@gmod/bbi

bbi-js

A parser for bigwig and bigbed file formats

Usage

If using locally

import {BigWig} from '@gmod/bbi'
const ti = new BigWig({
  path: 'volvox.bw'
})
await ti.getHeader()
const feats = await ti.getFeatures('chr1', 0, 100, { scale: 1 })

Documentation

BigWig/BigBed constructors

Accepts an object containing either

a) path - uses the LocalFile class in this repo b) url - uses the RemoteFile class in this repo c) filehandle - accepts some custom file handle class that you provide

BigWig

getFeatures(refName, start, end, opts)

opts.scale - 1 is the maximum zoom level, fractional values indicate a accessing multiple zoom levels based on pixelsPerBp opts.signal - an AbortSignal to halt processing opts.basesPerScale - inverse of opts.scale

returns a promise to an array of features

getFeatureStream(refName, start, end, opts)

Same as obove but returns an RxJS observable stream

BigBed

getFeatures(refName, start, end, opts)

opts.signal - an AbortSignal to halt processing

returns a promise to an array of features

note about BigBed file processing

The BigBed line contents can be parsed by @gmod/bed, it is not integrated with this module by default but for example

    import {BigBed} from '@gmod/bed'
    import BED from '@gmod/bed'

    const ti = new BigBed({
      filehandle: new LocalFile(require.resolve('./data/hg18.bb')),
    })
    const {autoSql} = await ti.getHeader()
    const feats = await ti.getFeatures('chr7', 0, 100000)
    const parser = new BED({autoSql})
    const lines = feats.map(f => parser.parseBedText('chr7', f.start, f.end, f.rest, 3))

Example output

        { refID: 'chr7',
          start: 75460,
          end: 116489,
          name: 'uc003sin.1',
          score: 0,
          strand: -1,
          thick_start: 75460,
          thick_end: 75460,
          reserved: '255,0,0',
          sp_id: 'AL137655' } ]

Documentation

See docs

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

Changelog

1.0.9 (2019-04-05)

• Added caching of networking requests (thanks @rbuels for the abortable-promise-cache module!)
• Fix some type errors on the range class
• Correct using span on fixed size wiggle types