From 1f3b8cd4a680781e3083e667b6c97c500ce603c7 Mon Sep 17 00:00:00 2001 From: Jim Robinson <933148+jrobinso@users.noreply.github.com> Date: Fri, 17 Nov 2023 20:04:42 -0800 Subject: [PATCH] * Add support for user settable window function (wig track) (#1734) * Summarize wig track with "mean" by default -- this was the case for bigwig until zoomed in, then "raw" values, now mean is used consistently --- dev/wig/encode.html | 52 - dev/wig/windowFunctions.html | 83 + js/bigwig/bwReader.js | 17 +- js/bigwig/bwSource.js | 6 +- js/bigwig/summarizeWigData.js | 69 - js/feature/textFeatureSource.js | 3 + js/feature/wigTrack.js | 216 +- js/tdf/tdfSource.js | 29 +- js/trackViewport.js | 28 +- test/data/wig/ENCFF000ARZ.wig | 127966 +++++++++++++++++++++++++++++ test/testWig.js | 80 + 11 files changed, 128353 insertions(+), 196 deletions(-) delete mode 100644 dev/wig/encode.html create mode 100644 dev/wig/windowFunctions.html delete mode 100644 js/bigwig/summarizeWigData.js create mode 100644 test/data/wig/ENCFF000ARZ.wig diff --git a/dev/wig/encode.html b/dev/wig/encode.html deleted file mode 100644 index 1fc7dc219..000000000 --- a/dev/wig/encode.html +++ /dev/null @@ -1,52 +0,0 @@ - - - - - IGV-JB - - - - - - - - - - -
- - - - - - diff --git a/dev/wig/windowFunctions.html b/dev/wig/windowFunctions.html new file mode 100644 index 000000000..5cf4c4846 --- /dev/null +++ b/dev/wig/windowFunctions.html @@ -0,0 +1,83 @@ + + + + + IGV-JB + + + + + + + + + + +
+ + + + + + diff --git a/js/bigwig/bwReader.js b/js/bigwig/bwReader.js index baa3b01b0..a17981104 100644 --- a/js/bigwig/bwReader.js +++ b/js/bigwig/bwReader.js @@ -30,7 +30,6 @@ import {BGZip, igvxhr, StringUtils} from "../../node_modules/igv-utils/src/index import {buildOptions, isDataURL} from "../util/igvUtils.js" import getDecoder from "./bbDecoders.js" import {parseAutoSQL} from "../util/ucscUtils.js" -import summarizeWigData from "./summarizeWigData.js" import Trix from "./trix.js" import BPTree from "./bpTree.js" @@ -131,7 +130,7 @@ class BWReader { })) // Parse data and return features - const allFeatures = [] + const features = [] for (let item of leafItems) { const uint8Array = new Uint8Array(arrayBuffer, item.dataOffset - start, item.dataSize) let plain @@ -141,22 +140,14 @@ class BWReader { } else { plain = uint8Array } - decodeFunction.call(this, new DataView(plain.buffer), chrIdx1, bpStart, chrIdx2, bpEnd, allFeatures, this.chromTree.idToName, windowFunction) + decodeFunction.call(this, new DataView(plain.buffer), chrIdx1, bpStart, chrIdx2, bpEnd, features, this.chromTree.idToName, windowFunction) } - allFeatures.sort(function (a, b) { + features.sort(function (a, b) { return a.start - b.start }) - // If we are reading "raw" wig data optionally summarize it with window function. - // Zoom level data is already summarized - if (decodeFunction === decodeWigData && - bpPerPixel && - ("mean" === windowFunction || "min" === windowFunction || "max" === windowFunction)) { - return summarizeWigData(allFeatures, bpPerPixel, windowFunction) - } else { - return allFeatures - } + return features } } diff --git a/js/bigwig/bwSource.js b/js/bigwig/bwSource.js index 9ecc29a80..c04307752 100755 --- a/js/bigwig/bwSource.js +++ b/js/bigwig/bwSource.js @@ -28,12 +28,14 @@ import pack from "../feature/featurePacker.js" class BWSource { + queryable = true + wgValues = {} + windowFunctions = ["mean", "min", "max"] + constructor(config, genome) { this.reader = new BWReader(config, genome) this.genome = genome this.format = config.format || "bigwig" - this.wgValues = {} - this.queryable = true } async getFeatures({chr, start, end, bpPerPixel, windowFunction}) { diff --git a/js/bigwig/summarizeWigData.js b/js/bigwig/summarizeWigData.js deleted file mode 100644 index ac777b190..000000000 --- a/js/bigwig/summarizeWigData.js +++ /dev/null @@ -1,69 +0,0 @@ -/** - * Summarize wig data in bins of size "bpPerPixel" with the given window function. - * - * @param features wig (numeric) data - * @param bpPerPixel size of bin in base pairs - * @param windowFunction mean, min, or max - * @returns {*|*[]} - */ -function summarizeWigData(features, bpPerPixel, windowFunction = "mean") { - - if (bpPerPixel <=1 || !features || features.length === 0) { - return features - } - - // Assumed features are sorted by position. Wig features cannot overlap. Note, UCSC "reductionLevel" == bpPerPixel - const chr = features[0].chr - const start = features[0].start - const sumData = [] - const weights = [] - const binSize = Math.floor(bpPerPixel) - const firstBin = Math.floor(start / binSize) - const summaryFeatures = [] - - for (let f of features) { - - const startBin = Math.floor(f.start / binSize) - const endBin = Math.floor(f.end / binSize) - - let startWeight, endWeight - if (endBin == startBin) { - startWeight = endWeight = (f.end - f.start) / binSize - } else { - startWeight = (1 - (f.start - startBin * binSize)) / binSize - endWeight = (f.end - endBin * binSize) / binSize - } - - // Loop through bins this feature overlaps, updating the weighted sum for each bin or min/max, depending on window function - for (let b = startBin - firstBin; b <= endBin - firstBin; b++) { - - const first = sumData[b] === undefined - switch (windowFunction) { - case "min": - sumData[b] = first ? f.value : Math.min(sumData[b], f.value) - break - case "max": - sumData[b] = first ? f.value : Math.max(sumData[b], f.value) - break - case "mean": - const weight = (b === startBin) ? startWeight : (b === endBin) ? endWeight : 1 - weights[b] = first ? weight : weights[b] + weight - const weightedValue = weight * f.value - sumData[b] = first ? weightedValue : sumData[b] + weightedValue - } - - } - } - - for (let b = 0; b < sumData.length; b++) { - let value = ("mean" === windowFunction) ? sumData[b] / weights[b] : sumData[b] - if (value > 0) { - summaryFeatures.push({chr, start: (firstBin + b) * binSize, end: (firstBin + b) * binSize, value}) - } - } - - return summaryFeatures - -} - -export default summarizeWigData \ No newline at end of file diff --git a/js/feature/textFeatureSource.js b/js/feature/textFeatureSource.js index 729a830a2..d7e196b93 100644 --- a/js/feature/textFeatureSource.js +++ b/js/feature/textFeatureSource.js @@ -151,6 +151,9 @@ class TextFeatureSource { const queryChr = genome ? genome.getChromosomeName(chr) : chr const isWholeGenome = ("all" === queryChr.toLowerCase()) + start = start || 0 + end = end || Number.MAX_SAFE_INTEGER + // Various conditions that can require a feature load // * view is "whole genome" but no features are loaded // * cache is disabled diff --git a/js/feature/wigTrack.js b/js/feature/wigTrack.js index 3f04fde77..d3afa6bb5 100755 --- a/js/feature/wigTrack.js +++ b/js/feature/wigTrack.js @@ -1,11 +1,12 @@ - import FeatureSource from './featureSource.js' +import FeatureSource from './featureSource.js' import TDFSource from "../tdf/tdfSource.js" import TrackBase from "../trackBase.js" import BWSource from "../bigwig/bwSource.js" import IGVGraphics from "../igv-canvas.js" import paintAxis from "../util/paintAxis.js" import {IGVColor, StringUtils} from "../../node_modules/igv-utils/src/index.js" -import summarizeWigData from "../bigwig/summarizeWigData.js" +import $ from "../vendor/jquery-3.3.1.slim.js" +import {createCheckbox} from "../igv-icons.js" const DEFAULT_COLOR = 'rgb(150, 150, 150)' @@ -16,12 +17,12 @@ class WigTrack extends TrackBase { height: 50, flipAxis: false, logScale: false, - windowFunction: 'none', + windowFunction: 'mean', graphType: 'bar', autoscale: true, normalize: undefined, scaleFactor: undefined, - overflowColor: `rgb(255,32,255)`, + overflowColor: `rgb(255, 32, 255)`, baselineColor: 'lightGray' } @@ -35,6 +36,7 @@ class WigTrack extends TrackBase { this.type = "wig" this.featureType = 'numeric' + this.resolutionAware = true this.paintAxis = paintAxis const format = config.format ? config.format.toLowerCase() : config.format @@ -43,20 +45,15 @@ class WigTrack extends TrackBase { delete config.featureSource } else if ("bigwig" === format) { this.featureSource = new BWSource(config, this.browser.genome) - this.resolutionAware = true - this.windowFunction = config.windowFunction || 'mean' } else if ("tdf" === format) { this.featureSource = new TDFSource(config, this.browser.genome) - this.resolutionAware = true - this.windowFunction = config.windowFunction || 'mean' } else { this.featureSource = FeatureSource(config, this.browser.genome) - this.resolutionAware = false } // Override autoscale default - if(config.max === undefined || config.autoscale === true) { + if (config.max === undefined || config.autoscale === true) { this.autoscale = true } else { this.dataRange = { @@ -73,13 +70,16 @@ class WigTrack extends TrackBase { } async getFeatures(chr, start, end, bpPerPixel) { + + const windowFunction = "points" === this.graphType ? "none" : this.windowFunction + const features = await this.featureSource.getFeatures({ chr, start, end, bpPerPixel, visibilityWindow: this.visibilityWindow, - windowFunction: this.windowFunction + windowFunction }) if (this.normalize && this.featureSource.normalizationFactor) { const scaleFactor = this.featureSource.normalizationFactor @@ -93,15 +93,14 @@ class WigTrack extends TrackBase { f.value *= scaleFactor } } - // If we are reading "raw" wig data optionally summarize it with window function. - // Bigwig data is already summarized - // if (!this.resolutionAware && - // ("mean" === this.windowFunction || "min" === this.windowFunction || "max" === this.windowFunction)) { - // return summarizeWigData(features, bpPerPixel, this.windowFunction) - // } else { - // return features - // } - return features + + // Summarize features to current resolution. This needs to be done here, rather than in the "draw" function, + // for group autoscale to work. + if (("mean" === windowFunction || "min" === windowFunction || "max" === windowFunction)) { + return summarizeData(features, start, bpPerPixel, windowFunction) + } else { + return features + } } menuItemList() { @@ -115,14 +114,44 @@ class WigTrack extends TrackBase { this.trackView.repaintViews() } - items.push({ label: 'Flip y-axis', click }) + items.push({label: 'Flip y-axis', click}) } items.push(...this.numericDataMenuItems()) + if("points" !== this.graphType) { + items.push(...this.wigSummarizationItems()) + } + return items } + wigSummarizationItems() { + + const menuItems = [] + menuItems.push('
') + + const windowFunctions = this.featureSource.windowFunctions ? + this.featureSource.windowFunctions.slice() : + ["mean", "min", "max"] + windowFunctions.push("none") + + menuItems.push("
Windowing function
") + for (const wf of windowFunctions) { + const object = $(createCheckbox(wf, this.windowFunction === wf)) + + function clickHandler() { + this.windowFunction = wf + this.trackView.updateViews() + } + + menuItems.push({object, click: clickHandler}) + } + + return menuItems + } + + async getHeader() { if (typeof this.featureSource.getHeader === "function") { @@ -163,10 +192,6 @@ class WigTrack extends TrackBase { const bpEnd = bpStart + pixelWidth * bpPerPixel + 1 const posColor = this.color || DEFAULT_COLOR - // let baselineColor - // if (typeof posColor === "string" && posColor.startsWith("rgb(")) { - // baselineColor = IGVColor.addAlpha(posColor, 0.2) - // } let lastNegValue = 1 const scaleFactor = this.getScaleFactor(this.dataRange.min, this.dataRange.max, options.pixelHeight, this.logScale) const yScale = (yValue) => this.logScale @@ -184,6 +209,7 @@ class WigTrack extends TrackBase { let lastPixelEnd = -1 let lastY const y0 = yScale(0) + for (let f of features) { if (f.end < bpStart) continue @@ -197,7 +223,7 @@ class WigTrack extends TrackBase { const rectEnd = Math.ceil((f.end - bpStart) / bpPerPixel) const width = Math.max(1, rectEnd - x) - const color = options.alpha ? IGVColor.addAlpha(this.getColorForFeature(f), options.alpha) : this.getColorForFeature(f) + const color = options.alpha ? IGVColor.addAlpha(this.getColorForFeature(f), options.alpha) : this.getColorForFeature(f) if (this.graphType === "line") { if (lastY !== undefined) { @@ -212,20 +238,20 @@ class WigTrack extends TrackBase { const px = x + width / 2 IGVGraphics.fillCircle(ctx, px, y, pointSize / 2, {"fillStyle": color, "strokeStyle": color}) - if(f.value > this.dataRange.max) { - IGVGraphics.fillCircle(ctx, px, pointSize/2, pointSize / 2, 3, {fillStyle: this.overflowColor}) - } else if(f.value < this.dataRange.min) { - IGVGraphics.fillCircle(ctx, px, pixelHeight-pointSize/2, pointSize / 2, 3, {fillStyle: this.overflowColor}) + if (f.value > this.dataRange.max) { + IGVGraphics.fillCircle(ctx, px, pointSize / 2, pointSize / 2, 3, {fillStyle: this.overflowColor}) + } else if (f.value < this.dataRange.min) { + IGVGraphics.fillCircle(ctx, px, pixelHeight - pointSize / 2, pointSize / 2, 3, {fillStyle: this.overflowColor}) } - } else { + } else { const height = Math.min(pixelHeight, y - y0) IGVGraphics.fillRect(ctx, x, y0, width, height, {fillStyle: color}) - if(f.value > this.dataRange.max) { + if (f.value > this.dataRange.max) { IGVGraphics.fillRect(ctx, x, 0, width, 3, {fillStyle: this.overflowColor}) - } else if(f.value < this.dataRange.min) { - IGVGraphics.fillRect(ctx, x, pixelHeight-3, width, 3, {fillStyle: this.overflowColor}) + } else if (f.value < this.dataRange.min) { + IGVGraphics.fillRect(ctx, x, pixelHeight - 3, width, 3, {fillStyle: this.overflowColor}) } } @@ -331,4 +357,126 @@ class WigTrack extends TrackBase { } +/** + * Summarize wig data in bins of size "bpPerPixel" with the given window function. + * + * @param features wig (numeric) data -- features cannot overlap, and are in ascending order by start position + * @param startBP bp start position for computing binned data + * @param bpPerPixel bp per pixel (bin) + * @param windowFunction mean, min, or max + * @returns {*|*[]} + */ +function summarizeData(features, startBP, bpPerPixel, windowFunction = "mean") { + + if (bpPerPixel <= 1 || !features || features.length === 0) { + return features + } + + // Assume features are sorted by position. Wig features cannot overlap. Note, UCSC "reductionLevel" == bpPerPixel + const chr = features[0].chr + const binSize = bpPerPixel + const summaryFeatures = [] + + const finishBin = (bin) => { + const start = startBP + bin.bin * binSize + const end = start + binSize + let value + switch (windowFunction) { + case "mean": + value = bin.sumData / bin.count + break + case "max": + value = bin.max + break + case "min": + value = bin.min + break + default: + throw Error(`Unknown window function: ${windowFunction}`) + } + const description = `${windowFunction} of ${bin.count} values` + summaryFeatures.push({chr, start, end, value, description}) + } + + let currentBinData + for (let f of features) { + + // Loop through bins this feature overlaps, updating the weighted sum for each bin or min/max, + // depending on window function + let startBin = Math.floor((f.start - startBP) / binSize) + const endBin = Math.floor((f.end - startBP) / binSize) + + if (!currentBinData) { + // First time + if (endBin > startBin) { + // Fill bins up to "endBin" + const start = startBP + startBin * binSize + const end = startBP + endBin * binSize + summaryFeatures.push({chr, start, end, value: f.value}) + } + currentBinData = new SummaryBinData(endBin, f.value) + + } else { + + if (startBin === currentBinData.bin) { + currentBinData.add(f.value) + startBin++ + } + + if (endBin > currentBinData.bin) { + + finishBin(currentBinData) + + // filler + if (endBin > startBin) { + const start = startBP + startBin * binSize + const end = startBP + endBin * binSize + summaryFeatures.push({chr, start, end, value: f.value}) + } + + currentBinData = new SummaryBinData(endBin, f.value) + } + } + } + finishBin(currentBinData) + + // Consolidate + const c = [] + let lastFeature = summaryFeatures[0] + for (let f of summaryFeatures) { + if (lastFeature.value === f.value) { + lastFeature.end = f.end + } else { + c.push(lastFeature) + lastFeature = f + } + } + c.push(lastFeature) + + return c + +} + +class SummaryBinData { + constructor(bin, value) { + this.bin = bin + this.sumData = value + this.count = 1 + this.min = value + this.max = value + } + + add(value) { + this.sumData += value + this.max = Math.max(value, this.max) + this.min = Math.min(value, this.min) + this.count++ + } + + get mean() { + return this.sumData / this.count + } +} + export default WigTrack +export {summarizeData} diff --git a/js/tdf/tdfSource.js b/js/tdf/tdfSource.js index 5b00c6e0b..490220714 100644 --- a/js/tdf/tdfSource.js +++ b/js/tdf/tdfSource.js @@ -26,19 +26,17 @@ import TDFReader from "./tdfReader.js" import GenomicInterval from "../genome/genomicInterval.js" -import summarizeWigData from "../bigwig/summarizeWigData.js" class TDFSource { searchable = false constructor(config, genome) { this.genome = genome - this.windowFunction = config.windowFunction || "mean" this.reader = new TDFReader(config, genome) this.queryable = true } - async getFeatures({chr, start, end, bpPerPixel}) { + async getFeatures({chr, start, end, bpPerPixel, windowFunction = "mean"}) { if (chr.toLowerCase() === "all") { const wgFeatures = [] @@ -48,7 +46,7 @@ class TDFSource { for (let c of genome.wgChromosomeNames) { const len = genome.getChromosome(c).bpLength bpPerPixel = len / 1000 - const chrFeatures = await this._getFeatures(c, 0, len, bpPerPixel) + const chrFeatures = await this._getFeatures(c, 0, len, bpPerPixel, windowFunction) if (chrFeatures) { for (let f of chrFeatures) { const wg = Object.assign({}, f) @@ -64,15 +62,10 @@ class TDFSource { return wgFeatures } else { - return this._getFeatures(chr, start, end, bpPerPixel) + return this._getFeatures(chr, start, end, bpPerPixel, windowFunction) } } - - async hasZoomDataFor(bpPerPixel) { - - } - - async _getFeatures(chr, start, end, bpPerPixel) { + async _getFeatures(chr, start, end, bpPerPixel, windowFunction) { const genomicInterval = new GenomicInterval(chr, start, end) const genome = this.genome @@ -94,7 +87,7 @@ class TDFSource { if (queryChr === undefined) queryChr = chr if (maxZoom === undefined) maxZoom = -1 - const wf = zoom > maxZoom ? "raw" : this.windowFunction + const wf = zoom > maxZoom ? "raw" : windowFunction const dataset = await this.reader.readDataset(queryChr, wf, zoom) if (dataset == null) { return [] @@ -125,18 +118,16 @@ class TDFSource { return a.start - b.start }) - // If we are reading "raw" wig data optionally summarize it with window function. - // Bigwig data is already summarized - if ("raw" === wf) { - return summarizeWigData(features, bpPerPixel, this.windowFunction) - } else { - return features - } + return features } get supportsWholeGenome() { return true } + + get windowFunctions() { + return this.reader.windowFunctions + } } function decodeBedTile(tile, chr, bpStart, bpEnd, bpPerPixel, features) { diff --git a/js/trackViewport.js b/js/trackViewport.js index 2e66835b1..025d35746 100644 --- a/js/trackViewport.js +++ b/js/trackViewport.js @@ -203,8 +203,9 @@ class TrackViewport extends Viewport { } } - const mr = track && (track.resolutionAware || "wig" === track.type) // wig tracks are potentially multiresolution (e.g. bigwig) - this.featureCache = new FeatureCache(chr, bpStart, bpEnd, referenceFrame.bpPerPixel, features, roiFeatures, mr) + const mr = track && (track.resolutionAware) // + const windowFunction = this.windowFunction + this.featureCache = new FeatureCache(chr, bpStart, bpEnd, referenceFrame.bpPerPixel, features, roiFeatures, mr, windowFunction) this.loading = false this.hideMessage() this.stopSpinner() @@ -223,6 +224,14 @@ class TrackViewport extends Viewport { } } + get track() { + return this.trackView.track + } + + get windowFunction() { + return this.track ? this.track.windowFunction : undefined + } + /** * Compute the genomic extent and needed pixelWidth to repaint the canvas for the current genomic state. * Normally the canvas is size 3X the width of the viewport, however there is no left-right panning for WGV so @@ -298,6 +307,7 @@ class TrackViewport extends Viewport { bpStart, bpEnd: bpEnd, bpPerPixel, + windowFunction: this.windowFunction, referenceFrame: this.referenceFrame, selection: this.selection, viewport: this, @@ -536,7 +546,7 @@ class TrackViewport extends Viewport { } async getFeatures(track, chr, start, end, bpPerPixel) { - if (this.featureCache && this.featureCache.containsRange(chr, start, end, bpPerPixel)) { + if (this.featureCache && this.featureCache.containsRange(chr, start, end, bpPerPixel, this.windowFunction)) { return this.featureCache.features } else if (typeof track.getFeatures === "function") { const features = await track.getFeatures(chr, start, end, bpPerPixel, this) @@ -556,14 +566,15 @@ class TrackViewport extends Viewport { this.referenceFrame.start < data.bpStart || this.referenceFrame.end > data.bpEnd || this.referenceFrame.chr !== data.referenceFrame.chr || - this.referenceFrame.bpPerPixel != data.bpPerPixel + this.referenceFrame.bpPerPixel != data.bpPerPixel || + this.windowFunction != data.windowFunction } needsReload() { if (!this.featureCache) return true const {chr, bpPerPixel} = this.referenceFrame const {bpStart, bpEnd} = this.repaintDimensions() - return (!this.featureCache.containsRange(chr, bpStart, bpEnd, bpPerPixel)) + return (!this.featureCache.containsRange(chr, bpStart, bpEnd, bpPerPixel, this.windowFunction)) } createZoomInNotice($parent) { @@ -871,7 +882,7 @@ function formatPopoverText(nameValues) { class FeatureCache { - constructor(chr, tileStart, tileEnd, bpPerPixel, features, roiFeatures, multiresolution) { + constructor(chr, tileStart, tileEnd, bpPerPixel, features, roiFeatures, multiresolution, windowFunction) { this.chr = chr this.bpStart = tileStart this.bpEnd = tileEnd @@ -879,9 +890,12 @@ class FeatureCache { this.features = features this.roiFeatures = roiFeatures this.multiresolution = multiresolution + this.windowFunction = windowFunction } - containsRange(chr, start, end, bpPerPixel) { + containsRange(chr, start, end, bpPerPixel, windowFunction) { + + if(windowFunction && windowFunction !== this.windowFunction) return false // For multi-resolution tracks allow for a 2X change in bpPerPixel const r = this.multiresolution ? this.bpPerPixel / bpPerPixel : 1 diff --git a/test/data/wig/ENCFF000ARZ.wig b/test/data/wig/ENCFF000ARZ.wig new file mode 100644 index 000000000..a1450d72c --- /dev/null +++ b/test/data/wig/ENCFF000ARZ.wig @@ -0,0 +1,127966 @@ +variableStep chrom=chr8 span=25 +59808276 1 +59808301 1.8 +59808326 1 +59808351 1 +59808376 1 +59808401 1 +59808426 1 +59808451 1 +59808476 1 +59808501 0.12 +59808551 0.96 +59808576 1 +59808601 1 +59808626 1.88 +59808651 2 +59808676 2 +59808701 2 +59808726 2 +59808751 1.04 +59808776 1.08 +59808801 2 +59808826 1.12 +59808851 1 +59808876 1 +59808901 1 +59808926 1 +59808951 1 +59808976 0.92 +59809351 0.72 +59809376 1 +59809401 1 +59809426 2 +59809451 2 +59809476 2.08 +59809501 3 +59809526 3 +59809551 2.28 +59809576 3 +59809601 3 +59809626 2 +59809651 2 +59809676 1.92 +59809701 1.52 +59809726 2 +59809751 2 +59809776 1 +59809801 1 +59809826 1 +59809851 1 +59809876 1.64 +59809901 1.48 +59809926 1 +59809951 1.56 +59809976 2 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+63918401 0.68 +63918426 1 +63918451 1 +63918476 1 +63918501 1 +63918526 1 +63918551 1 +63918576 1 +63918601 0.32 +63918751 0.8 +63918776 2 +63918801 2 +63918826 2 +63918851 2 +63918876 2.44 +63918901 3 +63918926 3 +63918951 2.2 +63918976 1.4 +63919001 2.96 +63919026 3 +63919051 3 +63919076 2.56 +63919101 2 +63919126 2 +63919151 3 +63919176 2.6 +63919201 1.36 +63919226 2 +63919251 2 +63919276 2 +63919301 2 +63919326 2 +63919351 1 +63919376 1 +63919401 0.68 diff --git a/test/testWig.js b/test/testWig.js index 067ac6621..ee83aaa65 100644 --- a/test/testWig.js +++ b/test/testWig.js @@ -2,6 +2,7 @@ import "./utils/mockObjects.js" import FeatureSource from "../js/feature/featureSource.js" import {assert} from 'chai' import {createGenome} from "./utils/Genome.js" +import {summarizeData} from "../js/feature/wigTrack.js" const genome = createGenome() @@ -53,4 +54,83 @@ suite("testWig", function () { }) }) + + /** + * Insure we get all features requested, but no more (i.e. no features out of interval) + */ + test("wig query", async function () { + + const url = "test/data/wig/ENCFF000ARZ.wig" + + const wigFeatureSource = FeatureSource({format: 'wig', url: url}, genome) + + const chr = "chr8" + const allFeatures = await wigFeatureSource.getFeatures({chr}) + assert.equal(allFeatures.length, 127840) + assert.equal(allFeatures[allFeatures.length - 1].start, 63919400) + + const start = 60879301 + 10 + const end = 60879526 + 10 + const queryFeatures = await wigFeatureSource.getFeatures({chr, start, end}) + assert.equal(10, queryFeatures.length) + }) + + test("wig summarize", async function () { + + const url = "test/data/wig/ENCFF000ARZ.wig" + + const wigFeatureSource = FeatureSource({format: 'wig', url: url}, genome) + + + //chr8:61,424,086-62,080,568 + const chr = "chr8" + const start = 61424086 + const end = 62080568 + + const bpPerPixel = (end - start) / 1000 + const binSize = bpPerPixel + + + const features = await wigFeatureSource.getFeatures({chr, start, end}) + assert.equal(features.length, 24546) + + let windowFunction = "mean" + let summarizedData = summarizeData(features, start, bpPerPixel, windowFunction) + assert.equal(summarizedData.length, 992) + + windowFunction = "min" + summarizedData = summarizeData(features, start, bpPerPixel, windowFunction) + assert.equal(summarizedData.length, 944) + + windowFunction = "max" + summarizedData = summarizeData(features, start, bpPerPixel, windowFunction) + assert.equal(summarizedData.length, 953) + + + // first bin + // console.log(features[0].start) + // const binEnd = start + bpPerPixel + // let sum = 0 + // let count = 0 + // let max = 0 + // + // const first = summarizedData[0] + // const firstBinStart = first.start + // const firstBinEnd = first.end + // + // for(let f of features) { + // if(f.end < firstBinStart) continue + // if(f.start > firstBinEnd) break + // max = Math.max(f.value, max) + // sum += f.value + // count++ + // } + // const avg = sum / count + // + // console.log(`bpPerPixel = ${bpPerPixel} first bin size = ${summarizedData[0].end-summarizedData[0].start}`) + // console.log(`${start}-${binEnd} ${summarizedData[0].start}-${summarizedData[0].end}`) + // console.log(`${avg} ${max} ${summarizedData[0].value}`) + + + }) }) \ No newline at end of file