@sjcrh/proteinpaint-shared 2.180.0 → 2.180.1

package/src/bulk.svjson.js

@@ -4,15 +4,15 @@
 //
 /////////////////////////////////
 
-import * as common from './common.js'
-import * as bulk from './bulk.js'
+import * as common from "./common.js"
+import * as bulk from "./bulk.js"
 
 // work for both sv/fusion
 // must tell if the data is fusion or sv
 
 export function parseheader(line, flag) {
-	const header = line.toLowerCase().split('\t')
-	if (header.length <= 1) return 'invalid file header for svjson'
+	const header = line.toLowerCase().split("\t")
+	if (header.length <= 1) return "invalid file header for svjson"
 	const htry = (...lst) => {
 		for (const a of lst) {
 			const j = header.indexOf(a)
@@ -20,21 +20,21 @@ export function parseheader(line, flag) {
 		}
 		return -1
 	}
-	let i = htry('sample')
-	if (i != -1) header[i] = 'sample'
-	i = htry('sampletype')
-	if (i != -1) header[i] = 'sampletype'
-	i = htry('patient')
-	if (i != -1) header[i] = 'patient'
-	i = htry('json', 'jsontext')
-	if (i == -1) return ['json missing from header']
-	header[i] = 'jsontext'
+	let i = htry("sample")
+	if (i != -1) header[i] = "sample"
+	i = htry("sampletype")
+	if (i != -1) header[i] = "sampletype"
+	i = htry("patient")
+	if (i != -1) header[i] = "patient"
+	i = htry("json", "jsontext")
+	if (i == -1) return ["json missing from header"]
+	header[i] = "jsontext"
 	return [null, header]
 }
 
 export function parseline(i, line, flag, header) {
-	if (line == '' || line[0] == '#') return
-	const lst = line.split('\t')
+	if (line == "" || line[0] == "#") return
+	const lst = line.split("\t")
 	const m = {}
 	const badlines = flag.svjson.badlines
 
@@ -42,7 +42,7 @@ export function parseline(i, line, flag, header) {
 		m[header[j]] = lst[j]
 	}
 	if (!m.jsontext) {
-		badlines.push([i, 'missing jsontext', lst])
+		badlines.push([i, "missing jsontext", lst])
 		return
 	}
 	if (bulk.parsesample(m, flag, i, lst, badlines)) {
@@ -52,7 +52,7 @@ export function parseline(i, line, flag, header) {
 	try {
 		json = JSON.parse(m.jsontext)
 	} catch (e) {
-		badlines.push([i, 'invalid JSON text', lst])
+		badlines.push([i, "invalid JSON text", lst])
 		return
 	}
 	// duplicating logic in pediatric.js
@@ -65,10 +65,10 @@ export function parseline(i, line, flag, header) {
 					dt: common.dtfusionrna,
 					class: common.mclassfusionrna,
 					isoform: pair.a.isoform,
-					mname: pair.b.name
+					mname: pair.b.name,
 				}
 				for (const k in m) {
-					if (k != 'jsontext') m2[k] = m[k]
+					if (k != "jsontext") m2[k] = m[k]
 				}
 				m2.pairlst = duplicate(json)
 				const n = pair.a.name.toUpperCase()
@@ -83,10 +83,10 @@ export function parseline(i, line, flag, header) {
 					dt: common.dtfusionrna,
 					class: common.mclassfusionrna,
 					isoform: pair.b.isoform,
-					mname: pair.a.name
+					mname: pair.a.name,
 				}
 				for (const k in m) {
-					if (k != 'jsontext') m2[k] = m[k]
+					if (k != "jsontext") m2[k] = m[k]
 				}
 				m2.pairlst = duplicate(json)
 				const n = pair.b.name.toUpperCase()
@@ -102,40 +102,42 @@ export function parseline(i, line, flag, header) {
 		switch (json.dt) {
 			case common.dtitd:
 				json.class = common.mclassitd
-				json.mname = 'ITD'
+				json.mname = "ITD"
 				break
 			case common.dtnloss:
 				json.class = common.mclassnloss
-				json.mname = 'N-loss'
+				json.mname = "N-loss"
 				break
 			case common.dtcloss:
 				json.class = common.mclasscloss
-				json.mname = 'C-loss'
+				json.mname = "C-loss"
 				break
 			case common.dtdel:
 				json.class = common.mclassdel
-				json.mname = 'Del'
+				json.mname = "Del"
 				break
 			case common.dtsv:
 				json.class = common.mclasssv
-				json.mname = 'SV'
+				json.mname = "SV"
 				break
 			default:
-				badlines.push([i, 'unknown datatype', lst])
+				badlines.push([i, "unknown datatype", lst])
 				return
 		}
 		// record only about a single gene
 		if (!json.gene) {
-			badlines.push([i, 'json.gene missing', lst])
+			badlines.push([i, "json.gene missing", lst])
 			return
 		}
 		flag.good++
 		for (const k in m) {
-			if (k != 'jsontext') {
+			if (k != "jsontext") {
 				json[k] = m[k]
 			}
 		}
-		const n = flag.geneToUpper ? json.gene.toUpperCase() : json.gene.toUpperCase()
+		const n = flag.geneToUpper
+			? json.gene.toUpperCase()
+			: json.gene.toUpperCase()
 		if (!flag.data[n]) {
 			flag.data[n] = []
 		}
@@ -148,7 +150,7 @@ function duplicate(lst) {
 	for (const pair of lst) {
 		const p = { a: {}, b: {} }
 		for (const k in pair) {
-			if (k != 'a' && k != 'b') p[k] = pair[k]
+			if (k != "a" && k != "b") p[k] = pair[k]
 		}
 		for (const k in pair.a) {
 			p.a[k] = pair.a[k]

package/src/bulk.trunc.js

@@ -4,12 +4,12 @@
 //
 ////////////////////////////////////
 
-import * as common from './common.js'
-import * as bulk from './bulk.js'
+import * as common from "./common.js"
+import * as bulk from "./bulk.js"
 
 export function parseheader(line, flag) {
-	const header = line.toLowerCase().split('\t')
-	if (header.length <= 1) return 'invalid header line for truncation'
+	const header = line.toLowerCase().split("\t")
+	if (header.length <= 1) return "invalid header line for truncation"
 	const htry = (...lst) => {
 		for (const e of lst) {
 			const j = header.indexOf(e)
@@ -17,74 +17,80 @@ export function parseheader(line, flag) {
 		}
 		return -1
 	}
-	let i = htry('gene')
-	if (i == -1) return 'gene missing from header'
-	header[i] = 'gene'
+	let i = htry("gene")
+	if (i == -1) return "gene missing from header"
+	header[i] = "gene"
 	i = htry(
-		'annovar_isoform',
-		'mrna_accession',
-		'mrna accession',
-		'refseq_mrna_id',
-		'annovar_sj_filter_isoform',
-		'refseq',
-		'isoform'
+		"annovar_isoform",
+		"mrna_accession",
+		"mrna accession",
+		"refseq_mrna_id",
+		"annovar_sj_filter_isoform",
+		"refseq",
+		"isoform"
 	)
-	if (i == -1) return 'isoform missing from header'
-	header[i] = 'isoform'
+	if (i == -1) return "isoform missing from header"
+	header[i] = "isoform"
 	let hasrnapos = false
-	i = htry('rnaposition')
+	i = htry("rnaposition")
 	if (i != -1) {
-		header[i] = 'rnaposition'
+		header[i] = "rnaposition"
 		hasrnapos = true
 	}
-	i = htry('losstype')
-	if (i == -1) return 'lossType missing from header'
-	header[i] = 'losstype'
+	i = htry("losstype")
+	if (i == -1) return "lossType missing from header"
+	header[i] = "losstype"
 	let hasgenomic = false
-	i = htry('chromosome', 'chr')
+	i = htry("chromosome", "chr")
 	if (i != -1) {
-		header[i] = 'chr'
-		i = htry('start', 'start_position', 'wu_hg19_pos', 'chr_position', 'position')
+		header[i] = "chr"
+		i = htry(
+			"start",
+			"start_position",
+			"wu_hg19_pos",
+			"chr_position",
+			"position"
+		)
 		if (i == -1) {
-			return 'genomic position missing from header'
+			return "genomic position missing from header"
 		}
-		header[i] = 'pos'
+		header[i] = "pos"
 		hasgenomic = true
 	}
 	if (!hasrnapos && !hasgenomic) {
-		return 'neither rnaposition nor genomic position is given'
+		return "neither rnaposition nor genomic position is given"
 	}
 
-	i = htry('sample', 'sample_name', 'tumor_sample_barcode')
-	if (i != -1) header[i] = 'sample'
-	i = htry('patient', 'donor', 'target_case_id')
-	if (i != -1) header[i] = 'patient'
-	i = htry('disease')
-	if (i != -1) header[i] = 'disease'
-	i = htry('origin')
-	if (i != -1) header[i] = 'origin'
-	i = htry('sampletype', 'sample type', 'sample_type')
-	if (i != -1) header[i] = 'sampletype'
+	i = htry("sample", "sample_name", "tumor_sample_barcode")
+	if (i != -1) header[i] = "sample"
+	i = htry("patient", "donor", "target_case_id")
+	if (i != -1) header[i] = "patient"
+	i = htry("disease")
+	if (i != -1) header[i] = "disease"
+	i = htry("origin")
+	if (i != -1) header[i] = "origin"
+	i = htry("sampletype", "sample type", "sample_type")
+	if (i != -1) header[i] = "sampletype"
 	flag.truncation.header = header
 	flag.truncation.loaded = true
 	return false
 }
 
 export function parseline(i, line, flag) {
-	if (line == '' || line[0] == '#') return
-	const lst = line.split('\t')
+	if (line == "" || line[0] == "#") return
+	const lst = line.split("\t")
 	const m = {}
 	for (let j = 0; j < flag.truncation.header.length; j++) {
 		m[flag.truncation.header[j]] = lst[j]
 	}
 	if (!m.gene) {
-		flag.truncation.badlines.push([i, 'missing gene', lst])
+		flag.truncation.badlines.push([i, "missing gene", lst])
 		return
 	}
 	if (m.rnaposition) {
 		const v = Number.parseInt(m.rnaposition)
 		if (Number.isNaN(v) || v < 0) {
-			flag.truncation.badlines.push([i, 'invalid rnaPosition value', lst])
+			flag.truncation.badlines.push([i, "invalid rnaPosition value", lst])
 			return
 		}
 		m.rnaposition = v
@@ -92,30 +98,30 @@ export function parseline(i, line, flag) {
 	if (m.pos) {
 		const v = Number.parseInt(m.pos)
 		if (Number.isNaN(v) || v < 0) {
-			flag.truncation.badlines.push([i, 'invalid genomic position', lst])
+			flag.truncation.badlines.push([i, "invalid genomic position", lst])
 			return
 		}
 		m.pos = v
 	}
 	if (!m.losstype) {
-		flag.truncation.badlines.push([i, 'missing lossType value', lst])
+		flag.truncation.badlines.push([i, "missing lossType value", lst])
 		return
 	}
-	if (m.losstype != 'n' && m.losstype != 'c') {
+	if (m.losstype != "n" && m.losstype != "c") {
 		flag.truncation.badlines.push([i, 'lossType value not "n" or "c"', lst])
 		return
 	}
 	if (bulk.parsesample(m, flag, i, lst, flag.truncation.badlines)) {
 		return
 	}
-	if (m.losstype == 'n') {
+	if (m.losstype == "n") {
 		m.dt = common.dtnloss
 		m.class = common.mclassnloss
-		m.mname = 'N-loss'
+		m.mname = "N-loss"
 	} else {
 		m.dt = common.dtcloss
 		m.class = common.mclasscloss
-		m.mname = 'C-loss'
+		m.mname = "C-loss"
 	}
 	flag.good++
 	const n = flag.geneToUpper ? m.gene.toUpperCase() : m.gene

package/src/clustering.js

@@ -1,34 +1,34 @@
 export const clusterMethodLst = [
 	{
-		label: 'Average',
-		value: 'average',
-		title: `Cluster by average value`
+		label: "Average",
+		value: "average",
+		title: `Cluster by average value`,
 	},
 	{
 		label: `Complete`,
-		value: 'complete',
-		title: `Use the complete clustering method`
+		value: "complete",
+		title: `Use the complete clustering method`,
 	},
 	{
 		label: `Single`,
-		value: 'single',
-		title: `Use the single clustering method`
+		value: "single",
+		title: `Use the single clustering method`,
 	},
 	{
 		label: `Ward.D`,
-		value: 'ward.D',
-		title: `Use the ward.D clustering method`
+		value: "ward.D",
+		title: `Use the ward.D clustering method`,
 	},
 	{
 		label: `Ward.D2`,
-		value: 'ward.D2',
-		title: `Use the ward.D2 clustering method`
+		value: "ward.D2",
+		title: `Use the ward.D2 clustering method`,
 	},
 	{
 		label: `Mcquitty`,
-		value: 'mcquitty',
-		title: `Use the Mcquity clustering method`
-	}
+		value: "mcquitty",
+		title: `Use the Mcquity clustering method`,
+	},
 	/* These methods are currently disabled because the dendrogram lines tend to cross one another.
 	{
 		label: `Centroid`,
@@ -44,23 +44,23 @@ export const clusterMethodLst = [
 ]
 export const distanceMethodLst = [
 	{
-		label: 'Euclidean',
-		value: 'euclidean',
-		title: `Calculate distance using euclidean method`
+		label: "Euclidean",
+		value: "euclidean",
+		title: `Calculate distance using euclidean method`,
 	},
 	{
-		label: 'Maximum',
-		value: 'maximum',
-		title: `Maximum distance between two components of x and y`
+		label: "Maximum",
+		value: "maximum",
+		title: `Maximum distance between two components of x and y`,
 	},
 	{
-		label: 'Manhattan',
-		value: 'manhattan',
-		title: `Calculate distance using the absolute distance between the two vectors`
+		label: "Manhattan",
+		value: "manhattan",
+		title: `Calculate distance using the absolute distance between the two vectors`,
 	},
 	{
-		label: 'Canberra',
-		value: 'canberra',
-		title: `Calculate distance using Canberra method`
-	}
+		label: "Canberra",
+		value: "canberra",
+		title: `Calculate distance using Canberra method`,
+	},
 ]