexedFasta } from '@gmod/indexedfasta'
    import { RemoteFile } from 'generic-filehandle'
    
    const t = new IndexedFasta({
      filehandle: new RemoteFile("http://yourside.com/test.fa"),
      faiFilehandle: new RemoteFile("http://yourside.com/test.fa.fai"),
    });
    const t = new BgzipIndexedFasta({
      filehandle: new RemoteFile("http://yourside.com/test.fa.gz"),
      faiFilehandle: new RemoteFile("http://yourside.com/test.fa.gz.fai"),
      gziFilehandle: new RemoteFile("http://yourside.com/test.fa.gz.gzi"),
    });
    

    In node.js you can also access remote files with generic-filehandle, but you would supply a fetch function e.g.

    import { IndexedFasta, BgzipIndexedFasta } from '@gmod/indexedfasta'
    import { RemoteFile } from 'generic-filehandle'
    import fetch from 'cross-fetch'
    
    const t = new IndexedFasta({
      filehandle: new RemoteFile("http://yourside.com/test.fa", {fetch}),
      faiFilehandle: new RemoteFile("http://yourside.com/test.fa.fai",{fetch}),
    });
    

    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 © Colin Diesh

    Install

    npm i @gmod/indexedfasta

    DownloadsWeekly Downloads

    418

    Version

    2.0.1

    License

    MIT

    Unpacked Size

    35.8 kB

    Total Files

    10

    Last publish

    Collaborators

    • nathandunn
    • rbuels
    • enuggetry
    • cmdcolin
    • garrettjstevens