@sjcrh/proteinpaint-server 2.193.0 → 2.195.0

package/dataset/termdb.test.js

@@ -448,6 +448,7 @@ function termdb_test_default() {
       },
       trackLst: {
         jsonFile: "files/hg38/TermdbTest/trackLst/facet.json",
+        facetTwLst: [{ id: "diaggrp" }, { id: "agedx" }],
         activeTracks: ["bw 1", "bed 1"]
       },
       chat: {}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.193.0",
+  "version": "2.195.0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -59,11 +59,11 @@
   },
   "dependencies": {
     "@sjcrh/augen": "2.190.0",
-    "@sjcrh/proteinpaint-python": "2.193.0",
+    "@sjcrh/proteinpaint-python": "2.194.0",
     "@sjcrh/proteinpaint-r": "2.190.0",
-    "@sjcrh/proteinpaint-rust": "2.193.0",
-    "@sjcrh/proteinpaint-shared": "2.192.0",
-    "@sjcrh/proteinpaint-types": "2.193.0",
+    "@sjcrh/proteinpaint-rust": "2.195.0",
+    "@sjcrh/proteinpaint-shared": "2.195.0",
+    "@sjcrh/proteinpaint-types": "2.195.0",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^12.4.1",

package/routes/termdb.diffMeth.js

@@ -14,7 +14,7 @@ function init({ genomes }) {
       const q = req.query;
       if (q.preAnalysis) {
         const { ds, term_results, term_results2 } = await resolveDaContext(q, genomes);
-        const groups = resolveDmSampleGroups(q, ds, term_results, term_results2);
+        const groups = await resolveDmSampleGroups(q, ds, term_results, term_results2);
         const group1Name = q.samplelst.groups[0].name;
         const group2Name = q.samplelst.groups[1].name;
         res.send({
@@ -67,7 +67,7 @@ async function getDmCacheResult(req, genomes) {
   return { result, cacheId };
 }
 async function runDmFresh(param, ds, term_results, term_results2) {
-  const groups = resolveDmSampleGroups(param, ds, term_results, term_results2);
+  const groups = await resolveDmSampleGroups(param, ds, term_results, term_results2);
   if (groups.alerts.length) throw new Error(groups.alerts.join(" | "));
   const q = ds.queries.dnaMethylation.promoter;
   const diffMethInput = {
@@ -97,7 +97,7 @@ async function runDmFresh(param, ds, term_results, term_results2) {
   };
   return cacheResult;
 }
-function resolveDmSampleGroups(param, ds, term_results, term_results2) {
+async function resolveDmSampleGroups(param, ds, term_results, term_results2) {
   if (param.samplelst?.groups?.length != 2)
     throw new Error("Exactly 2 sample groups are required for differential methylation analysis.");
   if (param.samplelst.groups[0].values?.length < 1)
@@ -107,8 +107,24 @@ function resolveDmSampleGroups(param, ds, term_results, term_results2) {
   const q = ds.queries.dnaMethylation?.promoter;
   if (!q) throw new Error("This dataset does not have promoter-level methylation data configured.");
   if (!q.file) throw new Error("Promoter methylation data file is not configured for this dataset.");
-  const g1 = buildGroupValues(param.samplelst.groups[0].values, q, ds, param.tw, param.tw2, term_results, term_results2);
-  const g2 = buildGroupValues(param.samplelst.groups[1].values, q, ds, param.tw, param.tw2, term_results, term_results2);
+  const g1 = await buildGroupValues(
+    param.samplelst.groups[0].values,
+    q,
+    ds,
+    param.tw,
+    param.tw2,
+    term_results,
+    term_results2
+  );
+  const g2 = await buildGroupValues(
+    param.samplelst.groups[1].values,
+    q,
+    ds,
+    param.tw,
+    param.tw2,
+    term_results,
+    term_results2
+  );
   const alerts = [];
   if (g1.names.length < 1) alerts.push("No samples in group 1 have methylation data available.");
   if (g2.names.length < 1) alerts.push("No samples in group 2 have methylation data available.");

package/routes/termdb.proteome.js

@@ -1,6 +1,13 @@
 import { get_ds_tdb } from "#src/termdb.js";
 import * as utils from "#src/utils.js";
 import { mayLimitSamples } from "#src/mds3.filter.js";
+function baseUniProtAcc(acc) {
+  if (!acc) return "";
+  const parts = acc.split("|");
+  const id = parts.length >= 2 ? parts[1] : acc;
+  const dash = id.indexOf("-");
+  return dash > 0 ? id.slice(0, dash) : id;
+}
 function init({ genomes }) {
   return async (req, res) => {
     const q = req.query;
@@ -70,6 +77,26 @@ function init({ genomes }) {
           }
         }
       }
+      const refAssay = ds.queries.proteome.proteinReferenceAssay;
+      if (refAssay) {
+        const refFcByKey = /* @__PURE__ */ new Map();
+        for (const e of cohorts) {
+          if (e.assayName !== refAssay || !Number.isFinite(e.foldChange)) continue;
+          const baseAcc = baseUniProtAcc(e.proteinAccession);
+          if (!baseAcc) continue;
+          const key = `${e.organism}|${e.cohortName}|${baseAcc}`;
+          const p = Number.isFinite(e.pValue) ? e.pValue : Infinity;
+          const cur = refFcByKey.get(key);
+          if (!cur || p < cur.p) refFcByKey.set(key, { fc: e.foldChange, p });
+        }
+        for (const e of cohorts) {
+          if (!e.PTMType) continue;
+          const baseAcc = baseUniProtAcc(e.proteinAccession);
+          if (!baseAcc) continue;
+          const ref = refFcByKey.get(`${e.organism}|${e.cohortName}|${baseAcc}`);
+          if (ref) e.proteinFoldChange = ref.fc;
+        }
+      }
       res.send({ protein: term.name, cohorts, sampleRegions: brConfig ? sampleRegions : void 0 });
     } catch (e) {
       if (e?.stack) console.log(e.stack);