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/** | ||
* Class for parsing chromosome bands for idiograms. | ||
* Format taken from https://github.com/hammerlab/idiogrammatik. | ||
* @flow | ||
*/ | ||
'use strict'; | ||
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import ContigInterval from '../ContigInterval'; | ||
import type {CoverageCount} from '../viz/pileuputils'; | ||
import _ from 'underscore'; | ||
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// chromosomal band (see https://github.com/hammerlab/idiogrammatik/blob/master/data/basic-chromosomes.json) | ||
// for an example | ||
export type Band = { | ||
start: number; | ||
end: number; | ||
name: string; | ||
value: string; | ||
} | ||
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class Chromosome { | ||
name: string; | ||
bands: Band[]; | ||
position: ContigInterval<string>; | ||
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constructor(chromosome: Object) { | ||
this.name = chromosome.name; | ||
this.bands = chromosome.bands; | ||
// create region for chromosome | ||
var start = _.min(this.bands, band => band.start).start; | ||
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var stop = _.max(this.bands, band => band.end).end; | ||
this.position = new ContigInterval(this.name, start, stop); | ||
} | ||
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getKey(): string { | ||
return this.name; | ||
} | ||
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getInterval(): ContigInterval<string> { | ||
return this.position; | ||
} | ||
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getCoverage(referenceSource: Object): CoverageCount { | ||
return { | ||
range: this.getInterval(), | ||
opInfo: null | ||
}; | ||
} | ||
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intersects(range: ContigInterval<string>): boolean { | ||
return range.intersects(this.position); | ||
} | ||
} | ||
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module.exports = Chromosome; |
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/** | ||
* Fetcher/parser for gzipped Cytoband files. Cytoband files can be downloaded | ||
* or accessed from http://hgdownload.cse.ucsc.edu/goldenpath for a genome build. | ||
* | ||
* extracts CONTIG, START, END, NAME and VALUE | ||
* | ||
* @flow | ||
*/ | ||
'use strict'; | ||
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import type AbstractFile from '../AbstractFile'; | ||
import type Q from 'q'; | ||
import _ from 'underscore'; | ||
import ContigInterval from '../ContigInterval'; | ||
import Chromosome from './chromosome'; | ||
import pako from 'pako/lib/inflate'; // for gzip inflation | ||
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function extractLine(cytoBandLine: string): Object { | ||
var split = cytoBandLine.split('\t'); | ||
return { | ||
contig: split[0], | ||
band: { | ||
start: Number(split[1]), | ||
end: Number(split[2]), | ||
name: split[3], | ||
value: split[4] | ||
} | ||
}; | ||
} | ||
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function groupedBandsToChromosome(grouped: Object[]): Chromosome { | ||
var bands = _.map(grouped, g => g.band); | ||
return new Chromosome( | ||
{name: grouped[0].contig, | ||
bands: bands, | ||
position: new ContigInterval(grouped[0].contig, bands[0].start, bands.slice(-1)[0].end)} | ||
); | ||
} | ||
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class ImmediateCytoBandFile { | ||
chrs: {[key:string]:Chromosome}; | ||
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constructor(chrs: {[key:string]:Chromosome}) { | ||
this.chrs = chrs; | ||
} | ||
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getFeaturesInRange(range: ContigInterval<string>): Chromosome { | ||
return this.chrs[range.contig]; | ||
} | ||
} | ||
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class CytoBandFile { | ||
remoteFile: AbstractFile; | ||
immediate: Q.Promise<ImmediateCytoBandFile>; | ||
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constructor(remoteFile: AbstractFile) { | ||
this.remoteFile = remoteFile; | ||
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this.immediate = this.remoteFile.getAll().then(bytes => { | ||
var txt = pako.inflate(bytes, {to: 'string'}); | ||
var txtLines = _.filter(txt.split('\n'), i => i); // gets rid of empty lines | ||
var lines = txtLines.map(extractLine); | ||
return lines; | ||
}).then(lines => { | ||
// group bands by contig | ||
var grouped = _.groupBy(lines, l => l.contig); | ||
var chrs = _.mapObject(grouped, g => groupedBandsToChromosome(g)); | ||
return new ImmediateCytoBandFile(chrs); | ||
}); | ||
this.immediate.done(); | ||
} | ||
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getFeaturesInRange(range: ContigInterval<string>): Q.Promise<Chromosome[]> { | ||
return this.immediate.then(immediate => { | ||
return immediate.getFeaturesInRange(range); | ||
}); | ||
} | ||
} | ||
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module.exports = { | ||
CytoBandFile | ||
}; |
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/** | ||
* A data source which implements generic JSON protocol. | ||
* Currently only used to load alignments. | ||
* @flow | ||
*/ | ||
'use strict'; | ||
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import type {DataSource} from '../sources/DataSource'; | ||
import Chromosome from '../data/chromosome'; | ||
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import _ from 'underscore'; | ||
import {Events} from 'backbone'; | ||
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import ContigInterval from '../ContigInterval'; | ||
import type {GenomeRange} from '../types'; | ||
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function create(json: string): DataSource<Chromosome> { | ||
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// parse json | ||
var parsedJson = JSON.parse(json); | ||
var chromosomes: Chromosome[] = []; | ||
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// fill chromosomes with json | ||
if (!_.isEmpty(parsedJson)) { | ||
chromosomes = _.values(parsedJson).map(chr => new Chromosome(chr)); | ||
} | ||
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function rangeChanged(newRange: GenomeRange) { | ||
// Data is already parsed, so immediately return | ||
var range = new ContigInterval(newRange.contig, newRange.start, newRange.stop); | ||
o.trigger('newdata', range); | ||
o.trigger('networkdone'); | ||
return; | ||
} | ||
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function getFeaturesInRange(range: ContigInterval<string>): Chromosome[] { | ||
return _.filter(chromosomes, chr => range.chrOnContig(chr.name)); | ||
} | ||
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var o = { | ||
rangeChanged, | ||
getFeaturesInRange, | ||
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on: () => {}, | ||
once: () => {}, | ||
off: () => {}, | ||
trigger: (string, any) => {} | ||
}; | ||
_.extend(o, Events); | ||
return o; | ||
} | ||
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module.exports = { | ||
create | ||
}; |
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/** | ||
* The "glue" between cytoBand.js and IdiogramTrack.js. | ||
* | ||
* Allows loading remote gzipped cytoband files into an Idiogram visualization. | ||
* | ||
* @flow | ||
*/ | ||
'use strict'; | ||
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import _ from 'underscore'; | ||
import {Events} from 'backbone'; | ||
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import ContigInterval from '../ContigInterval'; | ||
import Chromosome from '../data/chromosome'; | ||
import type {GenomeRange} from '../types'; | ||
import {CytoBandFile} from '../data/cytoBand'; | ||
import type {DataSource} from '../sources/DataSource'; | ||
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import RemoteFile from '../RemoteFile'; | ||
import utils from '../utils'; | ||
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var createFromCytoBandFile = function(remoteSource: CytoBandFile): DataSource<Chromosome> { | ||
// Local cache of genomic data. | ||
var contigMap: {[key:string]: Chromosome} = {}; | ||
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// This either adds or removes a 'chr' as needed. | ||
function normalizeRange(range: ContigInterval<string>): ContigInterval<string> { | ||
if (contigMap[range.contig] !== undefined) { | ||
return range; | ||
} | ||
var altContig = utils.altContigName(range.contig); | ||
if (contigMap[altContig] !== undefined) { | ||
return new ContigInterval(altContig, range.start(), range.stop()); | ||
} | ||
return range; | ||
} | ||
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function fetch(range: ContigInterval<string>) { | ||
remoteSource.getFeaturesInRange(range) | ||
.then(chr => { | ||
contigMap[chr.name] = chr; | ||
}).then(() => { | ||
o.trigger('newdata', range); | ||
}).done(); | ||
} | ||
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function getFeaturesInRange(range: ContigInterval<string>): Chromosome[] { | ||
return [contigMap[normalizeRange(range).contig]]; | ||
} | ||
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var o = { | ||
// The range here is 0-based, inclusive | ||
rangeChanged: function(newRange: GenomeRange) { | ||
// Check if this interval is already in the cache. | ||
if ( contigMap[newRange.contig] !== undefined ) { | ||
return; | ||
} | ||
fetch(new ContigInterval(newRange.contig, newRange.start, newRange.stop)); | ||
}, | ||
getFeaturesInRange, | ||
// These are here to make Flow happy. | ||
on: () => {}, | ||
once: () => {}, | ||
off: () => {}, | ||
trigger: (status: string, param: any) => {} | ||
}; | ||
_.extend(o, Events); // Make this an event emitter | ||
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return o; | ||
}; | ||
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function create(url:string): DataSource<Chromosome> { | ||
if (!url) { | ||
throw new Error(`Missing URL from track: ${url}`); | ||
} | ||
return createFromCytoBandFile(new CytoBandFile(new RemoteFile(url))); | ||
} | ||
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module.exports = { | ||
create, | ||
createFromCytoBandFile, | ||
}; |
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