@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

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

BigWig

getFeatures(refName, start, end, opts)

• refName - a name of a chromosome in the file
• start - a 0-based half open start coordinate
• end - a 0-based half open end coordinate
• 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.

Example:

const feats = await bigwig.getFeatures('chr1', 0, 100)
// returns array of features with start, end, score
// coordinates on returned data are are 0-based half open
// no conversion to 1-based as in wig is done)
// note refseq is not returned on the object, it is clearly chr1 from the query though

getFeatureStream(refName, start, end, opts)

Same getFeatures but returns an RxJS observable stream, useful for very large queries

const observer = await bigwig.getFeatureStream('chr1', 0, 100)
observer.subscribe(chunk => { /* chunk contains array of features with start, end, score */ }, errorCallback, finishCallback)

BigBed

getFeatures(refName, start, end, opts)

• refName - a name of a chromosome in the file
• start - a 0-based half open start coordinate
• end - a 0-based half open end coordinate
• 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, coordinates are 0-based half open as in BED

        { 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

1.0.10 (2019-04-09)

• Fix misinterpretation of variable step wig files in this module (the span is not variable in variable step files, only the step, use bedGraphToBigWig for variable span)
• Improved docs