@sjcrh/proteinpaint-client 2.223.0 → 2.224.0

package/dist/chunk-O3XTTT4K.js

@@ -0,0 +1,217 @@
+import {
+  dofetch,
+  dofetch2
+} from "./chunk-KBTFT76L.js";
+import {
+  contigNameNoChr2
+} from "./chunk-WJLRU5OF.js";
+
+// tracks/hic/data/parseData.ts
+async function hicParseFile(hic, debugmode, errList = []) {
+  if (debugmode) window["hic"] = hic;
+  if (hic.tklst) {
+    const lst = [];
+    for (const t of hic.tklst) {
+      if (!t.type) {
+        errList.push("type missing from one of the tracks accompanying HiC");
+      } else {
+        t.iscustom = true;
+        lst.push(t);
+      }
+    }
+    if (lst.length) {
+      hic.tklst = lst;
+    } else {
+      delete hic.tklst;
+    }
+  }
+  if (hic.enzyme) {
+    if (hic.genome.hicenzymefragment) {
+      let frag = null;
+      for (const f of hic.genome.hicenzymefragment) {
+        if (f.enzyme == hic.enzyme) {
+          frag = f;
+          break;
+        }
+      }
+      if (frag) {
+        hic.enzymefile = frag.file;
+      } else {
+        errList.push("unknown enzyme: " + hic.enzyme);
+        delete hic.enzyme;
+      }
+    } else {
+      errList.push("no enzyme fragment information available for this genome");
+      delete hic.enzyme;
+    }
+  }
+  try {
+    if (hic.sv && hic.sv.file) {
+      const re = await dofetch(hic.hostURL + "/textfile", {
+        method: "POST",
+        body: JSON.stringify({ file: hic.sv.file, jwt: hic.jwt })
+      });
+      const data2 = re.json();
+      const [err2, header, items] = parseSV(data2.text);
+      if (err2) throw { message: "Error parsing SV: " + err2 };
+      hic.sv.header = header;
+      hic.sv.items = items;
+    }
+    const data = await dofetch2("hicstat?" + (hic.file ? "file=" + hic.file : "url=" + hic.url));
+    if (data.error) {
+      errList.push(data.error);
+      return;
+    }
+    const err = hicparsestat(hic, data.out);
+    if (err) throw { message: err };
+  } catch (err) {
+    errList.push(err.message || err);
+    if (err.stack) {
+      console.log(err.stack);
+    }
+  }
+  return hic;
+}
+function parseSV(txt) {
+  const lines = txt.trim().split(/\r?\n/);
+  const [err, header] = parseSVheader(lines[0]);
+  if (err) return ["header error: " + err];
+  const items = [];
+  for (let i = 1; i < lines.length; i++) {
+    const line = lines[i];
+    if (line[0] == "#") continue;
+    const [e, m] = parseSVline(line, header);
+    if (e) return ["line " + (i + 1) + " error: " + e];
+    items.push(m);
+  }
+  return [null, header, items];
+}
+function parseSVheader(line) {
+  const header = line.toLowerCase().split("	");
+  if (header.length <= 1) return "invalid file header for fusions";
+  const htry = (...lst) => {
+    for (const a of lst) {
+      const j = header.indexOf(a);
+      if (j != -1) return j;
+    }
+    return -1;
+  };
+  let i = htry("chr_a", "chr1", "chra");
+  if (i == -1) return "chr_A missing from header";
+  header[i] = "chr1";
+  i = htry("chr_b", "chr2", "chrb");
+  if (i == -1) return "chr_B missing from header";
+  header[i] = "chr2";
+  i = htry("pos_a", "position_a", "position1", "posa");
+  if (i == -1) return "pos_a missing from header";
+  header[i] = "position1";
+  i = htry("pos_b", "position_b", "position2", "posb");
+  if (i == -1) return "pos_b missing from header";
+  header[i] = "position2";
+  i = htry("strand_a", "orta", "orienta");
+  if (i == -1) return "strand_a missing from header";
+  header[i] = "strand1";
+  i = htry("strand_b", "ortb", "orientb");
+  if (i == -1) return "strand_b missing from header";
+  header[i] = "strand2";
+  i = htry("numreadsa");
+  if (i != -1) header[i] = "reads1";
+  i = htry("numreadsb");
+  if (i != -1) header[i] = "reads2";
+  return [null, header];
+}
+function parseSVline(line, header) {
+  const lst = line.split("	");
+  const m = {};
+  for (let j = 0; j < header.length; j++) {
+    m[header[j]] = lst[j];
+  }
+  if (!m.chr1) return ["missing chr1"];
+  if (m.chr1.toLowerCase().indexOf("chr") != 0) {
+    m.chr1 = "chr" + m.chr1;
+  }
+  if (!m.chr2) return ["missing chr2"];
+  if (m.chr2.toLowerCase().indexOf("chr") != 0) {
+    m.chr2 = "chr" + m.chr2;
+  }
+  if (!m.position1) return ["missing position1"];
+  let v = Number.parseInt(m.position1);
+  if (Number.isNaN(v) || v <= 0) return ["position1 invalid value"];
+  m.position1 = v;
+  if (!m.position2) return ["missing position2"];
+  v = Number.parseInt(m.position2);
+  if (Number.isNaN(v) || v <= 0) return ["position2 invalid value"];
+  m.position2 = v;
+  if (m.reads1) {
+    v = Number.parseInt(m.reads1);
+    if (Number.isNaN(v)) return ["reads1 invalid value"];
+    m.reads1 = v;
+  }
+  if (m.reads2) {
+    v = Number.parseInt(m.reads2);
+    if (Number.isNaN(v)) return ["reads2 invalid value"];
+    m.reads2 = v;
+  }
+  return [null, m];
+}
+function hicparsestat(hic, j) {
+  if (!j) return "cannot stat hic file";
+  hic.normalization = j.normalization;
+  hic.version = j.version;
+  if (!j.Chromosomes) return "Chromosomes not found in file stat";
+  if (!Array.isArray(j.chrorder)) return ".chrorder[] missing";
+  if (j.chrorder.length == 0) return ".chrorder[] empty array";
+  hic.chrorder = j.chrorder;
+  if (!j["Base pair-delimited resolutions"]) return "Base pair-delimited resolutions not found in file stat";
+  if (!Array.isArray(j["Base pair-delimited resolutions"])) return "Base pair-delimited resolutions should be array";
+  hic.bpresolution = j["Base pair-delimited resolutions"];
+  if (!j["Fragment-delimited resolutions"]) return "Fragment-delimited resolutions not found in file stat";
+  if (!Array.isArray(j["Fragment-delimited resolutions"])) return "Fragment-delimited resolutions is not array";
+  hic.fragresolution = j["Fragment-delimited resolutions"];
+  const chrlst = [];
+  for (const chr in j.Chromosomes) {
+    chrlst.push(chr);
+  }
+  const [nochrcount, haschrcount] = contigNameNoChr2(hic.genome, chrlst);
+  if (nochrcount + haschrcount == 0) return "chromosome names do not match with genome build";
+  if (nochrcount > 0) {
+    hic.nochr = true;
+    for (let i = 0; i < hic.chrorder.length; i++) hic.chrorder[i] = "chr" + hic.chrorder[i];
+  }
+  hic.chrlst = [];
+  for (const chr of hic.genome.majorchrorder) {
+    const c2 = hic.nochr ? chr.replace("chr", "") : chr;
+    if (chrlst.indexOf(c2) != -1) {
+      hic.chrlst.push(chr);
+    }
+  }
+}
+function hicparsefragdata(items) {
+  const id2coord = /* @__PURE__ */ new Map();
+  let min = null, max;
+  for (const i of items) {
+    if (!i.rest || !i.rest[0]) {
+      return ["items[].rest data problem"];
+    }
+    const id = Number.parseInt(i.rest[0]);
+    if (Number.isNaN(id)) {
+      return [i.start + "." + i.stop + " invalid fragment id: " + i.rest[0]];
+    }
+    id2coord.set(id, [i.start, i.stop]);
+    if (min == null) {
+      min = id;
+      max = id;
+    } else {
+      min = Math.min(min, id);
+      max = Math.max(max, id);
+    }
+  }
+  return [null, id2coord, min, max];
+}
+
+export {
+  hicParseFile,
+  hicparsestat,
+  hicparsefragdata
+};
+//# sourceMappingURL=chunk-O3XTTT4K.js.map

package/dist/chunk-OJH2LKPN.js

@@ -0,0 +1,299 @@
+import {
+  first_genetrack_tolist,
+  gmmode,
+  sayerror
+} from "./chunk-U45YALDI.js";
+import {
+  dofetch3
+} from "./chunk-KBTFT76L.js";
+import {
+  codon_stop,
+  nt2aa,
+  proteinDomainColorScale
+} from "./chunk-WJLRU5OF.js";
+import {
+  select_default
+} from "./chunk-I6Y4O3RR.js";
+
+// common/snp.js
+async function string2snp(genome, str) {
+  const data = await dofetch3("snp", {
+    method: "POST",
+    body: JSON.stringify({ byName: true, genome: genome.name, lst: [str] })
+  });
+  if (data.error) throw data.error;
+  if (!data.results || data.results.length == 0) throw str + ": not a SNP";
+  for (const i of data.results) {
+    const chr = genome.chrlookup[i.chrom.toUpperCase()];
+    if (chr && chr.major) {
+      return {
+        chr: i.chrom,
+        start: i.chromStart,
+        stop: i.chromEnd
+      };
+    }
+  }
+  const r = data.results[0];
+  return {
+    chr: r.chrom,
+    start: r.chromStart,
+    stop: r.chromEnd
+  };
+}
+
+// src/block.init.js
+async function block_init_default(arg) {
+  if (!arg.holder) throw "No holder for block.init";
+  if (!arg.genome) throw "no genome";
+  if (arg.holder instanceof Element) arg.holder = select_default(arg.holder);
+  if (!arg.tklst) arg.tklst = [];
+  if (arg.query) {
+    await step1_findgm(arg);
+    return;
+  }
+  if (arg.model && arg.allmodels) {
+    await step2_getseq(arg);
+    return;
+  }
+}
+async function step1_findgm(arg) {
+  const wait = arg.holder.append("p").style("font-size", "2em").style("color", "#858585").text("Searching for " + arg.query + " ...");
+  const data = await dofetch3("genelookup", {
+    body: { deep: 1, input: arg.query, genome: arg.genome.name }
+  });
+  if (!data) throw "querying genes: server error";
+  if (data.error) throw "error querying genes: " + data.error;
+  if (!data.gmlst || data.gmlst.length == 0) {
+    if (arg.genome.hasSNP) {
+      try {
+        const r = await string2snp(arg.genome, arg.query);
+        wait.remove();
+        const par = {
+          genome: arg.genome,
+          holder: arg.holder,
+          chr: r.chr,
+          start: Math.max(0, r.start - 300),
+          stop: r.start + 300,
+          nobox: true,
+          tklst: arg.tklst,
+          debugmode: arg.debugmode
+        };
+        first_genetrack_tolist(arg.genome, par.tklst);
+        const b = await import("./block-LYSTIZKO.js");
+        const block = new b.Block(par);
+        block.addhlregion(r.chr, r.start, r.stop - 1);
+      } catch (e) {
+        wait.text("Not a gene or SNP: " + arg.query);
+      }
+    } else {
+      wait.text("No match to gene: " + arg.query);
+    }
+    return;
+  }
+  wait.remove();
+  arg.allmodels = data.gmlst;
+  for (const m of arg.allmodels) {
+    if (m.isoform.toUpperCase() == (data.found_isoform ? data.found_isoform.toUpperCase() : arg.query.toUpperCase())) {
+      arg.model = m;
+      await step2_getseq(arg);
+      return;
+    }
+  }
+  const defaultisoforms = [];
+  for (const m of arg.allmodels) {
+    if (!m.isoform) throw "isoform missing from one gene model: " + JSON.stringify(m);
+    const n = m.isoform.toUpperCase();
+    if (arg.genome.isoformcache.has(n)) {
+      let nothas = true;
+      for (const m2 of arg.genome.isoformcache.get(n)) {
+        if (m2.chr == m.chr && m2.start == m.start && m2.stop == m.stop && m2.strand == m.strand) {
+          nothas = false;
+          break;
+        }
+      }
+      if (nothas) {
+        arg.genome.isoformcache.get(n).push(m);
+      }
+    } else {
+      arg.genome.isoformcache.set(n, [m]);
+    }
+    if (m.isoform.toUpperCase() == arg.query.toUpperCase()) {
+      defaultisoforms.push(m);
+      break;
+    }
+    if (m.isdefault) {
+      defaultisoforms.push(m);
+    }
+  }
+  if (defaultisoforms.length == 1) {
+    arg.model = defaultisoforms[0];
+  } else if (defaultisoforms.length > 1) {
+    for (const m of defaultisoforms) {
+      if (m.chr == "chrY") {
+        continue;
+      }
+      const chr = arg.genome.chrlookup[m.chr.toUpperCase()];
+      if (!chr) {
+        continue;
+      }
+      if (!chr.major) {
+        continue;
+      }
+      arg.model = m;
+      break;
+    }
+    if (!arg.model) {
+      arg.model = defaultisoforms[0];
+    }
+  }
+  if (!arg.model) {
+    arg.model = arg.allmodels[0];
+  }
+  await step2_getseq(arg);
+}
+async function step2_getseq(arg) {
+  if (arg.model.genomicseq) {
+    checker();
+    step2_getpdomain(arg);
+    return;
+  }
+  const par = {
+    genome: arg.genome.name,
+    coord: arg.model.chr + ":" + (arg.model.start + 1) + "-" + arg.model.stop
+  };
+  const data = await dofetch3("ntseq", { method: "POST", body: JSON.stringify(par) });
+  if (!data) throw "getting sequence: server error";
+  if (data.error) throw "getting sequence: " + data.error;
+  if (!data.seq) throw "no nt seq???";
+  arg.model.genomicseq = data.seq.toUpperCase();
+  arg.model.aaseq = nt2aa(arg.model);
+  checker();
+  await step2_getpdomain(arg);
+  function checker() {
+    if (arg.model.aaseq) {
+      const stop = arg.model.aaseq.indexOf(codon_stop);
+      const cdslen = arg.model.cdslen - (arg.model.startCodonFrame ? 3 - arg.model.startCodonFrame : 0);
+      if (stop != -1 && stop < cdslen / 3 - 1) {
+        sayerror(arg.holder, "Translating " + arg.model.isoform + " ends at " + stop + " AA, expecting " + cdslen / 3);
+      }
+    }
+  }
+}
+async function step2_getpdomain(arg) {
+  const isoform2gm = /* @__PURE__ */ new Map();
+  for (const m of arg.allmodels) {
+    if (!m.pdomains) {
+      m.pdomains = [];
+      m.domain_hidden = {};
+      if (!isoform2gm.has(m.isoform)) isoform2gm.set(m.isoform, []);
+      isoform2gm.get(m.isoform).push(m);
+    }
+  }
+  if (isoform2gm.size == 0) {
+    await step3(arg);
+    return;
+  }
+  const data = await dofetch3("pdomain", {
+    method: "POST",
+    body: JSON.stringify({ genome: arg.genome.name, isoforms: [...isoform2gm.keys()] })
+  });
+  if (data.error) throw "error getting protein domain: " + data.error;
+  if (!Array.isArray(data.lst)) throw ".lst[] not array";
+  for (const a of data.lst) {
+    for (const m of isoform2gm.get(a.name)) {
+      m.pdomains = a.pdomains;
+      if (arg.hidePdomain) {
+        for (const i of a.pdomains) {
+          m.domain_hidden[i.name + i.description] = 1;
+        }
+      }
+    }
+  }
+  if (arg.geneDomains) {
+    if (typeof arg.geneDomains != "object") throw "geneDomains not object";
+    for (const isoform in arg.geneDomains) {
+      const lst = isoform2gm.get(isoform);
+      if (!lst) throw `unknown isoform ${isoform} from geneDomains{}`;
+      for (const g of lst) {
+        if (!g.pdomains) g.pdomains = [];
+        if (!Array.isArray(arg.geneDomains[isoform])) throw `geneDomains[${isoform}] not array`;
+        for (const b of arg.geneDomains[isoform]) {
+          if (typeof b != "object") throw "element from geneDomains[] not object";
+          if (!Number.isInteger(b.start)) throw "start not integer from geneDomains[]";
+          if (!Number.isInteger(b.stop)) throw "stop not integer from geneDomains[]";
+          if (b.start > b.stop) throw "start>stop from geneDomains[]";
+          if (!b.name) b.name = "Custom domain";
+          if (!g.pdomains.find((a) => a.start == b.start && a.stop == b.stop && a.name == b.name)) g.pdomains.push(b);
+        }
+      }
+    }
+  }
+  const s = proteinDomainColorScale();
+  for (const lst of isoform2gm.values()) {
+    for (const g of lst) {
+      for (const d of g.pdomains || []) {
+        if (!d.color) d.color = s(d.name + d.description);
+      }
+    }
+  }
+  await step3(arg);
+}
+async function step3(arg) {
+  let mode = arg.gmmode;
+  if (!mode) {
+    if (arg.model.cdslen) {
+      mode = gmmode.protein;
+    } else {
+      mode = gmmode.exononly;
+    }
+  }
+  if (arg.dataset) {
+    if (!Array.isArray(arg.dataset)) throw "dataset is not array";
+    for (const dsname of arg.dataset) {
+      if (arg.genome.datasets[dsname] && !arg.genome.datasets[dsname].legacyDsIsUninitiated) continue;
+      const d = await dofetch3(`getDataset?genome=${arg.genome.name}&dsname=${dsname}`);
+      if (d.error) throw `invalid name from dataset[]: ${d.error}`;
+      if (!d.ds) throw ".ds missing";
+      const ds = arg.genome.datasets[d.ds.label];
+      Object.assign(ds, d.ds);
+      const _ = await import("./legacyDataset-IEFWFVS6.js");
+      _.validate_oldds(ds);
+      delete ds.legacyDsIsUninitiated;
+    }
+  }
+  const b = await import("./block-LYSTIZKO.js");
+  arg.__blockInstance = new b.Block({
+    genome: arg.genome,
+    holder: arg.holder,
+    nobox: true,
+    usegm: arg.model,
+    gmstackheight: 37,
+    allgm: arg.allmodels,
+    datasetlst: arg.dataset,
+    legacyDsFilter: arg.legacyDsFilter,
+    mset: arg.mset,
+    hlaachange: arg.hlaachange,
+    hlvariants: arg.hlvariants,
+    hlregions: arg.hlregions,
+    aarange: arg.aarange,
+    gmmode: mode,
+    hidedatasetexpression: arg.hidedatasetexpression,
+    hidegenecontrol: arg.hidegenecontrol,
+    hidegenelegend: arg.hidegenelegend,
+    variantPageCall_snv: arg.variantPageCall_snv,
+    datasetqueries: arg.datasetqueries,
+    samplecart: arg.samplecart,
+    debugmode: arg.debugmode,
+    tklst: arg.tklst,
+    mclassOverride: arg.mclassOverride,
+    hide_dsHandles: arg.hide_dsHandles,
+    onloadalltk_always: arg.onloadalltk_always,
+    onAddRemoveTk: arg.onAddRemoveTk
+  });
+}
+
+export {
+  string2snp,
+  block_init_default
+};
+//# sourceMappingURL=chunk-OJH2LKPN.js.map

package/dist/chunk-PZKO4FL3.js

@@ -0,0 +1,50 @@
+import {
+  runproteinpaint
+} from "./chunk-64RXHMGN.js";
+
+// test/front.helpers.js
+var serverData = /* @__PURE__ */ Object.create(null);
+function getRunPp(appname = "", defaultArgs = {}, _host = "http://localhost:3000") {
+  const host = window.testHost || _host;
+  const arg = {
+    host: window.testHost || _host,
+    noheader: 1,
+    nobox: true,
+    debug: 1,
+    norecover: true
+  };
+  if (appname == "mass" || appname == "termdb") {
+    defaultArgs.debounceInterval = 0;
+  }
+  if (appname) arg[appname] = defaultArgs;
+  else copyMerge(arg, defaultArgs);
+  const argStr = JSON.stringify(arg);
+  return function runpp(overrides = {}) {
+    const argCopy = JSON.parse(argStr);
+    if (appname) copyMerge(argCopy[appname], overrides);
+    else copyMerge(argCopy, overrides);
+    if (appname && defaultArgs.fetchOpts) {
+      argCopy[appname].fetchOpts = defaultArgs.fetchOpts;
+    }
+    return runproteinpaint(Object.assign(argCopy, { serverData }));
+  };
+}
+function copyMerge(base, ...args) {
+  const target = typeof base == "string" ? JSON.parse(base) : base;
+  for (const arg of args) {
+    if (arg) {
+      const source = typeof base == "string" ? JSON.parse(JSON.stringify(arg)) : arg;
+      for (const key in source) {
+        if (key === "__proto__" || key === "constructor" || key === "prototype") continue;
+        if (!target[key] || Array.isArray(target[key]) || typeof target[key] !== "object") target[key] = source[key];
+        else copyMerge(target[key], source[key]);
+      }
+    }
+  }
+  return target;
+}
+
+export {
+  getRunPp
+};
+//# sourceMappingURL=chunk-PZKO4FL3.js.map