diff --git a/index.html b/index.html
index 1eee441..45e7168 100644
--- a/index.html
+++ b/index.html
@@ -572,14 +572,14 @@
const { TabixIndexedFile } = window.gmodTABIX
- const primateAiUrls = {
+ const lookupTableUrls = {
'37': 'https://storage.googleapis.com/spliceai-lookup-reference-data/PrimateAI_3D.hg19.with_gene_thresholds.txt.gz',
- '38': 'https://storage.googleapis.com/spliceai-lookup-reference-data/PrimateAI_3D.hg38.with_gene_thresholds.txt.gz',
+ '38': 'https://storage.googleapis.com/spliceai-lookup-reference-data/PrimateAI_and_PromoterAI_scores.hg38.tsv.gz',
}
- const primateAiTables = {
- '37': new TabixIndexedFile({ url: primateAiUrls['37'], tbiUrl: `${primateAiUrls['37']}.tbi` }),
- '38': new TabixIndexedFile({ url: primateAiUrls['38'], tbiUrl: `${primateAiUrls['38']}.tbi` }),
+ const lookupTables = {
+ '37': new TabixIndexedFile({ url: lookupTableUrls['37'], tbiUrl: `${lookupTableUrls['37']}.tbi` }),
+ '38': new TabixIndexedFile({ url: lookupTableUrls['38'], tbiUrl: `${lookupTableUrls['38']}.tbi` }),
}
const getUCSCBrowserUrl = (genomeVersion, chrom, pos) => {
@@ -977,6 +977,7 @@
const generateOtherPredictorsTable = async (normalizedVariant, variantConsequence, variant, genomeVersion) => {
/* Generate the results table to show either the SpliceAI or Pangolin scores */
+ console.log(`Generating other scores table for ${normalizedVariant} from ${lookupTableUrls[genomeVersion]}`)
const variantTokens = (normalizedVariant || "---").split("-")
const chrom = `chr${variantTokens[0].replace("chr", "")}`
@@ -984,28 +985,37 @@
const ref = variantTokens[2]
const alt = variantTokens[3]
- //console.log("Querying", chrom, pos, ref, alt, "from", primateAiUrls[genomeVersion])
const otherPredictorScores = []
- await primateAiTables[genomeVersion].getLines(chrom, pos-1, pos, line => {
+ await lookupTables[genomeVersion].getLines(chrom, pos-1, pos, line => {
+ //console.log("Got line:", line)
const fields = line.split('\t')
const lineChrom = fields[0]
const linePos = parseInt(fields[1])
const lineRef = fields[2]
const lineAlt = fields[3]
- console.log(lineChrom, linePos, lineRef, lineAlt, 'vs', chrom, pos, ref, alt)
+ //console.log("`Got scores`:", fields)
if (linePos != pos || lineRef != ref || lineAlt != alt) {
return
}
- const score = parseFloat(fields[4])
- const percentile = parseFloat(fields[5])
- const genePercentilethreshold = parseFloat(fields[6])
- otherPredictorScores.push({
- 'name': 'PrimateAI-3D',
- 'score': score,
- 'percentile': percentile,
- 'genePercentileThreshold': genePercentilethreshold,
- })
+ const percentile = parseFloat(fields[4])
+ const genePercentilethreshold = parseFloat(fields[5])
+ //console.log("PrimateAI-3D", percentile, genePercentilethreshold)
+ if (!isNaN(percentile)) {
+ otherPredictorScores.push({
+ 'name': 'PrimateAI-3D',
+ 'percentile': percentile,
+ 'genePercentileThreshold': genePercentilethreshold,
+ })
+ }
+ const promoterAiScore = parseFloat(fields[6])
+ //console.log("PromoterAI", promoterAiScore)
+ if (!isNaN(promoterAiScore)) {
+ otherPredictorScores.push({
+ 'name': 'PromoterAI',
+ 'score': promoterAiScore,
+ })
+ }
},)
const tableRows = []
@@ -1017,30 +1027,36 @@
`
- const primateAiThreshold1 = 0.867
- const primateAiThreshold2 = 0.79
- const primateAiThreshold3 = 0.484
-
- const mapPrimateAiScoreToColor = (record) => {
- if (record.score >= record.genePercentileThreshold) { // + 0.1) {
- return "#fccfb8"
- //} else if (record.score >= record.genePercentileThreshold - 0.1) {
- // return "#fff19d"
- //} else {
- return "#ffffff"
- }
- }
const helpTextForPredictorScores = {
- "PrimateAI-3D": `PrimateAI-3D gene-specific thresholds are provided by the authors. Scores above this threshold are annotated as likely deleterious.`,
+ "PrimateAI-3D": `PrimateAI-3D gene-specific thresholds are provided by the authors. Values above the threshold are annotated as likely deleterious.`,
+ "PromoterAI": `PromoterAI scores range from -1 to 1 with 0 meaning no activity, negative values are under-expression and positive values are over-expression. A threshold of +/-0.1 is used for high sensitivity, and +/-0.5 for high precision.`,
}
const colorMapForPredictorScores = {
- "PrimateAI-3D": mapPrimateAiScoreToColor,
+ "PrimateAI-3D": (record) => {
+ if (record.percentile >= record.genePercentileThreshold) { // + 0.1) {
+ return "#fccfb8"
+ //} else if (record.percentile >= record.genePercentileThreshold - 0.1) {
+ // return "#fff19d"
+ //} else {
+ return "#ffffff"
+ }
+ },
+ "PromoterAI": (record) => {
+ const absScore = Math.abs(record.score)
+ if (absScore >= 0.5) {
+ return "#fccfb8"
+ } else if (absScore >= 0.1) {
+ return "#fff19d"
+ } else {
+ return "#ffffff"
+ }
+ },
}
$(`#other-predictors-header`).nextAll().remove()
- const firstColumn = `
-
+ let firstColumn = `
+ |
${variant}
${normalizedVariantDiv}
| `
@@ -1051,7 +1067,20 @@
`)
} else {
for (const otherPredictor of otherPredictorScores) {
- let row = `
+ let row
+ if (otherPredictor.name == "PromoterAI") {
+ row = `
+ ${firstColumn}
+ |
+ ${otherPredictor.name}
+ |
+
+ ${otherPredictor.score.toFixed(3)}
+
+ |
+
`
+ } else if (otherPredictor.name == "PrimateAI-3D") {
+ row = `
${firstColumn}
|
${otherPredictor.name}
@@ -1061,8 +1090,9 @@
|
`
-
- tableRows.push(row)
+ }
+ tableRows.push(row)
+ firstColumn = " | "
}
}
$(`#other-predictors-header`).after(tableRows.join(""))