@sjcrh/proteinpaint-client 2.220.0 → 2.221.0

package/dist/block.tk.junction.textmatrixui-P4WXTAZR.js

@@ -0,0 +1,190 @@
+import {
+  first_genetrack_tolist,
+  newpane3,
+  renderSandboxFormDiv,
+  tkt
+} from "./chunk-WD7FZ5EE.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-WXSMUSU7.js";
+import "./chunk-CNFTQSNE.js";
+import "./chunk-RIHO7ZD5.js";
+import "./chunk-TVJOSRCH.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import "./chunk-4TJO2DGU.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-MHWYRNGA.js";
+import "./chunk-JHLF2ZC2.js";
+import "./chunk-WJLRU5OF.js";
+import "./chunk-HBNB5TRH.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-4OLM3KSB.js";
+import "./chunk-PWYMHUXY.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-HS5PO5ZQ.js";
+
+// src/block.tk.junction.textmatrixui.js
+function block_tk_junction_textmatrixui_default(genomes, hostURL, jwt, holder) {
+  let pane, inputdiv, gselect, filediv, saydiv, visualdiv;
+  if (holder !== void 0) [inputdiv, gselect, filediv, saydiv, visualdiv] = renderSandboxFormDiv(holder, genomes);
+  else {
+    ;
+    [pane, inputdiv, gselect, filediv, saydiv, visualdiv] = newpane3(100, 100, genomes);
+    pane.header.text("Splice junctions by sample matrix visualization");
+  }
+  filediv.append("p").text("Enter junction-by-sample read count matrix data:");
+  const ul = filediv.append("ul").style("color", "#858585").style("font-size", ".8em");
+  ul.append("li").text("The matrix is tab-delimited, junctions on rows, samples on columns.");
+  ul.append("li").text("First row lists sample names");
+  ul.append("li").text("Each row is one junction, with read count in each sample");
+  ul.append("li").text("Junction position example: chr21:39739570:+,chr21:39817327:+[,type], the type is optional");
+  ul.append("li").text("Junction start and stop positions are 1-based and should be exonic bases but not intronic.");
+  const ta1 = filediv.append("div").append("textarea").attr("rows", 6).attr("cols", 50).attr("placeholder", "junction-by-sample matrix");
+  setTimeout(() => ta1.node().focus(), 1100);
+  const p = filediv.append("p");
+  p.append("button").text("Submit").on("click", () => {
+    saydiv.text("");
+    const gn = gselect.options[gselect.selectedIndex].innerHTML;
+    const genomeobj = genomes[gn];
+    if (!genomeobj) {
+      saydiv.text("invalid genome name: " + gn);
+      return;
+    }
+    const v = ta1.property("value");
+    if (v == "") {
+      return;
+    }
+    const [err, junctions, samples] = junction_parsematrix(v, genomeobj);
+    if (err) {
+      saydiv.text(err);
+      return;
+    }
+    const range = /* @__PURE__ */ new Map();
+    for (const j of junctions) {
+      if (!range.has(j.chr)) {
+        range.set(j.chr, {
+          chr: j.chr,
+          start: j.start,
+          stop: j.stop
+        });
+      }
+      range.get(j.chr).start = Math.min(j.start, range.get(j.chr).start);
+      range.get(j.chr).stop = Math.max(j.stop, range.get(j.chr).stop);
+    }
+    const arange = [...range][0][1];
+    const tracks = [
+      {
+        type: tkt.junction,
+        name: "Junction",
+        fixeddata: junctions,
+        tracks: [
+          {
+            samplecount: samples.length
+          }
+        ],
+        iscustom: true
+      }
+    ];
+    first_genetrack_tolist(genomeobj, tracks);
+    import("./block-GLF6QNKY.js").then(
+      (b) => new b.Block({
+        hostURL,
+        jwt,
+        holder: holder !== void 0 ? holder : pane.body.append("div"),
+        genome: genomeobj,
+        chr: arange.chr,
+        start: arange.start,
+        stop: Math.min(arange.start + 1e5, arange.stop),
+        nobox: true,
+        tklst: tracks
+      })
+    );
+    inputdiv.remove();
+  });
+  p.append("button").text("Clear").on("click", () => {
+    ta1.property("value", "");
+  });
+  filediv.append("p").html("<a href=https://www.dropbox.com/s/xu52ke9cify24hw/junction.txt?dl=0 target=_blank>Example file</a>");
+}
+function junction_parsematrix(text, gn) {
+  const lines = text.trim().split("\n");
+  if (lines.length <= 1) {
+    return ["input should be at least 2 lines"];
+  }
+  const lst = lines[0].split("	");
+  const samples = [];
+  for (let i = 1; i < lst.length; i++) {
+    samples.push({
+      tkid: Math.random().toString(),
+      type: tkt.junction,
+      name: lst[i]
+    });
+  }
+  const junctions = [];
+  for (let i = 1; i < lines.length; i++) {
+    const jstr = lines[i].split("	")[0];
+    const [e, j] = junction_parsecoord(jstr, gn);
+    if (e) return ["Error parsing junction " + jstr + ": " + e];
+    j.data = [];
+    junctions.push(j);
+  }
+  if (junctions.length == 0) {
+    return ["No valid junctions"];
+  }
+  for (let i = 1; i < lines.length; i++) {
+    const lst2 = lines[i].split("	");
+    for (let j = 1; j < lst2.length; j++) {
+      if (lst2[j] == "") {
+        continue;
+      }
+      const readcount = Number.parseInt(lst2[j]);
+      if (Number.isNaN(readcount) || readcount < 0) {
+        return ["invalid read count " + lst2[j] + " at line " + (i + 1)];
+      }
+      if (readcount == 0) {
+        continue;
+      }
+      junctions[i - 1].data.push({
+        tkid: samples[j - 1].tkid,
+        sample: samples[j - 1].name,
+        v: readcount
+      });
+    }
+  }
+  return [null, junctions, samples];
+}
+function junction_parsecoord(s, g) {
+  const lst = s.split(",");
+  if (lst.length < 2) return ["expecting two fields separated by comma"];
+  const a = lst[0].split(":"), b = lst[1].split(":"), jtype = lst[2];
+  if (a.length != 3) return ["left position not 3 fields by :"];
+  if (b.length != 3) return ["right position not 3 fields by :"];
+  if (a[0] != b[0]) return ["disagreeing chromosomes"];
+  const pos1 = Number.parseInt(a[1]);
+  const pos2 = Number.parseInt(b[1]);
+  if (isNaN(pos1)) return ["invalid position 1"];
+  if (isNaN(pos2)) return ["invalid position 2"];
+  const start = Math.min(pos1, pos2) - 1;
+  const stop = Math.max(pos1, pos2) - 1;
+  let name = a[0].toLowerCase();
+  if (name.indexOf("chr") != 0) {
+    name = "chr" + name;
+  }
+  const chr = g.chrlookup[name.toUpperCase()];
+  if (!chr) return ["invalid chromosome"];
+  if (start <= 0 || start >= chr.len) return ["position 1 out of bound"];
+  if (stop <= 0 || stop >= chr.len) return ["position 2 out of bound"];
+  if (start >= stop) return ["start greater than stop"];
+  const j = { chr: chr.name, start, stop };
+  if (jtype) {
+    j.type = jtype;
+  }
+  return [null, j];
+}
+export {
+  block_tk_junction_textmatrixui_default as default
+};
+//# sourceMappingURL=block.tk.junction.textmatrixui-P4WXTAZR.js.map

package/dist/block.tk.ld-3PQ4O2AE.js

@@ -0,0 +1,90 @@
+import {
+  showLDlegend
+} from "./chunk-YPBY37KD.js";
+import {
+  legend_newrow
+} from "./chunk-VBTBUXXX.js";
+import "./chunk-V2OJLJSK.js";
+import "./chunk-VLIOMJDR.js";
+import "./chunk-WD7FZ5EE.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-WXSMUSU7.js";
+import "./chunk-CNFTQSNE.js";
+import "./chunk-RIHO7ZD5.js";
+import "./chunk-TVJOSRCH.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import {
+  dofetch3
+} from "./chunk-4TJO2DGU.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-MHWYRNGA.js";
+import "./chunk-JHLF2ZC2.js";
+import "./chunk-WJLRU5OF.js";
+import "./chunk-HBNB5TRH.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-4OLM3KSB.js";
+import "./chunk-PWYMHUXY.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import {
+  rgb_default
+} from "./chunk-Q5RDQNIT.js";
+import "./chunk-HS5PO5ZQ.js";
+
+// src/block.tk.ld.js
+async function loadTk(tk, block) {
+  if (tk.uninitiated) {
+    makeTk(tk, block);
+  }
+  block.tkcloakon(tk);
+  try {
+    const arg = {
+      genome: block.genome.name,
+      file: tk.file,
+      rglst: block.tkarg_rglst(tk),
+      width: block.width,
+      devicePixelRatio: window.devicePixelRatio > 1 ? window.devicePixelRatio : 1
+    };
+    const data = await dofetch3("tkld", { method: "POST", body: arg });
+    if (data.error) throw data.error;
+    tk.rglstG.selectAll("*").remove();
+    let tkheight = 0;
+    for (const r of data.rglst) {
+      const g = tk.rglstG.append("g");
+      if (r.rangetoobig) {
+        r.text_rangetoobig = g.append("text").text(r.rangetoobig).attr("text-anchor", "middle").attr("dominant-baseline", "central").attr("x", r.width / 2);
+        tkheight = Math.max(tkheight, 50);
+        continue;
+      }
+      if (r.img) {
+        g.append("image").attr("width", r.width).attr("height", r.img.height).attr("xlink:href", r.img.src);
+        tkheight = Math.max(tkheight, r.img.height);
+        continue;
+      }
+    }
+    tk.height_main = tk.toppad + tkheight + tk.bottompad;
+    block.tkcloakoff(tk, {});
+  } catch (e) {
+    tk.height_main = 50;
+    block.tkcloakoff(tk, { error: e.message || e });
+  }
+  block.block_setheight(tk);
+}
+function makeTk(tk, block) {
+  delete tk.uninitiated;
+  tk.rglstG = tk.glider.append("g");
+  const [tr, td] = legend_newrow(block, tk.name);
+  tk.tr_legend = tr;
+  tk.legend = {
+    div: td.append("div")
+  };
+  tk.legend.div.html("LD r<sup>2</sup>");
+  const scale = rgb_default("white", "red");
+  showLDlegend(tk.legend.div, scale);
+}
+export {
+  loadTk
+};
+//# sourceMappingURL=block.tk.ld-3PQ4O2AE.js.map