@sjcrh/proteinpaint-server 2.191.5 → 2.192.0

package/genome/hg38.base.js

@@ -112,6 +112,14 @@ function getHg38() {
         file: "anno/hicFragment/hic.NcoI.hg38.gz"
       }
     ],
+    // sources of blacklisted genomic regions (artifact-prone / germline-CNV loci),
+    // consumed e.g. by GRIN2 to drop genes lying in these regions before recurrence testing
+    blacklists: [
+      { name: "ENCODE blacklist", file: "anno/encodeBlacklist.hg38.bed.gz" },
+      { name: "Segmental duplications", file: "anno/genomicSuperDups.hg38.bed.gz" },
+      { name: "Assembly gaps", file: "anno/gaps.hg38.bed.gz" },
+      { name: "Common germline CNVs (DGV)", file: "anno/dgvCommon.hg38.bed.gz" }
+    ],
     geneset: [
       {
         name: "Cancer Gene Census",

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.191.5",
+  "version": "2.192.0",
   "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": "2.191.0",
+    "@sjcrh/proteinpaint-python": "2.192.0",
     "@sjcrh/proteinpaint-r": "2.190.0",
-    "@sjcrh/proteinpaint-rust": "2.191.4",
-    "@sjcrh/proteinpaint-shared": "2.191.4",
-    "@sjcrh/proteinpaint-types": "2.191.4",
+    "@sjcrh/proteinpaint-rust": "2.192.0",
+    "@sjcrh/proteinpaint-shared": "2.192.0",
+    "@sjcrh/proteinpaint-types": "2.192.0",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^12.4.1",

package/routes/termdb.proteome.js

@@ -12,6 +12,9 @@ function init({ genomes }) {
       const term = q.term?.term || q.term;
       if (!term?.name) throw "term.name missing";
       const cohorts = [];
+      const brConfig = ds.queries.proteome.brainRegions;
+      const regionRemap = brConfig?.regionValueRemap || {};
+      const sampleRegions = {};
       for (const organismName in ds.queries.proteome.organisms) {
         const organism = ds.queries.proteome.organisms[organismName];
         for (const assayName in organism.assays) {
@@ -43,20 +46,31 @@ function init({ genomes }) {
             const prior = assay.cohorts[cohortName].prior;
             for (const entry of cohortData.allEntries || []) {
               const s2v = entry.s2v;
+              const sampleRegionsRaw = entry.sampleRegionsRaw || {};
               const stats = getCohortStats(s2v, controlSampleIds, prior);
               delete entry.s2v;
+              delete entry.sampleRegionsRaw;
               entry.foldChange = stats.foldChange;
               entry.pValue = stats.pValue;
               entry.testedN = stats.testedN;
               entry.controlN = stats.controlN;
               if (assay.mclassOverride) entry.mclassOverride = assay.mclassOverride;
               if (organism.genomeName) entry.genomeName = organism.genomeName;
+              if (brConfig) {
+                entry.sampleIds = Object.keys(s2v);
+                for (const sid in sampleRegionsRaw) {
+                  const raw = sampleRegionsRaw[sid];
+                  if (raw == null) continue;
+                  const code = regionRemap[String(raw)] ?? String(raw);
+                  if (brConfig.regions[code] !== void 0) sampleRegions[sid] = code;
+                }
+              }
               cohorts.push(entry);
             }
           }
         }
       }
-      res.send({ protein: term.name, cohorts });
+      res.send({ protein: term.name, cohorts, sampleRegions: brConfig ? sampleRegions : void 0 });
     } catch (e) {
       if (e?.stack) console.log(e.stack);
       res.send({ error: e.message || e });
@@ -324,13 +338,14 @@ function countDistinctSamples(db, filters) {
 function queryDbRows(db, matchColumn, matchValue, filters) {
   const { conditions, params } = buildFilterClause(filters);
   const allConditions = [`${matchColumn} = ? COLLATE NOCASE`, ...conditions];
-  const sql = `SELECT organism, disease, identifier, protein_accession, isoform, modsite, gene, sample, value
+  const sql = `SELECT organism, disease, identifier, protein_accession, isoform, modsite, gene, sample, value, brain_region
 		FROM proteome_abundance
 		WHERE ${allConditions.join(" AND ")}`;
   return db.prepare(sql).all(matchValue, ...params);
 }
 async function getProteomeValuesFromCohort(ds, param, q) {
   const db = ds.queries.proteome.db;
+  const hasBrainRegions = !!q.brainRegions;
   const { assay, cohort, organism } = param.dataTypeDetails;
   const organismConfig = q.organisms?.[organism];
   if (!organismConfig) throw `queries.proteome invalid organism: ${organism}`;
@@ -403,10 +418,14 @@ async function getProteomeValuesFromCohort(ds, param, q) {
             isoform: row.isoform,
             // refSeq transcript ID mapped from protein_accession
             geneName: row.gene,
-            s2v: {}
+            s2v: {},
+            // raw brain_region per sample id (only when brainRegions is configured);
+            // remapped + finalized into entry.sampleRegions in the route's init().
+            sampleRegionsRaw: hasBrainRegions ? {} : void 0
           });
         }
         entryMap.get(row.identifier).s2v[sid] = row.value;
+        if (hasBrainRegions) entryMap.get(row.identifier).sampleRegionsRaw[sid] = row.brain_region;
       }
       for (const entry of entryMap.values()) allEntries.push(entry);
     } else {
@@ -445,6 +464,8 @@ async function getProteomeValuesFromCohort(ds, param, q) {
 }
 export {
   countDistinctSamples,
+  getCohortStats,
   init,
+  queryDbRows,
   validate_query_proteome
 };

package/routes/termdb.violinBox.js

@@ -4,7 +4,7 @@ import { run_R } from "@sjcrh/proteinpaint-r";
 import { getData } from "../src/termdb.matrix.js";
 import { createCanvas } from "canvas";
 import { getOrderedLabels } from "../src/termdb.barchart.js";
-import { getDescrStats, getStdDev, getMean } from "./termdb.descrstats.ts";
+import { getDescrStats, getStdDev, getMean } from "#routes/termdb.descrstats.ts";
 import { isNumericTerm } from "#shared/terms.js";
 import { boxplot_getvalue } from "../src/utils.js";
 import { roundValueAuto } from "#shared/roundValue.js";