Merge pull request #115 from molgenis/feat/sample_tree_categories

Add sample decision tree categories
molgenis · Nov 13, 2024 · ecfb27b · ecfb27b
2 parents b0e8fbd + 7dd3220
commit ecfb27b
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Showing 4 changed files with 103 additions and 40 deletions.
diff --git a/package.json b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@molgenis/vip-report-api",
-  "version": "6.0.1",
+  "version": "6.1.0",
   "description": "TypeScript Report API for Variant Call Format (VCF) Report Templates",
   "scripts": {
     "build": "tsc --build",

diff --git a/src/__tests__/apiClient.test.ts b/src/__tests__/apiClient.test.ts
@@ -183,6 +183,51 @@ beforeEach(() => {
   api = new ApiClient(reportData as unknown as EncodedReport);
 });
 
+test("postProcess - sample tree categories", async () => {
+  const metadata = await api.getRecordsMeta();
+  expect(metadata.format["VIPC_S"].categories).toEqual({
+    U1: {
+      description: "Usable: probably",
+      label: "U1",
+    },
+    U2: {
+      description: "Usable: maybe",
+      label: "U2",
+    },
+    U3: {
+      description: "Usable: probably not",
+      label: "U3",
+    },
+  });
+});
+
+test("postProcess - decision tree categories", async () => {
+  const metadata = await api.getRecordsMeta();
+  const csqItems = metadata.info.CSQ?.nested?.items;
+  const csqItem = csqItems.find((item) => item.id === "VIPC");
+  expect(csqItem.categories).toEqual({
+    B: {
+      label: "B",
+    },
+    LB: {
+      label: "LB",
+    },
+    LP: {
+      label: "LP",
+    },
+    LQ: {
+      description: "Low quality variants.",
+      label: "LQ",
+    },
+    P: {
+      label: "P",
+    },
+    VUS: {
+      label: "VUS",
+    },
+  });
+});
+
 test("getAppMeta", async () => {
   const metadata = await api.getAppMetadata();
   expect(metadata).toEqual(

diff --git a/src/__tests__/trio.vcf b/src/__tests__/trio.vcf
@@ -8,9 +8,11 @@
 ##INFO=<ID=n_string4,Number=1,Type=String,Description="n_string4">
 ##INFO=<ID=n_array0,Number=.,Type=String,Description="n_array0">
 ##INFO=<ID=n_object0,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: n_string1|n_string2">
+##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|VIPC">
 ##FORMAT=<ID=DP,Number=1,Type=String,Description="Depth">
 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=VIPC_S,Number=.,Type=String,Description="VIP decision tree classification.">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Patient	Mother	Father
 1	10042538	.	C	T	.	PASS	n_array0=c,,d,b;n_number2=1;n_object0=dummy|c,dummy|,dummy|d,dummy|b;n_string0=a;n_string3=b;n_string4=b	GT:DP:AD	1|0:50:45,5	0|0:10:10,0	0|0:10:10,0
 1	16376412	.	G	A	.	PASS	n_array0=b,c,a;n_bool3;n_bool6;n_bool7;n_number2=0;n_object0=dummy|b,dummy|c,dummy|a;n_string0=a;n_string3=a;n_string4=A	GT:DP:AD	0|1:10:0,0	1|0:11:11,0	1|0:11:11,0
diff --git a/src/apiClient.ts b/src/apiClient.ts
@@ -110,19 +110,10 @@ export class ApiClient implements Api {
   }
 
   private postProcessReportData(reportData: ReportData): ReportData {
-    if (!reportData.decisionTree) {
-      return reportData;
-    }
-    const csqItems = reportData.metadata.records.info.CSQ?.nested?.items;
-    if (!csqItems) {
-      return reportData;
-    }
-
-    // make VIPC categorical with categories based on tree exit nodes
-    const csqItem = csqItems.find((item) => item.id === "VIPC");
-    if (csqItem) {
-      csqItem.type = "CATEGORICAL";
-      csqItem.categories = Object.values(reportData.decisionTree.nodes)
+    // make VIPC_S categorical with categories based on sample tree exit nodes
+    const vipc_s = reportData.metadata.records.format["VIPC_S"];
+    if (vipc_s && reportData.sampleTree !== undefined) {
+      vipc_s.categories = Object.values(reportData.sampleTree.nodes)
         .filter((node) => node.type === "LEAF")
         .map((node) => node as LeafNode)
         .reduce(
@@ -132,39 +123,64 @@ export class ApiClient implements Api {
           }),
           {},
         );
-      csqItem.required = true;
+
+      vipc_s.type = "CATEGORICAL";
     }
 
-    // make HPO categorical with categories based on phenotypes
-    const hpoItem = csqItems.find((item) => item.id === "HPO");
-    if (hpoItem) {
-      const categories = reportData.data.phenotypes
-        ? (reportData.data.phenotypes as Phenotype[])
-            .flatMap((phenotype) => phenotype.phenotypicFeaturesList)
-            .map((phenotype) => phenotype.type.id)
-            .filter((v, i, a) => a.indexOf(v) === i)
-            .sort()
-        : [];
-      if (categories.length > 0) {
-        hpoItem.type = "CATEGORICAL";
-        const categories: CategoryRecord = (reportData.data.phenotypes as Phenotype[])
-          .flatMap((phenotype) => phenotype.phenotypicFeaturesList)
-          .reduce(
-            (acc, phenotype) => ({
-              ...acc,
-              [phenotype.type.id]: { label: phenotype.type.label },
-            }),
-            {},
-          );
-        hpoItem.categories = Object.keys(categories)
-          .sort()
+    const csqItems = reportData.metadata.records.info.CSQ?.nested?.items;
+    if (!csqItems) {
+      return reportData;
+    }
+
+    // make VIPC categorical with categories based on tree exit nodes
+    const csqItem = csqItems.find((item) => item.id === "VIPC");
+    if (csqItem) {
+      if (reportData.decisionTree) {
+        csqItem.type = "CATEGORICAL";
+        csqItem.categories = Object.values(reportData.decisionTree.nodes)
+          .filter((node) => node.type === "LEAF")
+          .map((node) => node as LeafNode)
           .reduce(
-            (acc, categoryId) => ({
+            (acc, node) => ({
               ...acc,
-              [categoryId]: categories[categoryId],
+              [node.class]: { label: node.class, description: node.description },
             }),
             {},
           );
+        csqItem.required = true;
+      }
+
+      // make HPO categorical with categories based on phenotypes
+      const hpoItem = csqItems.find((item) => item.id === "HPO");
+      if (hpoItem) {
+        const categories = reportData.data.phenotypes
+          ? (reportData.data.phenotypes as Phenotype[])
+              .flatMap((phenotype) => phenotype.phenotypicFeaturesList)
+              .map((phenotype) => phenotype.type.id)
+              .filter((v, i, a) => a.indexOf(v) === i)
+              .sort()
+          : [];
+        if (categories.length > 0) {
+          hpoItem.type = "CATEGORICAL";
+          const categories: CategoryRecord = (reportData.data.phenotypes as Phenotype[])
+            .flatMap((phenotype) => phenotype.phenotypicFeaturesList)
+            .reduce(
+              (acc, phenotype) => ({
+                ...acc,
+                [phenotype.type.id]: { label: phenotype.type.label },
+              }),
+              {},
+            );
+          hpoItem.categories = Object.keys(categories)
+            .sort()
+            .reduce(
+              (acc, categoryId) => ({
+                ...acc,
+                [categoryId]: categories[categoryId],
+              }),
+              {},
+            );
+        }
       }
     }