@sjcrh/proteinpaint-client 2.191.4 → 2.193.0

package/dist/chunk-FABY3ISP.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/disco/launch.adhoc.ts"],
+  "sourcesContent": ["import type { Genome } from '#types'\nimport type { Selection } from 'd3-selection'\nimport { appInit } from '../plot.app'\nimport { showErrorsWithCounter } from '../../dom/sayerror'\nimport { mclass } from '#shared/common.js'\n\ntype SnvEntry = {\n\tdt: 1\n\tchr: string\n\tposition: number\n\tgene: string\n\tmname: string\n\tclass: string\n\tvafs?: Array<{ id: string; totalCount: number; altCount: number }>\n}\ntype CnvEntry = {\n\tdt: 4\n\tchr: string\n\tstart: number\n\tstop: number\n\tvalue: number\n}\ntype SvEntry4Cols = {\n\tdt: number\n\tchrA: string\n\tposA: number\n\tchrB: string\n\tposB: number\n}\n\ntype SvEntry6Cols = {\n\tdt: number\n\tchrA: string\n\tposA: number\n\tgeneA: string\n\tchrB: string\n\tposB: number\n\tgeneB: string\n}\n\ntype SvEntry = SvEntry4Cols | SvEntry6Cols\n\ntype MutationListEntry = SnvEntry | CnvEntry | SvEntry\n\n/** When disco is embedded, the arguments below are nested under arg.disco */\nexport type DiscoPlotArgs = {\n\t/**optional array of preparsed mutation events, from runpp() */\n\tmlst?: MutationListEntry[]\n\n\t/**tabular text of snv data, with follow columns.\n\t1. chr\n\t2. position\n\t3. gene\n\t4. aachange\n\t5. class\n\tOptionally, provide DNA total/alt read counts in columns 6-7 and RNA total/alt \n\tread counts in columns 8-9.\n\teach line is parsed into an object:\n\t{dt:1, chr:, position:, gene:, class:} */\n\tsnvText?: string\n\t/**tp path to a text file of same content as snvText */\n\tsnvFile?: string\n\t/**url of a text file of same content as snvText */\n\tsnvUrl?: string\n\n\t/**tabular text of sv/fusion data, with follow columns\n\t1. chrA\n\t2. posA\n\t3. geneA\n\t4. chrB\n\t5. posB\n\t6. geneB\n\teach line is parsed into an object:\n\t{dt:2, chrA, posA, geneA, chrB, posB, geneB} */\n\tsvText?: string\n\tsvFile?: string\n\tsvUrl?: string\n\n\t/**tabular text of cnv data, with following columns\n\t1. chr\n\t2. start\n\t3. stop\n\t4. value\n\teach line is parsed into an object\n\t{chr, start, stop, value} */\n\tcnvText?: string\n\tcnvFile?: string\n\tcnvUrl?: string\n\tsettings?: any\n}\n\n//... more datatypes can be added later\n\n/**\n * parse input data into mlst[] and pass to disco\n * TODO display data error on ui\n * TODO later make this script a native part of disco, so that runpp() directly invokes plot.app.js...\n * @param arg\n * @param genomeObj\n * @param holder\n * @returns\n */\n\nexport async function launch(arg: DiscoPlotArgs, genomeObj: Genome, holder: Selection<HTMLDivElement, any, any, any>) {\n\tconst [mlst, errors] = await getMlst(arg)\n\n\tif (errors?.length) {\n\t\treturn showErrorsWithCounter(errors, holder)\n\t}\n\n\tconst opts = {\n\t\tholder,\n\t\tvocabApi: {\n\t\t\t// api is required by plot.app.js, so create a mock one for the adhoc data\n\t\t\tvocab: { terms: [] },\n\t\t\tmain: () => {\n\t\t\t\treturn //fix so linter doesn't yell while this is in development\n\t\t\t},\n\t\t\tgetTermdbConfig: () => {\n\t\t\t\treturn {}\n\t\t\t}\n\t\t},\n\t\tstate: {\n\t\t\targs: {\n\t\t\t\tdata: mlst,\n\t\t\t\tgenome: genomeObj\n\t\t\t},\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'Disco',\n\t\t\t\t\tsubfolder: 'disco',\n\t\t\t\t\textension: 'ts',\n\t\t\t\t\t/** NOTE: Users should only override the settings in the default\n\t\t\t\t\t * settings.Disco:{}, not the entire settings:{} object.*/\n\t\t\t\t\toverrides: { Disco: arg?.settings || {} }\n\t\t\t\t}\n\t\t\t]\n\t\t}\n\t}\n\n\tconst plotAppApi = await appInit(opts)\n\treturn plotAppApi\n}\n\n/**\n * from multiple possible data sources, parse mutation events and put everything into one array and return, for disco rendering\n * app drawer will supply data for \"snvText, svText, cnvText\"\n * while the \"File\" and \"Url\" can come from url parameters e.g. host?disco=1&snvFile=path/to/file\n * @param arg\n * @returns\n */\nasync function getMlst(arg: DiscoPlotArgs): Promise<[MutationListEntry[], string[] | null]> {\n\tif (Array.isArray(arg.mlst)) {\n\t\t// has preformatted in runpp()\n\t\treturn [arg.mlst, null]\n\t}\n\n\t// parse data from text and files and append to one mlst[] array\n\tconst mlst = [] as MutationListEntry[]\n\tconst errors = [] as string[]\n\n\tif (arg.snvText) parseSnvText(arg.snvText, mlst, errors)\n\tif (arg.svText) parseSvText(arg.svText, mlst, errors)\n\tif (arg.cnvText) parseCnvText(arg.cnvText, mlst, errors)\n\n\t// if (arg.snvFile) {\n\t// }\n\t// if (arg.snvUrl) {\n\t// }\n\t// if (arg.svFile) {\n\t// }\n\t// if (arg.svUrl) {\n\t// }\n\t// if (arg.cnvFile) {\n\t// }\n\t// if (arg.cnvUrl) {\n\t// }\n\n\treturn [mlst, errors]\n}\n\nfunction parseSnvText(text: string, mlst: MutationListEntry[], errors: string[]) {\n\t// TODO share a parser for snvindel text file with samples (with header line and non-fixed columns), but should not require sample here\n\tfor (const line of text.trim().split('\\n')) {\n\t\tconst l = line.trim().split('\\t')\n\n\t\tif (![5, 7, 9].includes(l.length)) {\n\t\t\terrors.push('snv input not equal to 5, 7, or 9 columns')\n\t\t\tcontinue\n\t\t}\n\n\t\tlet m: SnvEntry\n\t\ttry {\n\t\t\tm = {\n\t\t\t\tdt: 1,\n\t\t\t\tchr: l[0],\n\t\t\t\tposition: Number(l[1]),\n\t\t\t\tgene: l[2],\n\t\t\t\tmname: l[3],\n\t\t\t\tclass: validateMutation(l[4], errors)\n\t\t\t}\n\t\t\tconst vafs = parseOptionalVafs(l, errors)\n\t\t\tif (vafs.length) m.vafs = vafs\n\t\t} catch (e: any) {\n\t\t\terrors.push(e)\n\t\t\tcontinue\n\t\t}\n\t\tmlst.push(m)\n\t}\n}\n\nfunction parseOptionalVafs(line: string[], errors: string[]) {\n\tconst vafs: Array<{ id: string; totalCount: number; altCount: number }> = []\n\tconst addVaf = (id: string, totalIndex: number, altIndex: number) => {\n\t\tif (line.length <= altIndex) return\n\t\tconst totalCount = Number(line[totalIndex])\n\t\tconst altCount = Number(line[altIndex])\n\t\tif (\n\t\t\t!Number.isInteger(totalCount) ||\n\t\t\t!Number.isInteger(altCount) ||\n\t\t\ttotalCount <= 0 ||\n\t\t\taltCount < 0 ||\n\t\t\taltCount > totalCount\n\t\t) {\n\t\t\terrors.push(`${id} total/alt counts must be integers with total > 0, alt >= 0, and alt cannot exceed total`)\n\t\t\treturn\n\t\t}\n\n\t\tvafs.push({ id, totalCount, altCount })\n\t}\n\n\taddVaf('DNA', 5, 6)\n\taddVaf('RNA', 7, 8)\n\treturn vafs\n}\n\nfunction parseSvText(text: string, mlst: MutationListEntry[], errors: string[]) {\n\tfor (const line of text.trim().split('\\n')) {\n\t\tconst l = line.trim().split('\\t')\n\t\tif (l.length < 4 || l.length > 6) {\n\t\t\terrors.push('sv input not equal to 4 or 6 columns')\n\t\t\tcontinue\n\t\t}\n\t\tlet m: SvEntry\n\t\ttry {\n\t\t\tconst length: number = l.length\n\t\t\tif (length == 4) {\n\t\t\t\tm = {\n\t\t\t\t\tdt: 2,\n\t\t\t\t\tchrA: l[0],\n\t\t\t\t\tposA: Number(l[1]),\n\t\t\t\t\tchrB: l[2],\n\t\t\t\t\tposB: Number(l[3])\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\tm = {\n\t\t\t\t\tdt: 2,\n\t\t\t\t\tchrA: l[0],\n\t\t\t\t\tposA: Number(l[1]),\n\t\t\t\t\tgeneA: l[2],\n\t\t\t\t\tchrB: l[3],\n\t\t\t\t\tposB: Number(l[4]),\n\t\t\t\t\tgeneB: l[5]\n\t\t\t\t}\n\t\t\t}\n\t\t} catch (e: any) {\n\t\t\terrors.push(e)\n\t\t\tcontinue\n\t\t}\n\t\tmlst.push(m)\n\t}\n}\n\nfunction parseCnvText(text: string, mlst: MutationListEntry[], errors: string[]) {\n\tfor (const line of text.trim().split('\\n')) {\n\t\tconst l = line.trim().split('\\t')\n\t\tif (l.length != 4) {\n\t\t\terrors.push('cnv input not equal to 4 columns')\n\t\t\tcontinue\n\t\t}\n\t\tlet m: CnvEntry\n\t\ttry {\n\t\t\tm = {\n\t\t\t\tdt: 4,\n\t\t\t\tchr: l[0],\n\t\t\t\tstart: Number(l[1]),\n\t\t\t\tstop: Number(l[2]),\n\t\t\t\tvalue: Number(l[3])\n\t\t\t}\n\t\t} catch (e: any) {\n\t\t\terrors.push(e)\n\t\t\tcontinue\n\t\t}\n\t\tmlst.push(m)\n\t}\n}\n\nfunction validateMutation(mutation: string, errors: string[]) {\n\tconst mut2check = mutation.toLowerCase()\n\tconst foundMutation = Object.values(mclass).find(\n\t\t(m: any) => m.key.toLowerCase() === mut2check || m.label.toLowerCase() === mut2check\n\t) as any\n\tif (foundMutation) {\n\t\treturn foundMutation.key\n\t} else {\n\t\terrors.push(`Invalid mutation class: ${mutation}`)\n\t}\n}\n"],
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+  "names": []
+}

package/dist/chunk-FOPHIWFD.js

@@ -0,0 +1,100 @@
+import {
+  SearchHandler,
+  fillTermWrapper,
+  table2col,
+  termsettingInit
+} from "./chunk-L7VDSIM7.js";
+
+// plots/summarizeMutationDiagnosis.ts
+async function makeChartBtnMenu(holder, chartsInstance) {
+  let dictTw;
+  {
+    const t = chartsInstance.app.vocabApi.termdbConfig.defaultTw4correlationPlot?.disease;
+    if (!t) throw "defaultTw4correlationPlot missing";
+    dictTw = structuredClone(t);
+    await fillTermWrapper(dictTw, chartsInstance.app.vocabApi);
+  }
+  const table = table2col({
+    holder: holder.append("div"),
+    margin: "0px 10px 10px 10px",
+    cellPadding: "10px"
+  });
+  {
+    const [td1, td2] = table.addRow();
+    td1.text("Mutation Variable");
+    const searchDiv = td2.append("div");
+    const geneSearchInst = new SearchHandler();
+    geneSearchInst.init({
+      holder: searchDiv,
+      app: chartsInstance.app,
+      // required to supply "opts.app.vocabApi" for the search ui
+      genomeObj: chartsInstance.app.opts.genome,
+      msg: "Hit ENTER to launch plot.",
+      callback: async (geneTw) => {
+        await fillTermWrapper(geneTw, chartsInstance.app.vocabApi);
+        launchPlot({
+          tw1: dictTw,
+          tw2: geneTw,
+          chartsInstance,
+          holder
+        });
+      }
+    });
+    searchDiv.style("padding", "0px 0px 5px 0px");
+  }
+  {
+    const [td1, td2] = table.addRow();
+    td1.text("Compare Mutations Against");
+    const pillDiv = td2.append("div"), waitDiv = td2.append("div").style("font-size", ".7em").text("LOADING ...");
+    const pill = await termsettingInit({
+      menuOptions: "{edit,replace}",
+      /** presumably this usecase let it restrict to dictionary term ui, and hide genomic queries
+      target="filter" works for gdc since in gdc ds it is overriding filter to dict
+      but is not a general fix for non-gdc ds, which Replace menu will launch genomic+dict options
+      maybe this is okay for non-gdc ds as the default dictTw is meaningful
+      */
+      usecase: { target: "filter" },
+      vocabApi: chartsInstance.app.vocabApi,
+      holder: pillDiv,
+      callback: async (tw) => {
+        waitDiv.text("LOADING ...");
+        try {
+          await pill.main(tw);
+          dictTw = tw;
+          waitDiv.text("Click to edit/replace the variable before searching gene.");
+        } catch (e) {
+          waitDiv.text("Error: " + (e.message || e));
+        }
+      }
+    });
+    try {
+      await fillTermWrapper(dictTw, chartsInstance.app.vocabApi);
+      await pill.main(dictTw);
+      waitDiv.text("Click to edit/replace the variable before searching gene.");
+    } catch (e) {
+      waitDiv.text("Error: " + (e.message || e));
+    }
+  }
+}
+function launchPlot({ tw1, tw2, chartsInstance, holder }) {
+  const chart = {
+    config: {
+      chartType: tw1?.term?.type == "survival" ? "survival" : "summary",
+      // TODO define sandbox header with gene+term name
+      term: tw1,
+      term2: tw2
+    }
+  };
+  chartsInstance.plotCreate(chart);
+  holder.selectAll("*").remove();
+  holder.append("div").style("margin", "20px").text("LOADING CHART ...");
+  setTimeout(() => {
+    holder.style("display", "none");
+  }, 1e3);
+}
+
+export {
+  makeChartBtnMenu,
+  launchPlot
+};
+//# sourceMappingURL=chunk-FOPHIWFD.js.map

package/dist/chunk-FVX76DZS.js

@@ -0,0 +1,203 @@
+import {
+  tkt
+} from "./chunk-L7VDSIM7.js";
+import {
+  stratinput
+} from "./chunk-PF4DSFDR.js";
+import {
+  stratify_default
+} from "./chunk-VQZ2Z5YU.js";
+
+// src/vcf.tkconvert.js
+function vcf2dstk(arg) {
+  const ds = {
+    id2vcf: {},
+    label: arg.name || "Unnamed VCF file"
+  };
+  let vcfobj;
+  if (arg.file) {
+    const id = Math.random().toString();
+    vcfobj = {
+      file: arg.file,
+      indexURL: arg.indexURL,
+      vcfid: id
+    };
+    ds.id2vcf[id] = vcfobj;
+  } else if (arg.url) {
+    const id = Math.random().toString();
+    vcfobj = {
+      url: arg.url,
+      indexURL: arg.indexURL,
+      vcfid: id
+    };
+    ds.id2vcf[id] = vcfobj;
+  } else {
+    return ["no .file or .url"];
+  }
+  vcfobj.headernotloaded = true;
+  if (arg.samplenamemap) {
+    vcfobj.samplenamemap = arg.samplenamemap;
+  }
+  if (arg.variant2img) {
+    if (!arg.variant2img.path) return [".path missing from .variant2img{}"];
+  }
+  const tk = {
+    type: tkt.ds,
+    // to be loaded by loadvcftk() as a custom track, rather than "/dsdata" for official ds
+    isvcf: true,
+    name: ds.label,
+    ds,
+    populationfrequencyfilter: arg.populationfrequencyfilter,
+    vcfinfofilter: arg.vcfinfofilter,
+    itemlabelname: arg.itemlabelname,
+    viewrangeupperlimit: arg.viewrangeupperlimit,
+    variant2img: arg.variant2img,
+    axisheight: arg.axisheight
+  };
+  if (arg.url4variant) {
+    const err = check_url4variant(arg.url4variant);
+    if (err) return [".url4variant error: " + err];
+    tk.url4variant = arg.url4variant;
+  }
+  if (arg.button4variant) {
+    const err = check_button4variant(arg.button4variant);
+    if (err) return [".button4variant error: " + err];
+    tk.button4variant = arg.button4variant;
+  }
+  if (arg.sampleannotation) {
+    const sn = arg.sampleannotation;
+    if (!sn.annotation) return [".annotation{} missing from .sampleannotation"];
+    if (sn.levels) {
+      if (!Array.isArray(sn.levels)) return [".sampleannotation.levels should be array"];
+      const lst = [];
+      for (const sample in sn.annotation) {
+        const o = { sample_name: sample };
+        for (const k in sn.annotation[sample]) {
+          o[k] = sn.annotation[sample][k];
+        }
+        lst.push(o);
+      }
+      const nodes = stratinput(lst, sn.levels);
+      sn.root = stratify_default()(nodes);
+      sn.root.sum((i) => i.value);
+    }
+    if (sn.variantsunburst) {
+      if (!sn.levels) return [".levels missing when .variantsunburst is on from .sampleannotation"];
+    }
+    tk.ds.cohort = sn;
+  }
+  if (arg.vcfcohorttrack) {
+    if (!arg.vcfcohorttrack.file && !arg.vcfcohorttrack.url) return ["no .file or .url provided from .vcfcohorttrack"];
+    tk.ds.vcfcohorttrack = arg.vcfcohorttrack;
+  }
+  if (arg.germline2dvafplot) {
+    if (!arg.germline2dvafplot.individualkey) return [".individualkey missing from germline2dvafplot"];
+    if (!arg.germline2dvafplot.sampletypekey) return [".sampletypekey missing from germline2dvafplot"];
+    if (!arg.germline2dvafplot.xsampletype) return [".xsampletype missing from germline2dvafplot"];
+    if (!arg.germline2dvafplot.yleftsampletype) return [".yleftsampletype missing from germline2dvafplot"];
+    if (arg.germline2dvafplot.yrightsampletype) {
+      if (arg.germline2dvafplot.yrightsampletype == arg.germline2dvafplot.yleftsampletype)
+        return [".yrightsampletype should not be same as yleftsampletype"];
+    }
+    tk.ds.germline2dvafplot = arg.germline2dvafplot;
+  }
+  if (arg.vaf2coverageplot) {
+    if (arg.vaf2coverageplot.categorykey) {
+      if (!arg.vaf2coverageplot.categories)
+        return [".categories missing when .categorykey is in use for .vaf2coverageplot"];
+    }
+    tk.ds.vaf2coverageplot = arg.vaf2coverageplot;
+  }
+  if (arg.genotype2boxplot) {
+    if (arg.genotype2boxplot.boxplotvaluekey) {
+    } else if (arg.genotype2boxplot.sampleannotationkey) {
+      if (!tk.ds.cohort) return ["sampleannotation missing when using genotype2boxplot.sampleannotationkey"];
+      if (!tk.ds.cohort.annotation)
+        return ["sampleannotation.annotation missing when using genotype2boxplot.sampleannotationkey"];
+      let found = false;
+      for (const k in tk.ds.cohort.annotation) {
+        if (arg.genotype2boxplot.sampleannotationkey in tk.ds.cohort.annotation[k]) {
+          found = true;
+          break;
+        }
+      }
+      if (!found) return [arg.genotype2boxplot.sampleannotationkey + " not found in any sample annotation"];
+    } else {
+      return ["incomplete instruction for genotype2boxplot"];
+    }
+    tk.ds.genotype2boxplot = arg.genotype2boxplot;
+  }
+  if (arg.discardsymbolicallele) {
+    tk.ds.discardsymbolicallele = true;
+  }
+  if (arg.samplebynumericvalue) {
+    if (!arg.samplebynumericvalue.attrkey) return ["attrkey missing from samplebynumericvalue"];
+    if (!tk.ds.cohort) return ["sampleannotation missing when using samplebynumericvalue"];
+    if (!tk.ds.cohort.annotation) return ["sampleannotation.annotation missing when using samplebynumericvalue"];
+    let found = false;
+    for (const k in tk.ds.cohort.annotation) {
+      if (Number.isFinite(tk.ds.cohort.annotation[k][arg.samplebynumericvalue.attrkey])) {
+        found = true;
+        break;
+      }
+    }
+    if (!found) return ["samplebynumericvalue.attrkey not found in any sample annotation"];
+    tk.ds.samplebynumericvalue = arg.samplebynumericvalue;
+  }
+  {
+    const g = arg.genotypebynumericvalue;
+    if (g) {
+      if (!g.refref) return [tk.name + ": refref missing from genotypebynumericvalue"];
+      if (!g.refalt) return [tk.name + ": refalt missing from genotypebynumericvalue"];
+      if (!g.altalt) return [tk.name + ": altalt missing from genotypebynumericvalue"];
+      if (!g.refref.infokey) return [tk.name + ": refref.infokey missing from genotypebynumericvalue"];
+      if (!g.refalt.infokey) return [tk.name + ": refalt.infokey missing from genotypebynumericvalue"];
+      if (!g.altalt.infokey) return [tk.name + ": altalt.infokey missing from genotypebynumericvalue"];
+      if (g.refref.genotypeCountInfokey || g.refalt.genotypeCountInfokey || g.altalt.genotypeCountInfokey) {
+        if (!g.refref.genotypeCountInfokey)
+          return [tk.name + ": genotypeCountInfokey missing from genotypebynumericvalue.refref{}"];
+        if (!g.refalt.genotypeCountInfokey)
+          return [tk.name + ": genotypeCountInfokey missing from genotypebynumericvalue.refalt{}"];
+        if (!g.altalt.genotypeCountInfokey)
+          return [tk.name + ": genotypeCountInfokey missing from genotypebynumericvalue.altalt{}"];
+      }
+      tk.ds.genotypebynumericvalue = g;
+    }
+  }
+  if (arg.pointdown) {
+    tk.aboveprotein = false;
+  }
+  if (arg.dstk_novcferror) {
+    tk.dstk_novcferror = true;
+  }
+  return [null, tk];
+}
+function check_url4variant(lst) {
+  if (!Array.isArray(lst)) return "value is not an array";
+  for (const item of lst) {
+    if (!item.makeurl) {
+      return ".makeurl missing";
+    }
+    if (typeof item.makeurl != "function") {
+      return ".makeurl must be a function";
+    }
+  }
+  return false;
+}
+function check_button4variant(lst) {
+  if (!Array.isArray(lst)) return "value is not an array";
+  for (const item of lst) {
+    if (!item.makebutton) {
+      return ".makebutton missing";
+    }
+    if (typeof item.makebutton != "function") {
+      return ".makebutton must be a function";
+    }
+  }
+  return false;
+}
+
+export {
+  vcf2dstk
+};
+//# sourceMappingURL=chunk-FVX76DZS.js.map