@sjcrh/proteinpaint-shared 2.78.0-0

package/src/bulk.trunc.js

@@ -0,0 +1,126 @@
+////////////////////////////////////
+//
+//  shared between client and server
+//
+////////////////////////////////////
+
+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 htry = (...lst) => {
+		for (const e of lst) {
+			const j = header.indexOf(e)
+			if (j != -1) return j
+		}
+		return -1
+	}
+	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'
+	)
+	if (i == -1) return 'isoform missing from header'
+	header[i] = 'isoform'
+	let hasrnapos = false
+	i = htry('rnaposition')
+	if (i != -1) {
+		header[i] = 'rnaposition'
+		hasrnapos = true
+	}
+	i = htry('losstype')
+	if (i == -1) return 'lossType missing from header'
+	header[i] = 'losstype'
+	let hasgenomic = false
+	i = htry('chromosome', 'chr')
+	if (i != -1) {
+		header[i] = 'chr'
+		i = htry('start', 'start_position', 'wu_hg19_pos', 'chr_position', 'position')
+		if (i == -1) {
+			return 'genomic position missing from header'
+		}
+		header[i] = 'pos'
+		hasgenomic = true
+	}
+	if (!hasrnapos && !hasgenomic) {
+		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'
+	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')
+	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])
+		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])
+			return
+		}
+		m.rnaposition = v
+	}
+	if (m.pos) {
+		const v = Number.parseInt(m.pos)
+		if (Number.isNaN(v) || v < 0) {
+			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])
+		return
+	}
+	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') {
+		m.dt = common.dtnloss
+		m.class = common.mclassnloss
+		m.mname = 'N-loss'
+	} else {
+		m.dt = common.dtcloss
+		m.class = common.mclasscloss
+		m.mname = 'C-loss'
+	}
+	flag.good++
+	const n = flag.geneToUpper ? m.gene.toUpperCase() : m.gene
+	if (!(n in flag.data)) {
+		flag.data[n] = []
+	}
+	flag.data[n].push(m)
+}

package/src/clustering.js

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+export const clusterMethodLst = [
+	{
+		label: 'Average',
+		value: 'average',
+		title: `Cluster by average value`
+	},
+	{
+		label: `Complete`,
+		value: 'complete',
+		title: `Use the complete clustering method`
+	},
+	{
+		label: `Single`,
+		value: 'single',
+		title: `Use the single clustering method`
+	},
+	{
+		label: `Ward.D`,
+		value: 'ward.D',
+		title: `Use the ward.D clustering method`
+	},
+	{
+		label: `Ward.D2`,
+		value: 'ward.D2',
+		title: `Use the ward.D2 clustering method`
+	},
+	{
+		label: `Mcquitty`,
+		value: 'mcquitty',
+		title: `Use the Mcquity clustering method`
+	}
+	/* These methods are currently disabled because the dendrogram lines tend to cross one another.
+	{
+		label: `Centroid`,
+		value: 'centroid',
+		title: `Use the centroid clustering method`
+	},
+    	{
+		label: `Median`,
+		value: 'median',
+		title: `Use the median clustering method`
+	}
+        */
+]
+export const distanceMethodLst = [
+	{
+		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: 'Manhattan',
+		value: 'manhattan',
+		title: `Calculate distance using the absolute distance between the two vectors`
+	},
+	{
+		label: 'Canberra',
+		value: 'canberra',
+		title: `Calculate distance using Canberra method`
+	}
+]