@sjcrh/proteinpaint-server 2.44.0 → 2.46.0

package/dataset/clinvar.hg19.js

@@ -1,54 +1,55 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-var clinvar_js_1 = require("./clinvar.js");
-exports.default = {
-    isMds3: true,
-    dsinfo: [
-        { k: 'Source', v: '<a href=http://www.ncbi.nlm.nih.gov/clinvar/ target=_blank>NCBI ClinVar</a>' },
-        { k: 'Data type', v: 'SNV/Indel' },
-        { k: 'Gene annotation', v: 'VEP version 100' },
-        { k: 'Download date', v: 'May 2023' }
-    ],
-    genome: 'hg19',
-    queries: {
-        snvindel: {
-            forTrack: true,
-            byrange: {
-                bcffile: 'hg19/clinvar.hg19.bcf.gz',
-                infoFields: [
-                    {
-                        name: 'Clinical Significance',
-                        key: 'CLNSIG',
-                        categories: clinvar_js_1.clinsig,
-                        separator: '|'
-                    }
-                ]
-            },
-            ssmUrl: {
-                base: 'https://www.ncbi.nlm.nih.gov/clinvar/variation/',
-                namekey: 'vcf_id',
-                linkText: 'ClinVar',
-                shownSeparately: true
-            },
-            infoUrl: [{ base: 'https://www.ncbi.nlm.nih.gov/snp/rs', key: 'RS' }]
-        }
-    }
-    /*
-    vcfinfofilter: {
-        setidx4mclass: 0,
-        setidx4numeric: 1,
-        lst: [
-            {
-                name: 'Clinical significance',
-                locusinfo: {
-                    key: 'CLNSIG'
-                },
-                categories: clinvar.clinsig
-            },
-            clinvar.AF.AF_EXAC,
-            clinvar.AF.AF_ESP,
-            clinvar.AF.AF_TGP
+import { clinsig } from "./clinvar.js";
+var clinvar_hg19_default = {
+  isMds3: true,
+  dsinfo: [
+    { k: "Source", v: "<a href=http://www.ncbi.nlm.nih.gov/clinvar/ target=_blank>NCBI ClinVar</a>" },
+    { k: "Data type", v: "SNV/Indel" },
+    { k: "Gene annotation", v: "VEP version 100" },
+    { k: "Download date", v: "May 2023" }
+  ],
+  genome: "hg19",
+  queries: {
+    snvindel: {
+      forTrack: true,
+      byrange: {
+        bcffile: "hg19/clinvar.hg19.bcf.gz",
+        infoFields: [
+          {
+            name: "Clinical Significance",
+            key: "CLNSIG",
+            categories: clinsig,
+            separator: "|"
+          }
         ]
-    },
-*/
+      },
+      ssmUrl: {
+        base: "https://www.ncbi.nlm.nih.gov/clinvar/variation/",
+        namekey: "vcf_id",
+        linkText: "ClinVar",
+        shownSeparately: true
+      },
+      infoUrl: [{ base: "https://www.ncbi.nlm.nih.gov/snp/rs", key: "RS" }]
+    }
+  }
+  /*
+  	vcfinfofilter: {
+  		setidx4mclass: 0,
+  		setidx4numeric: 1,
+  		lst: [
+  			{
+  				name: 'Clinical significance',
+  				locusinfo: {
+  					key: 'CLNSIG'
+  				},
+  				categories: clinvar.clinsig
+  			},
+  			clinvar.AF.AF_EXAC,
+  			clinvar.AF.AF_ESP,
+  			clinvar.AF.AF_TGP
+  		]
+  	},
+  */
+};
+export {
+  clinvar_hg19_default as default
 };

package/dataset/clinvar.hg38.js

@@ -1,77 +1,78 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-var clinvar_js_1 = require("./clinvar.js");
-exports.default = {
-    isMds3: true,
-    dsinfo: [
-        { k: 'Source', v: '<a href=http://www.ncbi.nlm.nih.gov/clinvar/ target=_blank>NCBI ClinVar</a>' },
-        { k: 'Data type', v: 'SNV/Indel' },
-        { k: 'Gene annotation', v: 'VEP version 100' },
-        { k: 'Download date', v: 'May 2023' }
-    ],
-    genome: 'hg38',
-    viewModes: [
-        {
-            byInfo: 'gnomAD_AF',
-            inuse: true
-        },
-        {
-            byInfo: 'gnomAD_AF_afr'
-        }
-    ],
-    queries: {
-        snvindel: {
-            forTrack: true,
-            byrange: {
-                bcffile: 'hg38/clinvar.hg38.bcf.gz',
-                // list of info fields with special configurations
-                infoFields: [
-                    {
-                        name: 'Clinical significance',
-                        key: 'CLNSIG',
-                        categories: clinvar_js_1.clinsig,
-                        separator: '|'
-                    },
-                    {
-                        name: 'gnomAD_AF',
-                        key: 'gnomAD_AF'
-                    },
-                    {
-                        name: 'gnomAD_AF_afr',
-                        key: 'gnomAD_AF_afr'
-                    }
-                ]
-            },
-            ssmUrl: {
-                base: 'https://www.ncbi.nlm.nih.gov/clinvar/variation/',
-                namekey: 'vcf_id',
-                linkText: 'ClinVar',
-                shownSeparately: true
-            },
-            infoUrl: [
-                {
-                    base: 'https://www.ncbi.nlm.nih.gov/snp/rs',
-                    key: 'RS'
-                }
-            ]
-        }
+import { clinsig } from "./clinvar.js";
+var clinvar_hg38_default = {
+  isMds3: true,
+  dsinfo: [
+    { k: "Source", v: "<a href=http://www.ncbi.nlm.nih.gov/clinvar/ target=_blank>NCBI ClinVar</a>" },
+    { k: "Data type", v: "SNV/Indel" },
+    { k: "Gene annotation", v: "VEP version 100" },
+    { k: "Download date", v: "May 2023" }
+  ],
+  genome: "hg38",
+  viewModes: [
+    {
+      byInfo: "gnomAD_AF",
+      inuse: true
+    },
+    {
+      byInfo: "gnomAD_AF_afr"
     }
-    /*
-    vcfinfofilter: {
-        setidx4mclass: 0,
-        setidx4numeric: 1,
-        lst: [
-            {
-                name: 'Clinical significance',
-                locusinfo: {
-                    key: 'CLNSIG'
-                },
-                categories: clinvar.clinsig
-            },
-            clinvar.AF.AF_EXAC,
-            clinvar.AF.AF_ESP,
-            clinvar.AF.AF_TGP
+  ],
+  queries: {
+    snvindel: {
+      forTrack: true,
+      byrange: {
+        bcffile: "hg38/clinvar.hg38.bcf.gz",
+        // list of info fields with special configurations
+        infoFields: [
+          {
+            name: "Clinical significance",
+            key: "CLNSIG",
+            categories: clinsig,
+            separator: "|"
+          },
+          {
+            name: "gnomAD_AF",
+            key: "gnomAD_AF"
+          },
+          {
+            name: "gnomAD_AF_afr",
+            key: "gnomAD_AF_afr"
+          }
         ]
+      },
+      ssmUrl: {
+        base: "https://www.ncbi.nlm.nih.gov/clinvar/variation/",
+        namekey: "vcf_id",
+        linkText: "ClinVar",
+        shownSeparately: true
+      },
+      infoUrl: [
+        {
+          base: "https://www.ncbi.nlm.nih.gov/snp/rs",
+          key: "RS"
+        }
+      ]
     }
-    */
+  }
+  /*
+  vcfinfofilter: {
+  	setidx4mclass: 0,
+  	setidx4numeric: 1,
+  	lst: [
+  		{
+  			name: 'Clinical significance',
+  			locusinfo: {
+  				key: 'CLNSIG'
+  			},
+  			categories: clinvar.clinsig
+  		},
+  		clinvar.AF.AF_EXAC,
+  		clinvar.AF.AF_ESP,
+  		clinvar.AF.AF_TGP
+  	]
+  }
+  */
+};
+export {
+  clinvar_hg38_default as default
 };

package/dataset/clinvar.js

@@ -1,49 +1,166 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.AF = exports.clinsig = void 0;
-exports.clinsig = {
-    Affects: { color: '#ccc', label: 'Affects', desc: "Variants that cause a non-disease phenotype, such as lactose intolerance." },
-    Benign: { color: '#43ac6a', label: 'Benign', textcolor: 'white', desc: "The variant is reported to be benign." },
-    'Benign/Likely_benign': { color: '#43ac6a', label: 'Benign/Likely benign', textcolor: 'white', desc: "The variant is reported to be benign/likely benign by different submitters." },
-    Likely_benign: { color: '#5bc0de', label: 'Likely benign', textcolor: 'white', desc: "The variant is reported to be likely benign." },
-    Conflicting_interpretations_of_pathogenicity: { color: '#90C3D4', label: 'Conflicting interpretations of pathogenicity', desc: "The variant has conflicting clinical assertions from different submitters." },
-    Likely_pathogenic: { color: '#e99002', label: 'Likely pathogenic', textcolor: 'white', desc: "The variant is reported to be likely pathogenic." },
-    'Likely_pathogenic,_low_penetrance': { color: '#e99002', label: 'Likely pathogenic/Low penetrance', desc: "The variant is reported to be likely pathogenic with low penetrance." },
-    '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." },
-    Likely_risk_allele: { color: '#e99002', label: 'Likely risk allele', desc: "" },
-    Pathogenic: { color: '#f04124', label: 'Pathogenic', textcolor: 'white', desc: "The variant is reported to be pathogenic." },
-    '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." },
-    '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." },
-    'Pathogenic/Likely_pathogenic': { color: '#f04124', label: 'Pathogenic/Likely pathogenic', textcolor: 'white', desc: "The variant is reported to be pathogenic/likely pathogenic by different submitters." },
-    '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." },
-    'Pathogenic/Likely_risk_allele': { color: '#f04124', label: 'Pathogenic/Likely risk allele', desc: "The variant is reported pathogenic/likely risk allele by different submitters." },
-    'Pathogenic/Pathogenic,_low_penetrance': { color: '#f04124', label: 'Pathogenic/Low penetrance', desc: "The variant is reported pathogenic with low penetrance." },
-    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." },
-    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." },
-    '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." },
-    association: { color: '#ccc', label: 'Association', desc: "Variants identified in a GWAS study and further interpreted for their clinical significance." },
-    association_not_found: { color: '#ccc', label: 'Association not found', desc: "No significant GWAS association study found." },
-    confers_sensitivity: { color: '#ccc', label: 'Confers sensitivity', desc: "" },
-    drug_response: { color: 'gold', label: 'Drug response', textcolor: 'white', desc: "The variant is reported to affect a drug response." },
-    not_provided: { color: '#ccc', label: 'Not provided', desc: "Clinical significance for the variant has not been provided by the submitter." },
-    other: { color: '#ccc', label: 'Other', desc: "The variant has some other clinical significance, such as protective, association, confers sensitivity." },
-    protective: { color: '#ccc', label: 'Protective', desc: "Variants that decrease the risk of a disorder, including infections." },
-    risk_factor: { color: '#ccc', label: 'Risk factor', desc: "The variant is reported to be a risk factor for a particular disease." },
+const clinsig = {
+  Affects: {
+    color: "#ccc",
+    label: "Affects",
+    desc: "Variants that cause a non-disease phenotype, such as lactose intolerance."
+  },
+  Benign: { color: "#43ac6a", label: "Benign", textcolor: "white", desc: "The variant is reported to be benign." },
+  "Benign/Likely_benign": {
+    color: "#43ac6a",
+    label: "Benign/Likely benign",
+    textcolor: "white",
+    desc: "The variant is reported to be benign/likely benign by different submitters."
+  },
+  Likely_benign: {
+    color: "#5bc0de",
+    label: "Likely benign",
+    textcolor: "white",
+    desc: "The variant is reported to be likely benign."
+  },
+  Conflicting_interpretations_of_pathogenicity: {
+    color: "#90C3D4",
+    label: "Conflicting interpretations of pathogenicity",
+    desc: "The variant has conflicting clinical assertions from different submitters."
+  },
+  Likely_pathogenic: {
+    color: "#e99002",
+    label: "Likely pathogenic",
+    textcolor: "white",
+    desc: "The variant is reported to be likely pathogenic."
+  },
+  "Likely_pathogenic,_low_penetrance": {
+    color: "#e99002",
+    label: "Likely pathogenic/Low penetrance",
+    desc: "The variant is reported to be likely pathogenic with low penetrance."
+  },
+  "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."
+  },
+  Likely_risk_allele: { color: "#e99002", label: "Likely risk allele", desc: "" },
+  Pathogenic: {
+    color: "#f04124",
+    label: "Pathogenic",
+    textcolor: "white",
+    desc: "The variant is reported to be pathogenic."
+  },
+  "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."
+  },
+  "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."
+  },
+  "Pathogenic/Likely_pathogenic": {
+    color: "#f04124",
+    label: "Pathogenic/Likely pathogenic",
+    textcolor: "white",
+    desc: "The variant is reported to be pathogenic/likely pathogenic by different submitters."
+  },
+  "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."
+  },
+  "Pathogenic/Likely_risk_allele": {
+    color: "#f04124",
+    label: "Pathogenic/Likely risk allele",
+    desc: "The variant is reported pathogenic/likely risk allele by different submitters."
+  },
+  "Pathogenic/Pathogenic,_low_penetrance": {
+    color: "#f04124",
+    label: "Pathogenic/Low penetrance",
+    desc: "The variant is reported pathogenic with low penetrance."
+  },
+  Uncertain_risk_allele: {
+    color: "#aaa",
+    label: "Uncertain risk allele",
+    textcolor: "white",
+    desc: "A genetic change affecting an allele whose impact on the individual\u2019s disease risk is not yet known."
+  },
+  Uncertain_significance: {
+    color: "#aaa",
+    label: "Uncertain significance",
+    textcolor: "white",
+    desc: "A genetic change whose impact on the individual\u2019s disease risk is not yet known."
+  },
+  "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."
+  },
+  association: {
+    color: "#ccc",
+    label: "Association",
+    desc: "Variants identified in a GWAS study and further interpreted for their clinical significance."
+  },
+  association_not_found: {
+    color: "#ccc",
+    label: "Association not found",
+    desc: "No significant GWAS association study found."
+  },
+  confers_sensitivity: { color: "#ccc", label: "Confers sensitivity", desc: "" },
+  drug_response: {
+    color: "gold",
+    label: "Drug response",
+    textcolor: "white",
+    desc: "The variant is reported to affect a drug response."
+  },
+  not_provided: {
+    color: "#ccc",
+    label: "Not provided",
+    desc: "Clinical significance for the variant has not been provided by the submitter."
+  },
+  other: {
+    color: "#ccc",
+    label: "Other",
+    desc: "The variant has some other clinical significance, such as protective, association, confers sensitivity."
+  },
+  protective: {
+    color: "#ccc",
+    label: "Protective",
+    desc: "Variants that decrease the risk of a disorder, including infections."
+  },
+  risk_factor: {
+    color: "#ccc",
+    label: "Risk factor",
+    desc: "The variant is reported to be a risk factor for a particular disease."
+  }
 };
-exports.AF = {
-    AF_EXAC: {
-        name: 'ExAC frequency',
-        locusinfo: { key: 'AF_EXAC' },
-        numericfilter: [{ side: '<', value: 0.0001 }, { side: '<', value: 0.001 }, { side: '<', value: 0.01 }]
-    },
-    AF_ESP: {
-        name: 'GO-ESP frequency',
-        locusinfo: { key: 'AF_ESP' },
-        numericfilter: [{ side: '<', value: 0.0001 }, { side: '<', value: 0.001 }, { side: '<', value: 0.01 }]
-    },
-    AF_TGP: {
-        name: '1000 Genomes frequency',
-        locusinfo: { key: 'AF_TGP' },
-        numericfilter: [{ side: '<', value: 0.0001 }, { side: '<', value: 0.001 }, { side: '<', value: 0.01 }]
-    }
+const AF = {
+  AF_EXAC: {
+    name: "ExAC frequency",
+    locusinfo: { key: "AF_EXAC" },
+    numericfilter: [
+      { side: "<", value: 1e-4 },
+      { side: "<", value: 1e-3 },
+      { side: "<", value: 0.01 }
+    ]
+  },
+  AF_ESP: {
+    name: "GO-ESP frequency",
+    locusinfo: { key: "AF_ESP" },
+    numericfilter: [
+      { side: "<", value: 1e-4 },
+      { side: "<", value: 1e-3 },
+      { side: "<", value: 0.01 }
+    ]
+  },
+  AF_TGP: {
+    name: "1000 Genomes frequency",
+    locusinfo: { key: "AF_TGP" },
+    numericfilter: [
+      { side: "<", value: 1e-4 },
+      { side: "<", value: 1e-3 },
+      { side: "<", value: 0.01 }
+    ]
+  }
+};
+export {
+  AF,
+  clinsig
 };