@sjcrh/proteinpaint-shared 2.187.0 → 2.188.1

package/src/bulk.del.js

@@ -1,124 +0,0 @@
-////////////////////////////////////
-//
-//  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 intragenic deletion"
-	const htry = (...lst) => {
-		for (const i of lst) {
-			const j = header.indexOf(i)
-			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"
-	i = htry("rnaposition")
-	if (i != -1) {
-		header[i] = "rnaposition"
-		i = htry("rnadellength")
-		if (i == -1) return "rnadellength is required when rnaPosition is used"
-		header[i] = "rnadellength"
-	}
-	i = htry("chromosome", "chr")
-	if (i != -1) {
-		header[i] = "chr"
-		i = htry("chr_start")
-		if (i == -1) return "chr_start is required when chr is used"
-		header[i] = "chrpos1"
-		i = htry("chr_stop")
-		if (i == -1) return "chr_stop is required when chr is used"
-		header[i] = "chrpos2"
-	}
-
-	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.del.header = header
-	flag.del.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.del.header.length; j++) {
-		if (lst[j] == undefined) break
-		m[flag.del.header[j]] = lst[j]
-	}
-	if (!m.gene) {
-		flag.del.badlines.push([i, "missing gene", lst])
-		return
-	}
-	if (m.rnaposition) {
-		let v = Number.parseInt(m.rnaposition)
-		if (Number.isNaN(v) || v < 0) {
-			flag.del.badlines.push([i, "invalid rnaPosition value", lst])
-			return
-		}
-		m.rnaposition = v
-		if (!m.rnadellength) {
-			flag.del.badlines.push([i, "missing rnaDellength value", lst])
-			return
-		}
-		v = Number.parseInt(m.rnadellength)
-		if (Number.isNaN(v) || v < 0) {
-			flag.del.badlines.push([i, "invalid rnaDellength value", lst])
-			return
-		}
-		m.rnadellength = v
-	}
-	if (m.chr) {
-		let v = Number.parseInt(m.chrpos1)
-		if (Number.isNaN(v) || v < 0) {
-			flag.del.badlines.push([i, "invalid chr_start value", lst])
-			return
-		}
-		m.chrpos1 = v
-		v = Number.parseInt(m.chrpos2)
-		if (Number.isNaN(v) || v < 0) {
-			flag.del.badlines.push([i, "invalid chr_stop value", lst])
-			return
-		}
-		m.chrpos2 = v
-	}
-
-	if (bulk.parsesample(m, flag, i, lst, flag.del.badlines)) {
-		return
-	}
-	m.dt = common.dtdel
-	m.class = common.mclassdel
-	m.mname = "DEL"
-	flag.good++
-	var n = flag.geneToUpper ? m.gene.toUpperCase() : m.gene
-	if (!(n in flag.data)) {
-		flag.data[n] = []
-	}
-	flag.data[n].push(m)
-}

package/src/bulk.itd.js

@@ -1,123 +0,0 @@
-////////////////////////////////////
-//
-//  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 ITD"
-	const htry = (...lst) => {
-		for (const i of lst) {
-			const j = header.indexOf(i)
-			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"
-	i = htry("rnaposition")
-	if (i != -1) {
-		header[i] = "rnaposition"
-		i = htry("rnaduplength")
-		if (i == -1) return "rnaduplength is required when rnaposition is present"
-		header[i] = "rnaduplength"
-	}
-	i = htry("chromosome", "chr")
-	if (i != -1) {
-		header[i] = "chr"
-		i = htry("chr_start")
-		if (i == -1) return "chr_start is required when chr is present"
-		header[i] = "chrpos1"
-		i = htry("chr_stop")
-		if (i == -1) return "chr_stop is required when chr is present"
-		header[i] = "chrpos2"
-	}
-
-	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.itd.header = header
-	flag.itd.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.itd.header.length; j++) {
-		if (lst[j] == undefined) break
-		m[flag.itd.header[j]] = lst[j]
-	}
-	if (!m.gene) {
-		flag.itd.badlines.push([i, "missing gene", lst])
-		return
-	}
-	if (m.rnaposition) {
-		let v = Number.parseInt(m.rnaposition)
-		if (Number.isNaN(v) || v < 0) {
-			flag.itd.badlines.push([i, "invalid rnaPosition value", lst])
-			return
-		}
-		m.rnaposition = v
-		if (!m.rnaduplength) {
-			flag.itd.badlines.push([i, "missing rnaDuplength value", lst])
-			return
-		}
-		v = Number.parseInt(m.rnaduplength)
-		if (Number.isNaN(v) || v < 0) {
-			flag.itd.badlines.push([i, "invalid rnaDuplength value", lst])
-			return
-		}
-		m.rnaduplength = v
-	}
-	if (m.chr) {
-		let v = Number.parseInt(m.chrpos1)
-		if (Number.isNaN(v) || v < 0) {
-			flag.itd.badlines.push([i, "invalid chr_start value", lst])
-			return
-		}
-		m.chrpos1 = v
-		v = Number.parseInt(m.chrpos2)
-		if (Number.isNaN(v) || v < 0) {
-			flag.itd.badlines.push([i, "invalid chr_stop value", lst])
-			return
-		}
-		m.chrpos2 = v
-	}
-	if (bulk.parsesample(m, flag, i, lst, flag.itd.badlines)) {
-		return
-	}
-	m.dt = common.dtitd
-	m.class = common.mclassitd
-	m.mname = "ITD"
-	flag.good++
-	var n = flag.geneToUpper ? m.gene.toUpperCase() : m.gene
-	if (!(n in flag.data)) {
-		flag.data[n] = []
-	}
-	flag.data[n].push(m)
-}

package/src/bulk.js

@@ -1,197 +0,0 @@
-////////////////////////////////////
-//
-//  shared between client and server
-//
-////////////////////////////////////
-
-import * as common from "./common.js"
-
-export default {}
-
-export function init_bulk_flag(genome) {
-	if (!genome) {
-		return null
-	}
-	const mclasslabel2key = {}
-	for (const n in common.mclass) {
-		mclasslabel2key[common.mclass[n].label.toUpperCase()] = n
-	}
-	return {
-		genome: genome,
-		mclasslabel2key: mclasslabel2key,
-		data: {},
-		sample2disease: {}, // (proof) k: sample, v: disease
-		// will only record this when origin is used
-		patient2st: {},
-		// k: patient, v: { k: sampletype, v: sample }
-		// new sample names always override old
-		good: 0,
-		geneToUpper: true, // option to not force uppercase on gene names
-		snv: {
-			loaded: false,
-			header: null,
-			badlines: [],
-			// jinghui: based on missense/silent ratio of entire dataset to decide whether to include silent when importing...
-			// hard-coded class codes
-			missense: 0,
-			silent: 0,
-		},
-		svjson: {
-			loaded: false,
-			header: null,
-			badlines: [],
-		},
-		fusion: {
-			loaded: false,
-			header: null,
-			badlines: [],
-			original: [],
-		},
-		sv: {
-			loaded: false,
-			header: null,
-			badlines: [],
-			original: [],
-		},
-		cnv: {
-			loaded: false,
-			header: null,
-			badlines: [],
-		},
-		itd: {
-			loaded: false,
-			header: null,
-			badlines: [],
-		},
-		del: {
-			loaded: false,
-			header: null,
-			badlines: [],
-		},
-		truncation: {
-			loaded: false,
-			header: null,
-			badlines: [],
-		},
-	}
-}
-
-export function parsesample(m, flag, i, lst, badline) {
-	let variantorigin = common.moriginsomatic
-	if (m.sampletype) {
-		const s = m.sampletype.toLowerCase()
-		switch (s) {
-			case "relapse":
-				variantorigin = common.moriginrelapse
-				break
-			case "germline":
-				variantorigin = common.morigingermline
-				break
-			case "somatic":
-			case "diagnosis":
-				break
-		}
-		if (m.sample) {
-			if (m.patient) {
-				// good
-			} else {
-				m.patient = m.sample + " " + m.sampletype
-			}
-		} else {
-			if (m.patient) {
-				m.sample = m.patient + " " + m.sampletype
-			} else {
-				// neither sample or patient, will quit later
-			}
-		}
-	} else {
-		if (m.patient) {
-			if (m.sample) {
-				m.sampletype = m.sample
-			} else {
-				m.sample = m.sampletype = m.patient
-			}
-		} else {
-			if (m.sample) {
-				m.sampletype = m.sample
-			} else {
-				// no patient/sample, will quit later
-			}
-		}
-	}
-	if (m.origin) {
-		// override existing variantorigin
-		const s = m.origin.toLowerCase()
-		switch (s) {
-			case "r":
-			case "relapse":
-				variantorigin = common.moriginrelapse
-				m.isrim2 = true
-				break
-			case "g":
-			case "germline":
-				variantorigin = common.morigingermline
-				m.isrim1 = true
-				break
-			case "gp":
-			case "germline pathogenic":
-				variantorigin = common.morigingermlinepathogenic
-				m.isrim1 = true
-				break
-			case "gnp":
-			case "germline nonpathogenic":
-			case "germline non-pathogenic":
-				variantorigin = common.morigingermlinenonpathogenic
-				m.isrim1 = true
-				break
-			case "s":
-			case "somatic":
-			case "diagnosis":
-				variantorigin = common.moriginsomatic
-				break
-		}
-	}
-	m.origin = variantorigin
-
-	if (!m.sample && !m.patient) {
-		// will not go into sample table
-		return
-	}
-
-	const nopatientname = "no patient/individual name"
-	let p
-	if (m.patient) {
-		if (!flag.patient2st[m.patient]) {
-			flag.patient2st[m.patient] = {}
-		}
-		flag.patient2st[m.patient][m.sampletype] = m.sample
-	} else {
-		if (!flag.patient2st[nopatientname]) {
-			flag.patient2st[nopatientname] = {}
-		}
-		flag.patient2st[nopatientname][m.sampletype] = m.sample
-	}
-
-	if (m.sample) {
-		if (m.disease) {
-			if (m.sample in flag.sample2disease) {
-				if (m.disease != flag.sample2disease[m.sample]) {
-					flag.snv.badlines.push([
-						i,
-						'conflict of disease types for sample "' +
-							m.sample +
-							'": ' +
-							m.disease +
-							", " +
-							flag.sample2disease[m.sample],
-						lst,
-					])
-					return true
-				}
-			} else {
-				flag.sample2disease[m.sample] = m.disease
-			}
-		}
-	}
-	return false
-}

package/src/bulk.snv.js

@@ -1,271 +0,0 @@
-///////////////////////////////
-//
-//  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 file header for snv/indel"
-	const htry = (...args) => {
-		for (const s of args) {
-			const i = header.indexOf(s)
-			if (i != -1) return i
-		}
-		return -1
-	}
-	let i = htry(
-		"annovar_gene",
-		"annovar_sj_gene",
-		"gene",
-		"genename",
-		"gene_symbol",
-		"hugo_symbol"
-	)
-	if (i == -1) return "gene missing from header"
-	header[i] = "gene"
-	i = htry(
-		"annovar_aachange",
-		"amino_acid_change",
-		"annovar_sj_aachange",
-		"aachange",
-		"protein_change",
-		"variant"
-	)
-	if (i == -1) return "amino_acid_change missing from header"
-	header[i] = "mname"
-	i = htry(
-		"annovar_class",
-		"class",
-		"mclass",
-		"variant_class",
-		"variant_classification",
-		"annovar_sj_class"
-	)
-	if (i == -1) return "variant_class missing from header"
-	header[i] = "class"
-	i = htry("chromosome", "chr")
-	if (i == -1) return "chromosome missing from header"
-	header[i] = "chr"
-	i = htry("wu_hg19_pos", "start", "start_position", "chr_position", "position")
-	if (i == -1) return "start missing from header"
-	header[i] = "pos"
-	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"
-
-	// optional
-	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("quantitative_measurements")
-	if (i != -1) header[i] = "qmset"
-	// dna maf tumor
-	i = htry("mutant_reads_in_case", "mutant_in_tumor", "tumor_readcount_alt")
-	if (i != -1) header[i] = "maf_tumor_v1"
-	i = htry("total_reads_in_case", "total_in_tumor", "tumor_readcount_total")
-	if (i != -1) header[i] = "maf_tumor_v2"
-	// dna maf normal
-	i = htry(
-		"mutant_reads_in_control",
-		"mutant_in_normal",
-		"normal_readcount_alt"
-	)
-	if (i != -1) header[i] = "maf_normal_v1"
-	i = htry(
-		"total_reads_in_control",
-		"total_in_normal",
-		"normal_readcount_total"
-	)
-	if (i != -1) header[i] = "maf_normal_v2"
-	// rna maf
-	// cdna
-	i = htry("cdna_change")
-	if (i != -1) header[i] = "cdna_change"
-	i = htry("sampletype", "sample type", "sample_type")
-	if (i != -1) header[i] = "sampletype"
-	i = htry("origin")
-	if (i != -1) header[i] = "origin"
-	i = htry("cancer", "disease", "diagnosis")
-	if (i != -1) header[i] = "disease"
-	flag.snv.header = header
-	flag.snv.loaded = true
-	return false
-}
-
-export function parseline(linei, line, flag) {
-	if (line == "" || line[0] == "#") return
-	const lst = line.split("\t")
-	const m = {}
-	for (let j = 0; j < flag.snv.header.length; j++) {
-		if (lst[j] == undefined) break
-		m[flag.snv.header[j]] = lst[j]
-	}
-	if (!m.gene) {
-		flag.snv.badlines.push([linei, "missing gene", lst])
-		return
-	}
-	if (m.gene.toUpperCase() == "UNKNOWN") {
-		flag.snv.badlines.push([linei, "gene name is UNKNOWN", lst])
-		return
-	}
-	if (!m.isoform) {
-		flag.snv.badlines.push([linei, "missing isoform", lst])
-		return
-	}
-	if (!m.mname) {
-		m.mname = m.cdna_change
-		if (!m.mname) {
-			flag.snv.badlines.push([linei, "missing amino acid change", lst])
-			return
-		}
-	} else {
-		if (m.mname.indexOf("p.") == 0) {
-			m.mname = m.mname.replace(/^p\./, "")
-		}
-	}
-	if (!m.class) {
-		flag.snv.badlines.push([linei, "missing mutation class", lst])
-		return
-	}
-	let _c = flag.mclasslabel2key[m.class.toUpperCase()]
-	if (_c) {
-		m.class = _c
-	} else {
-		_c = common.mclasstester(m.class)
-		if (_c) {
-			m.class = _c
-		} else {
-			flag.snv.badlines.push([linei, "wrong mutation class: " + m.class, lst])
-			return
-		}
-	}
-	if (bulk.parsesample(m, flag, linei, lst, flag.snv.badlines)) {
-		return
-	}
-	if (!m.chr) {
-		flag.snv.badlines.push([linei, "missing chromosome", lst])
-		return
-	}
-	if (m.chr.toLowerCase().indexOf("chr") != 0) {
-		m.chr = "chr" + m.chr
-	}
-	if (!m.pos) {
-		flag.snv.badlines.push([linei, "missing chromosome position", lst])
-		return
-	}
-	const v = Number.parseInt(m.pos)
-	if (Number.isNaN(v)) {
-		flag.snv.badlines.push([linei, "invalid chromosome position", lst])
-		return
-	}
-	m.pos = v - 1
-
-	if (m.maf_tumor_v2 != undefined && m.maf_tumor_v1 != undefined) {
-		if (m.maf_tumor_v2 == "") {
-			// no value, do not parse
-		} else {
-			let v1 = Number.parseInt(m.maf_tumor_v1),
-				v2 = Number.parseInt(m.maf_tumor_v2)
-			if (Number.isNaN(v1) || Number.isNaN(v2)) {
-				flag.snv.badlines.push([
-					linei,
-					"invalid maf_tumor mutant and/or total read count",
-					lst,
-				])
-				return
-			}
-			m.maf_tumor = { f: v1 / v2, v1: v1, v2: v2 }
-		}
-		delete m.maf_tumor_v1
-		delete m.maf_tumor_v2
-	}
-
-	if (m.maf_normal_v1 != undefined && m.maf_normal_v2 != undefined) {
-		if (m.maf_normal_v2 == "") {
-			// no value
-		} else {
-			let v1 = Number.parseInt(m.maf_normal_v1),
-				v2 = Number.parseInt(m.maf_normal_v2)
-			if (Number.isNaN(v1) || Number.isNaN(v2)) {
-				flag.snv.badlines.push([
-					linei,
-					"invalid maf_normal mutant and/or total read count",
-					lst,
-				])
-				return
-			}
-			m.maf_normal = { f: v1 / v2, v1: v1, v2: v2 }
-		}
-		delete m.maf_normal_v1
-		delete m.maf_normal_v2
-	}
-
-	/*
-	if(m.qmset) {
-		try{
-			var v=JSON.parse(m.qmset)
-		} catch(e){
-			flag.snv.badlines.push([linei,'invalid JSON for quantitative_measurements',lst])
-			v=null
-		} finally {
-			if(v) {
-				if(typeof(v)!='object') {
-					flag.snv.badlines.push([linei,'value of quantitative_measurements must be an object',lst])
-					delete m.qmset
-				} else {
-					for(var n in v) {
-						if(!Array.isArray(v[n])) {
-							flag.snv.badlines.push([linei,'quantitative_measurements: "'+n+'" value must be an array',lst])
-							delete v[n]
-						} else {
-							var tmp=[]
-							v[n].forEach(function(v2){
-								if(typeof(v2)=='number') {
-									tmp.push({v:v2})
-								} else if(v2.v && typeof(v2.v)=='number') {
-									tmp.push(v2)
-								}
-							})
-							if(tmp.length) {
-								v[n]=tmp
-							} else {
-								flag.snv.badlines.push([linei,'quantitative_measurements: no valid value for "'+n+'"',lst])
-								delete v[n]
-							}
-						}
-					}
-					m.qmset=v
-				}
-			} else {
-				delete m.qmset
-			}
-		}
-	}
-	*/
-	flag.good++
-	// FIXME hard-coded M and S
-	if (m.class == "M") {
-		flag.snv.missense++
-	} else if (m.class == "S") {
-		flag.snv.silent++
-	}
-	const n = flag.geneToUpper ? m.gene.toUpperCase() : m.gene
-	if (!flag.data[n]) {
-		flag.data[n] = []
-	}
-	m.dt = common.dtsnvindel
-	flag.data[n].push(m)
-}