@sjcrh/proteinpaint-server 2.16.0 → 2.18.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dataset/clinvar.hg19.js +53 -51
- package/dataset/clinvar.hg38.js +60 -58
- package/dataset/clinvar.js +49 -55
- package/genome/CriGri.js +23 -1853
- package/genome/danRer10.js +48 -1108
- package/genome/dm3.js +47 -60
- package/genome/dm6.js +48 -1916
- package/genome/galGal5.js +48 -23522
- package/genome/galGal6.js +48 -512
- package/genome/hg19.js +210 -304
- package/genome/hg38.js +110 -474
- package/genome/hg38.test.js +42 -409
- package/genome/hgvirus.js +21 -43
- package/genome/mm10.js +70 -135
- package/genome/mm9.js +82 -118
- package/genome/rn6.js +49 -1000
- package/package.json +11 -7
- package/server.js +1 -1
- package/shared/common.js +4 -0
- package/src/serverconfig.js +10 -2
- package/utils/fastclust.R +16 -6
- package/genome/genome.sql +0 -54
package/dataset/clinvar.hg19.js
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"use strict";
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Object.defineProperty(exports, "__esModule", { value: true });
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var clinvar_js_1 = require("./clinvar.js");
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exports.default = {
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isMds3: true,
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dsinfo: [
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{ k: 'Source', v: '<a href=http://www.ncbi.nlm.nih.gov/clinvar/ target=_blank>NCBI ClinVar</a>' },
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{ k: 'Data type', v: 'SNV/Indel' },
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{ k: 'Gene annotation', v: 'VEP version 107' },
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{ k: 'Download date', v: 'July 2022' }
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],
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genome: 'hg19',
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queries: {
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snvindel: {
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forTrack: true,
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byrange: {
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bcffile: 'hg19/clinvar.hg19.hgvs_short.vep.bcf.gz',
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infoFields: [
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{
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name: 'Clinical Significance',
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key: 'CLNSIG',
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categories: clinvar_js_1.clinsig,
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separator: '|'
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}
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]
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},
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variantUrl: {
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base: 'https://www.ncbi.nlm.nih.gov/clinvar/variation/',
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key: 'vcf_id',
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linkText: 'ClinVar',
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shownSeparately: true
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},
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infoUrl: [{ base: 'https://www.ncbi.nlm.nih.gov/snp/rs', key: 'RS' }]
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}
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}
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/*
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vcfinfofilter: {
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setidx4mclass: 0,
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setidx4numeric: 1,
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lst: [
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{
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name: 'Clinical significance',
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locusinfo: {
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key: 'CLNSIG'
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},
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categories: clinvar.clinsig
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},
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clinvar.AF.AF_EXAC,
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clinvar.AF.AF_ESP,
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clinvar.AF.AF_TGP
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]
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},
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*/
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}
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};
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package/dataset/clinvar.hg38.js
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}
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"use strict";
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Object.defineProperty(exports, "__esModule", { value: true });
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var clinvar_js_1 = require("./clinvar.js");
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exports.default = {
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isMds3: true,
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dsinfo: [
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{ k: 'Source', v: '<a href=http://www.ncbi.nlm.nih.gov/clinvar/ target=_blank>NCBI ClinVar</a>' },
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{ k: 'Data type', v: 'SNV/Indel' },
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{ k: 'Gene annotation', v: 'VEP version 107' },
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{ k: 'Download date', v: 'July 2022' }
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],
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genome: 'hg38',
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queries: {
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snvindel: {
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forTrack: true,
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byrange: {
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bcffile: 'hg38/clinvar.hg38.hgvs_short.vep.bcf.gz',
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// list of info fields with special configurations
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infoFields: [
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{
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name: 'Clinical significance',
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key: 'CLNSIG',
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categories: clinvar_js_1.clinsig,
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separator: '|'
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}
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]
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},
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variantUrl: {
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base: 'https://www.ncbi.nlm.nih.gov/clinvar/variation/',
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key: 'vcf_id',
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linkText: 'ClinVar',
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shownSeparately: true
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},
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infoUrl: [
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{
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base: 'https://www.ncbi.nlm.nih.gov/snp/rs',
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key: 'RS'
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}
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]
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}
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}
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/*
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vcfinfofilter: {
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setidx4mclass: 0,
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setidx4numeric: 1,
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lst: [
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{
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name: 'Clinical significance',
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locusinfo: {
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key: 'CLNSIG'
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},
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categories: clinvar.clinsig
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},
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clinvar.AF.AF_EXAC,
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clinvar.AF.AF_ESP,
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clinvar.AF.AF_TGP
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]
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}
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*/
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};
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package/dataset/clinvar.js
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}
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AF_TGP: {
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name: '1000 Genomes frequency',
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locusinfo: { key: 'AF_TGP' },
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numericfilter: [{ side: '<', value: 0.0001 }, { side: '<', value: 0.001 }, { side: '<', value: 0.01 }]
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}
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}
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"use strict";
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Object.defineProperty(exports, "__esModule", { value: true });
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exports.AF = exports.clinsig = void 0;
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exports.clinsig = {
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Affects: { color: '#ccc', label: 'Affects', desc: "Variants that cause a non-disease phenotype, such as lactose intolerance." },
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Benign: { color: '#43ac6a', label: 'Benign', textcolor: 'white', desc: "The variant is reported to be benign." },
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'Benign/Likely_benign': { color: '#43ac6a', label: 'Benign/Likely benign', textcolor: 'white', desc: "The variant is reported to be benign/likely benign by different submitters." },
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Likely_benign: { color: '#5bc0de', label: 'Likely benign', textcolor: 'white', desc: "The variant is reported to be likely benign." },
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Conflicting_interpretations_of_pathogenicity: { color: '#90C3D4', label: 'Conflicting interpretations of pathogenicity', desc: "The variant has conflicting clinical assertions from different submitters." },
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Likely_pathogenic: { color: '#e99002', label: 'Likely pathogenic', textcolor: 'white', desc: "The variant is reported to be likely pathogenic." },
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'Likely_pathogenic,_low_penetrance': { color: '#e99002', label: 'Likely pathogenic/Low penetrance', desc: "The variant is reported to be likely pathogenic with low penetrance." },
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'Likely_pathogenic/Likely_risk_allele': { color: '#e99002', label: 'Likely pathogenic/Likely risk allele', desc: "The variant is reported to be likely pathogenic/likely risk allele by different submitters." },
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Likely_risk_allele: { color: '#e99002', label: 'Likely risk allele', desc: "" },
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Pathogenic: { color: '#f04124', label: 'Pathogenic', textcolor: 'white', desc: "The variant is reported to be pathogenic." },
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'Likely_pathogenic/Pathogenic,_low_penetrance': { color: '#f04124', label: 'Likely pathogenic/Pathogenic/Low penetrance', desc: "The variant is reported likely pathogenic/pathogenic with low penetrance by different submitters." },
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'Pathogenic/Likely_pathogenic/Pathogenic,_low_penetrance': { color: '#f04124', label: 'Pathogenic/Likely pathogenic/Low penetrance', desc: "The variant is reported likely pathogenic/pathogenic with low penetrance by different submitters." },
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'Pathogenic/Likely_pathogenic': { color: '#f04124', label: 'Pathogenic/Likely pathogenic', textcolor: 'white', desc: "The variant is reported to be pathogenic/likely pathogenic by different submitters." },
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'Pathogenic/Likely_pathogenic/Likely_risk_allele': { color: '#f04124', label: 'Pathogenic/Likely pathogenic/Likely risk allele', desc: "The variant is reported to be pathogenic, likely pathogenic or likely risk allele by different submitters." },
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'Pathogenic/Likely_risk_allele': { color: '#f04124', label: 'Pathogenic/Likely risk allele', desc: "The variant is reported pathogenic/likely risk allele by different submitters." },
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'Pathogenic/Pathogenic,_low_penetrance': { color: '#f04124', label: 'Pathogenic/Low penetrance', desc: "The variant is reported pathogenic with low penetrance." },
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Uncertain_risk_allele: { color: '#aaa', label: 'Uncertain risk allele', textcolor: 'white', desc: "A genetic change affecting an allele whose impact on the individual’s disease risk is not yet known." },
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Uncertain_significance: { color: '#aaa', label: 'Uncertain significance', textcolor: 'white', desc: "A genetic change whose impact on the individual’s disease risk is not yet known." },
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'Uncertain_significance/Uncertain_risk_allele': { color: '#aaa', label: 'Uncertain significance/Uncertain risk allele', desc: "The variant is reported of uncertain significance/uncertain risk allele by different submitters." },
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association: { color: '#ccc', label: 'Association', desc: "Variants identified in a GWAS study and further interpreted for their clinical significance." },
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association_not_found: { color: '#ccc', label: 'Association not found', desc: "No significant GWAS association study found." },
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confers_sensitivity: { color: '#ccc', label: 'Confers sensitivity', desc: "" },
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drug_response: { color: 'gold', label: 'Drug response', textcolor: 'white', desc: "The variant is reported to affect a drug response." },
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not_provided: { color: '#ccc', label: 'Not provided', desc: "Clinical significance for the variant has not been provided by the submitter." },
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other: { color: '#ccc', label: 'Other', desc: "The variant has some other clinical significance, such as protective, association, confers sensitivity." },
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protective: { color: '#ccc', label: 'Protective', desc: "Variants that decrease the risk of a disorder, including infections." },
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risk_factor: { color: '#ccc', label: 'Risk factor', desc: "The variant is reported to be a risk factor for a particular disease." },
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};
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exports.AF = {
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AF_EXAC: {
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name: 'ExAC frequency',
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locusinfo: { key: 'AF_EXAC' },
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numericfilter: [{ side: '<', value: 0.0001 }, { side: '<', value: 0.001 }, { side: '<', value: 0.01 }]
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},
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AF_ESP: {
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name: 'GO-ESP frequency',
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locusinfo: { key: 'AF_ESP' },
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numericfilter: [{ side: '<', value: 0.0001 }, { side: '<', value: 0.001 }, { side: '<', value: 0.01 }]
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},
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AF_TGP: {
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name: '1000 Genomes frequency',
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locusinfo: { key: 'AF_TGP' },
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numericfilter: [{ side: '<', value: 0.0001 }, { side: '<', value: 0.001 }, { side: '<', value: 0.01 }]
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}
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};
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