@sjcrh/proteinpaint-client 2.203.0 → 2.203.1

package/dist/chunk-2OEMKKLP.js

@@ -1,272 +0,0 @@
-import {
-  fillbar,
-  make_table_2col
-} from "./chunk-GQQ4R6BI.js";
-
-// src/block.mds.expressionstat.js
-var color_noinfo = "#858585";
-function init_config(cfg) {
-  if (!cfg.datatype) cfg.datatype = "FPKM";
-  if (!cfg.itemcolor) cfg.itemcolor = "green";
-  if (!cfg.ase) cfg.ase = {};
-  if (cfg.ase.qvalue == void 0) cfg.ase.qvalue = 0.05;
-  if (cfg.ase.meandelta_monoallelic == void 0) cfg.ase.meandelta_monoallelic = 0.3;
-  if (cfg.ase.asemarkernumber_biallelic == void 0) cfg.ase.asemarkernumber_biallelic = 0;
-  if (!cfg.ase.color_noinfo) cfg.ase.color_noinfo = color_noinfo;
-  if (!cfg.ase.color_uncertain) cfg.ase.color_uncertain = "#A8E0B5";
-  if (!cfg.ase.color_biallelic) cfg.ase.color_biallelic = "#40859C";
-  if (!cfg.ase.color_monoallelic) cfg.ase.color_monoallelic = "#d95f02";
-  if (!cfg.outlier) cfg.outlier = {};
-  if (cfg.outlier.pvalue_cutoff == void 0) cfg.outlier.pvalue_cutoff = 0.05;
-  if (cfg.outlier.rank_asehigh_cutoff == void 0) cfg.outlier.rank_asehigh_cutoff = 0.1;
-  if (!cfg.outlier.color_outlier) cfg.outlier.color_outlier = "#FF8875";
-  if (!cfg.outlier.color_outlier_asehigh) cfg.outlier.color_outlier_asehigh = "blue";
-}
-function measure(v, cfg) {
-  if (!cfg) return;
-  v.estat = {};
-  if (v.ase && cfg.ase) {
-    const qvalue = v.ase.qvalue || v.ase.geometricmean;
-    if (qvalue == void 0) {
-      v.estat.ase_noinfo = true;
-    } else if (qvalue <= cfg.ase.qvalue) {
-      if (v.ase.mean_delta >= cfg.ase.meandelta_monoallelic) {
-        v.estat.ase_monoallelic = true;
-      } else {
-        v.estat.ase_uncertain = true;
-      }
-    } else {
-      if (v.ase.ase_markers == cfg.ase.asemarkernumber_biallelic) {
-        v.estat.ase_biallelic = true;
-      } else {
-        v.estat.ase_uncertain = true;
-      }
-    }
-  } else {
-    v.estat.ase_noinfo = true;
-  }
-  if (v.outlier && cfg.outlier) {
-    if (v.outlier.test_whitelist) {
-      if (v.outlier.test_whitelist.pvalue <= cfg.outlier.pvalue_cutoff) {
-        v.estat.outlier = true;
-      } else {
-        if (v.estat.ase_monoallelic) {
-          if (Number.isInteger(v.outlier.test_whitelist.rank) && Number.isInteger(v.outlier.test_whitelist.size) && v.outlier.test_whitelist.rank / v.outlier.test_whitelist.size <= cfg.outlier.rank_asehigh_cutoff) {
-            v.estat.outlier_asehigh = true;
-            v.outlier.test_whitelist.asehigh = true;
-          }
-        }
-      }
-    } else if (v.outlier.test_biallelic) {
-      if (v.outlier.test_biallelic.pvalue <= cfg.outlier.pvalue_cutoff) {
-        v.estat.outlier = true;
-      } else {
-        if (v.estat.ase_monoallelic) {
-          if (Number.isInteger(v.outlier.test_biallelic.rank) && Number.isInteger(v.outlier.test_biallelic.size) && v.outlier.test_biallelic.rank / v.outlier.test_biallelic.size <= cfg.outlier.rank_asehigh_cutoff) {
-            v.estat.outlier_asehigh = true;
-            v.outlier.test_biallelic.asehigh = true;
-          }
-        }
-      }
-    } else if (v.outlier.test_entirecohort) {
-      if (v.outlier.test_entirecohort.pvalue <= cfg.outlier.pvalue_cutoff) {
-        v.estat.outlier = true;
-      } else {
-        if (v.estat.ase_monoallelic) {
-          if (Number.isInteger(v.outlier.test_entirecohort.rank) && Number.isInteger(v.outlier.test_entirecohort.size) && v.outlier.test_entirecohort.rank / v.outlier.test_entirecohort.size <= cfg.outlier.rank_asehigh_cutoff) {
-            v.estat.outlier_asehigh = true;
-            v.outlier.test_entirecohort.asehigh = true;
-          }
-        }
-      }
-    }
-  }
-}
-function showsingleitem_table(v, cfg, table) {
-  if (!v.estat) return;
-  if (cfg.no_ase) return;
-  if (v.ase) {
-    const tr = table.append("tr");
-    tr.append("td").attr("colspan", 2).style("background", ase_color(v, cfg)).style("color", "white").html(
-      (v.estat.ase_monoallelic ? "Mono-allelic" : v.estat.ase_biallelic ? "Bi-allelic" : "ASE uncertain") + "<br>(allele-specific expression)"
-    );
-    const lst = [
-      {
-        k: "#SNPs heterozygous in DNA",
-        v: v.ase.markers
-      },
-      {
-        k: "#SNPs showing ASE in RNA",
-        v: v.ase.ase_markers
-      },
-      {
-        k: "Mean delta of ASE SNPs",
-        v: v.ase.mean_delta
-      }
-    ];
-    if (v.ase.qvalue) {
-      lst.push({
-        k: "Q-value",
-        v: v.ase.qvalue
-      });
-    } else if (v.ase.geometricmean) {
-      lst.push({
-        k: "Geometric mean of binomial P-values of ASE SNPs",
-        v: v.ase.geometricmean
-      });
-    }
-    const td = tr.append("td");
-    make_table_2col(td, lst);
-  } else {
-    const tr = table.append("tr");
-    tr.append("td").attr("colspan", 3).style("background", cfg.ase.color_noinfo).style("color", "white").text("No info on allele-specific expression");
-  }
-  if (v.snps && v.snps.length > 0) {
-    const hetsnp = v.snps.filter((i) => i.dnacount && i.dnacount.ishet);
-    if (hetsnp.length > 0) {
-      const lst = [];
-      for (const m of hetsnp) {
-        lst.push(
-          "<tr><td>" + m.chr + ":" + (m.pos + 1) + " " + m.ref + ">" + m.alt + "</td><td>" + fillbar(null, { f: m.dnacount.f }) + " " + m.dnacount.ref + "/" + m.dnacount.alt + "</td><td>" + (m.rnacount.nocoverage ? '<span style="font-size:.8em;opacity:.5">No coverage</span>' : fillbar(null, { f: m.rnacount.f }) + " " + m.rnacount.ref + "/" + m.rnacount.alt) + "</td><td>" + (m.rnacount.pvalue || "-") + "</td></tr>"
-        );
-      }
-      table.append("tr").append("td").attr("colspan", 3).html(
-        '<table style="margin-top:10px;border:solid 1px #ededed;border-spacing:5px;"><tr style="opacity:.5"><td>SNP</td><td>DNA</td><td>RNA</td><td>Binomial test P-value</td></tr>' + lst.join("") + "</table>"
-      );
-    }
-  }
-  if (v.outlier) {
-    if (v.outlier.test_whitelist) {
-      const tr = table.append("tr");
-      tr.append("td").attr("colspan", 2).text("Outlier (white list)");
-      const lst = [];
-      for (const k in v.outlier.test_whitelist) {
-        lst.push({ k, v: v.outlier.test_whitelist[k] });
-      }
-      const td = tr.append("td");
-      make_table_2col(td, lst);
-      if (v.outlier.test_whitelist.asehigh) {
-        td.append("div").style("background", cfg.outlier.color_outlier_asehigh).style("padding", "2px 10px").style("color", "white").text("ASE high");
-      }
-    }
-    if (v.outlier.test_biallelic) {
-      const tr = table.append("tr");
-      tr.append("td").attr("colspan", 2).text("Outlier (biallelic)");
-      const lst = [];
-      for (const k in v.outlier.test_biallelic) {
-        lst.push({ k, v: v.outlier.test_biallelic[k] });
-      }
-      const td = tr.append("td");
-      make_table_2col(td, lst);
-      if (v.outlier.test_biallelic.asehigh) {
-        td.append("div").style("background", cfg.outlier.color_outlier_asehigh).style("padding", "2px 10px").style("color", "white").text("ASE high");
-      }
-    }
-    if (v.outlier.test_entirecohort) {
-      const tr = table.append("tr");
-      tr.append("td").attr("colspan", 2).text("Outlier (all samples)");
-      const lst = [];
-      for (const k in v.outlier.test_entirecohort) {
-        lst.push({ k, v: v.outlier.test_entirecohort[k] });
-      }
-      const td = tr.append("td");
-      make_table_2col(td, lst);
-      if (v.outlier.test_entirecohort.asehigh) {
-        td.append("div").style("background", cfg.outlier.color_outlier_asehigh).style("padding", "2px 10px").style("color", "white").text("ASE high");
-      }
-    }
-  }
-}
-function ase_color(v, cfg) {
-  if (cfg.no_ase) return color_noinfo;
-  if (!cfg.ase) return color_noinfo;
-  if (!v.estat) return cfg.ase.color_noinfo;
-  if (v.estat.ase_monoallelic) return cfg.ase.color_monoallelic;
-  if (v.estat.ase_biallelic) return cfg.ase.color_biallelic;
-  if (v.estat.ase_uncertain) return cfg.ase.color_uncertain;
-  return cfg.ase.color_noinfo;
-}
-function ui_config(holder, cfg, tk, call) {
-  const indent = 30;
-  {
-    const row = holder.append("div").style("margin-bottom", "5px");
-    row.append("span").html("If " + (tk.checkrnabam ? "p-value geometric mean" : "Q-VALUE") + " &le;&nbsp;");
-    row.append("input").attr("type", "number").style("width", "50px").property("value", cfg.ase.qvalue).on("keyup", (event) => {
-      if (event.code != "Enter" && event.code != "NumpadEnter") return;
-      let v = Number.parseFloat(event.target.value);
-      if (!v || v <= 0) {
-        return;
-      }
-      if (cfg.ase.qvalue == v) {
-        return;
-      }
-      cfg.ase.qvalue = v;
-      call();
-    });
-    row.append("span").html("&nbsp;:");
-  }
-  {
-    const row = holder.append("div").style("margin", "0px 5px 5px " + indent + "px");
-    row.append("span").html("If MEAN_DELTA &ge;&nbsp;");
-    row.append("input").attr("type", "number").style("width", "50px").property("value", cfg.ase.meandelta_monoallelic).on("keyup", (event) => {
-      if (event.code != "Enter" && event.code != "NumpadEnter") return;
-      let v = Number.parseFloat(event.target.value);
-      if (!v || v <= 0) {
-        return;
-      }
-      if (cfg.ase.meandelta_monoallelic == v) {
-        return;
-      }
-      cfg.ase.meandelta_monoallelic = v;
-      call();
-    });
-    row.append("span").html("&nbsp;:&nbsp;");
-  }
-  holder.append("div").style("margin", "0px 5px 5px " + indent * 2 + "px").html(
-    'Is <span style="background:' + cfg.ase.color_monoallelic + ';padding:1px 5px;color:white;">mono-allelic expression</span>'
-  );
-  holder.append("div").style("margin", "0px 5px 5px " + indent + "px").html("Else:");
-  holder.append("div").style("margin", "0px 5px 5px " + indent * 2 + "px").html(
-    'Is <span style="background:' + cfg.ase.color_uncertain + ';padding:1px 5px;color:white;">ASE uncertain</span>'
-  );
-  holder.append("div").style("margin", "0px 5px 5px 0px").html("Else:");
-  {
-    const row = holder.append("div").style("margin", "0px 5px 5px " + indent + "px");
-    row.append("span").html("If number of ASE markers &le;&nbsp;");
-    row.append("input").attr("type", "number").style("width", "50px").property("value", cfg.ase.asemarkernumber_biallelic).on("keyup", (event) => {
-      if (event.code != "Enter" && event.code != "NumpadEnter") return;
-      let v = Number.parseInt(event.target.value);
-      if (v < 0) {
-        return;
-      }
-      if (cfg.ase.asemarkernumber_biallelic == v) {
-        return;
-      }
-      cfg.ase.asemarkernumber_biallelic = v;
-      call();
-    });
-    row.append("span").html("&nbsp;:&nbsp;");
-  }
-  holder.append("div").style("margin", "0px 5px 5px " + indent * 2 + "px").html(
-    'Is <span style="background:' + cfg.ase.color_biallelic + ';padding:1px 5px;color:white;">bi-allelic expression</span>'
-  );
-  holder.append("div").style("margin", "0px 5px 5px " + indent + "px").html("Else:");
-  holder.append("div").style("margin", "0px 5px 5px " + indent * 2 + "px").html(
-    'Is <span style="background:' + cfg.ase.color_uncertain + ';padding:1px 5px;color:white;">ASE uncertain</span>'
-  );
-  holder.append("div").style("margin", "10px").append("button").text("Default ASE parameters").on("click", () => {
-    cfg.ase.qvalue = 0.05;
-    cfg.ase.meandelta_monoallelic = 0.3;
-    cfg.ase.asemarkernumber_biallelic = 0;
-    call();
-  });
-}
-
-export {
-  init_config,
-  measure,
-  showsingleitem_table,
-  ase_color,
-  ui_config
-};
-//# sourceMappingURL=chunk-2OEMKKLP.js.map

package/dist/chunk-34AV6DED.js

@@ -1,299 +0,0 @@
-import {
-  first_genetrack_tolist,
-  gmmode,
-  sayerror
-} from "./chunk-GQQ4R6BI.js";
-import {
-  dofetch3
-} from "./chunk-HENLCRVM.js";
-import {
-  codon_stop,
-  nt2aa,
-  proteinDomainColorScale
-} from "./chunk-4QBRVM4V.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-XYSUTBXJ.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-NVFYTQG4.js");
-      _.validate_oldds(ds);
-      delete ds.legacyDsIsUninitiated;
-    }
-  }
-  const b = await import("./block-XYSUTBXJ.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-34AV6DED.js.map