@gmod/bed

bed-js

Performs parsing of BED files including autoSql

Usage

Example

You can pipe your file through this programs parseLine function

var parser = new BED()
var text = fs.readFileSync('file.txt', 'utf8')
var results = text.split('\n').map(line => parser.parseLine(line))

BED parser with default schema

The default instantiation of the parser with new BED() simply parses lines assuming the fields come from the standard BED schema.

The default schema is the same 12 fields as UCSC

chrom
chromStart
chromEnd
name
score
strand
thickStart
thickEnd
itemRgb
blockCount
blockSizes
blockStarts

If only a subset of those are used, it just parses up to that, e.g. your line can just contain chrom, chromStart, chromEnd, name, score.

BED parser with alternative schema

If you have a BED format that corresponds to a different schema, you can specify from a list of default built in alternate schemas or specify an autoSql as a string

The alternative types by default include

bigInteract
bigMaf
bigPsl
bigNarrowPeak
bigGenePred
bigLink
bigChain
mafFrames
mafSummary

Specify this in the type for the BED constructor

const p = new BED({ type: 'bigGenePred' })
const line = 'chr1\t11868\t14409\tENST00000456328.2\t1000\t+\t11868\t11868\t255,128,0\t3\t359,109,1189,\t0,744,1352,\tDDX11L1\tnone\tnone\t-1,-1,-1,\tnone\tENST00000456328.2\tDDX11L1\tnone'
p.parseLine(line)
// above line outputs
      { refID: 'chr1',
        start: 11868,
        end: 14409,
        name: 'ENST00000456328.2',
        score: 1000,
        strand: 1,
        thick_start: 11868,
        thick_end: 11868,
        reserved: '255,128,0',
        block_count: 3,
        block_sizes: [ 359, 109, 1189 ],
        chrom_starts: [ 0, 744, 1352 ],
        name2: 'DDX11L1',
        cds_start_stat: 'none',
        cds_end_stat: 'none',
        exon_frames: [ -1, -1, -1 ],
        type: 'none',
        gene_name: 'ENST00000456328.2',
        gene_name2: 'DDX11L1',
        gene_type: 'none' }

BED parser with autoSql

If you have a BED format with a custom alternative schema with autoSql, or if you are using a BigBed file that contains autoSql (e.g. with @gmod/bbi then you can get it from header.autoSql) then you can supply this via the constructor

const p = new BED({ autoSql: /* your autosql formatted string here */ })

Your autosql will be validated against a grammar for autoSql and used in subsequent parseLine calls

Important notes

• BED parsing does not do any conversion of types beyond string vs int but helps assign keys to values
• Parsing does not convert blockStarts/blockEnds to gene features
• It does not parse header or track lines

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

1.0.1 (2019-04-02)

• Added BED12 support
• Improved documentation
• Fixed babel loader for webpack