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= f.rest.split('\t'), - // exons arrays sometimes have trailing commas - exonLengths = x[7].replace(/,*$/, '').split(',').map(Number), - exonStarts = x[8].replace(/,*$/, '').split(',').map(Number), - exons = _.zip(exonStarts, exonLengths) - .map(function([start, length]) { - return new Interval(f.start + start, f.start + start + length); - }); - - return { - position, - id: x[0], // e.g. ENST00000359597 - strand: x[2], // either + or - - codingRegion: new Interval(Number(x[3]), Number(x[4])), - geneId: x[9], - name: x[10], - exons - }; + x = f.rest.split('\t'), exons = []; + + if (x.length > 0 && x[0] !== "") { + // exons arrays sometimes have trailing commas + var exonLengths = x[7].replace(/,*$/, '').split(',').map(Number), + exonStarts = x[8].replace(/,*$/, '').split(',').map(Number); + exons = _.zip(exonStarts, exonLengths) + .map(function([start, length]) { + return new Interval(f.start + start, f.start + start + length); + }); + + return { + position, + id: x[0], // e.g. ENST00000359597 + strand: x[2], // either + or - + codingRegion: new Interval(Number(x[3]), Number(x[4])), + geneId: x[9], + name: x[10], + exons + }; + } else { + return { + position + }; + } } diff --git a/src/main/viz/GeneTrack.js b/src/main/viz/GeneTrack.js index 6ee6b740..c33ca897 100644 --- a/src/main/viz/GeneTrack.js +++ b/src/main/viz/GeneTrack.js @@ -57,7 +57,7 @@ function drawGeneName(ctx: CanvasRenderingContext2D, textIntervals: Interval[]) { var p = gene.position, centerX = 0.5 * (clampedScale(1 + p.start()) + clampedScale(1 + p.stop())); - var name = gene.name || gene.id; + var name = gene.name || gene.id || gene.position.toString(); var textWidth = ctx.measureText(name).width; var textInterval = new Interval(centerX - 0.5 * textWidth, centerX + 0.5 * textWidth); @@ -144,23 +144,25 @@ class GeneTrack extends React.Component { clampedScale(1 + gene.position.stop()), geneLineY + 0.5); // TODO: only compute all these intervals when data becomes available. - var exons = bedtools.splitCodingExons(gene.exons, gene.codingRegion); - exons.forEach(exon => { - ctx.fillRect(sc(1 + exon.start), - geneLineY - 3 * (exon.isCoding ? 2 : 1), - sc(exon.stop + 2) - sc(1 + exon.start), - 6 * (exon.isCoding ? 2 : 1)); - }); - - var introns = gene.position.interval.complementIntervals(gene.exons); - introns.forEach(range => { - drawArrow(ctx, clampedScale, range, geneLineY + 0.5, gene.strand); - }); - ctx.strokeStyle = style.GENE_COMPLEMENT_COLOR; - ctx.lineWidth = 2; - gene.exons.forEach(range => { - drawArrow(ctx, clampedScale, range, geneLineY + 0.5, gene.strand); - }); + if (gene.strand && gene.exons && gene.codingRegion) { + var exons = bedtools.splitCodingExons(gene.exons, gene.codingRegion); + exons.forEach(exon => { + ctx.fillRect(sc(1 + exon.start), + geneLineY - 3 * (exon.isCoding ? 2 : 1), + sc(exon.stop + 2) - sc(1 + exon.start), + 6 * (exon.isCoding ? 2 : 1)); + }); + + var introns = gene.position.interval.complementIntervals(gene.exons); + introns.forEach(range => { + drawArrow(ctx, clampedScale, range, geneLineY + 0.5, gene.strand); + }); + ctx.strokeStyle = style.GENE_COMPLEMENT_COLOR; + ctx.lineWidth = 2; + gene.exons.forEach(range => { + drawArrow(ctx, clampedScale, range, geneLineY + 0.5, gene.strand); + }); + } drawGeneName(ctx, clampedScale, geneLineY, gene, textIntervals); diff --git a/src/test/components-bigbed-test.js b/src/test/components-bigbed-test.js new file mode 100644 index 00000000..5c3c358b --- /dev/null +++ b/src/test/components-bigbed-test.js @@ -0,0 +1,102 @@ +/* @flow */ +'use strict'; + +import {expect} from 'chai'; +import dataCanvas from 'data-canvas'; + +import pileup from '../main/pileup'; +import {waitFor} from './async'; + +describe('pileup-bigBed', function() { + var tracks = [ + { + viz: pileup.viz.scale(), + data: pileup.formats.empty(), + name: 'Scale' + }, + { + viz: pileup.viz.location(), + data: pileup.formats.empty(), + name: 'Location' + }, + { + viz: pileup.viz.genome(), + isReference: true, + data: pileup.formats.twoBit({ + url: '/test-data/test.2bit' + }), + cssClass: 'a' + }, + { + viz: pileup.viz.genes(), + data: pileup.formats.bigBed({ + // This file contains the beginning of chr17 with only chr, start, stop. + // See test/data/README.md. + url: '/test-data/simple17.bb' + }), + name: "simple17", + cssClass: 'b' + } + ]; + + var testDiv = document.getElementById('testdiv'); + + beforeEach(() => { + dataCanvas.RecordingContext.recordAll(); // record all data canvases + }); + + afterEach(function() { + dataCanvas.RecordingContext.reset(); + testDiv.innerHTML = ''; // avoid pollution between tests. + }); + + it('should render reference genome and genes', function() { + this.timeout(5000); + + var div = document.createElement('div'); + div.setAttribute('style', 'width: 800px; height: 200px;'); + testDiv.appendChild(div); + + var p = pileup.create(div, { + range: {contig: 'chr17', start: 20391, stop: 20591}, + tracks: tracks + }); + + var {drawnObjects, drawnObjectsWith, callsOf} = dataCanvas.RecordingContext; + + // TODO: consider moving this into the data-canvas library + function hasCanvasAndObjects(div, selector) { + return div.querySelector(selector + ' canvas') && drawnObjects(div, selector).length > 0; + } + + var ready = (() => + hasCanvasAndObjects(div, '.reference') && + hasCanvasAndObjects(div, '.genes') + ); + + return waitFor(ready, 5000) + .then(() => { + var basepairs = drawnObjectsWith(div, '.reference', x => x.letter); + expect(basepairs).to.have.length.at.least(10); + + var geneTexts = callsOf(div, '.genes', 'fillText'); + expect(geneTexts).to.have.length(1); + expect(geneTexts[0][1]).to.equal('chr17:5821-31270'); + + // Note: there are no exons in simple bed + expect(callsOf(div, '.genes', 'fillRect')).to.have.length(0); + + expect(div.querySelector('div > .a').className).to.equal('track reference a'); + expect(div.querySelector('div > .b').className).to.equal('track genes b'); + + expect(p.getRange()).to.deep.equal({ + contig: 'chr17', + start: 20391, + stop: 20591 + }); + + p.destroy(); + }); + }); + }); + \ No newline at end of file diff --git a/src/test/data/BigBed-test.js b/src/test/data/BigBed-test.js index abf1a7bc..89e52e89 100644 --- a/src/test/data/BigBed-test.js +++ b/src/test/data/BigBed-test.js @@ -17,6 +17,10 @@ describe('BigBed', function() { return new BigBed('/test-data/simple17unc.bb'); // See test-data/README.md } + function getSimpleBigBed() { + return new BigBed('/test-data/simple17.bb'); // See test-data/README.md + } + it('should extract features in a range', function() { var bb = getTestBigBed(); @@ -66,6 +70,26 @@ describe('BigBed', function() { }); }); + it('should extract features from an simple BigBed', function () { + var bb = getSimpleBigBed(); + console.log(bb); + + return bb.getFeaturesInRange('chr17', 60000, 270000) + .then(features => { + // Here's what these three lines in the file look like: + // chr17 62296 202576 + // chr17 62296 202576 + // chr17 260433 264713 + expect(features).to.deep.equal( + [ + { contig: 'chr17', start: 62296, stop: 202576, rest: "" }, + { contig: 'chr17', start: 62296, stop: 202576, rest: "" }, + { contig: 'chr17', start: 260433, stop: 264713, rest: "" } + ] + ); + }); + }); + it('should have inclusive ranges', function() { // The matches looks like this: // chrX 151071196 151072363 RED