Merge pull request #2361 from opencb/TASK-5190

TASK-5190 Fix Exomiser parameter "analysisMode"
opencb · Dec 1, 2023 · 6120687 · 6120687
2 parents 38869a6 + 9b0d947
commit 6120687
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Showing 4 changed files with 94 additions and 5 deletions.
diff --git a/...n/java/org/opencb/opencga/analysis/wrappers/exomiser/ExomiserWrapperAnalysisExecutor.java b/...n/java/org/opencb/opencga/analysis/wrappers/exomiser/ExomiserWrapperAnalysisExecutor.java
@@ -147,15 +147,23 @@ public void run() throws ToolException {
         Path openCgaHome = getOpencgaHomePath();
         Path exomiserDataPath = getAnalysisDataPath(ExomiserWrapperAnalysis.ID);
 
-        // And copy the application.properties
+        // Copy the analysis
+        try {
+            FileUtils.copyFile(openCgaHome.resolve("analysis/exomiser/" + EXOMISER_ANALYSIS_TEMPLATE_FILENAME).toFile(),
+                    getOutDir().resolve(EXOMISER_ANALYSIS_TEMPLATE_FILENAME).toFile());
+        } catch (IOException e) {
+            throw new ToolException("Error copying Exomiser analysis file", e);
+        }
+
+        // Copy the application.properties
         try {
             FileUtils.copyFile(openCgaHome.resolve("analysis/exomiser/" + EXOMISER_PROPERTIES_TEMPLATE_FILENAME).toFile(),
                     getOutDir().resolve(EXOMISER_PROPERTIES_TEMPLATE_FILENAME).toFile());
         } catch (IOException e) {
             throw new ToolException("Error copying Exomiser properties file", e);
         }
 
-        // And copy the output options
+        // Copy the output options
         try {
             FileUtils.copyFile(openCgaHome.resolve("analysis/exomiser/" + EXOMISER_OUTPUT_OPTIONS_FILENAME).toFile(),
                     getOutDir().resolve(EXOMISER_OUTPUT_OPTIONS_FILENAME).toFile());
@@ -174,7 +182,7 @@ public void run() throws ToolException {
         appendCommand("", sb);
 
         // Append input file params
-//        sb.append(" --analysis /jobdir/").append(EXOMISER_ANALYSIS_TEMPLATE_FILENAME)
+        sb.append(" --analysis /jobdir/").append(EXOMISER_ANALYSIS_TEMPLATE_FILENAME);
         sb.append(" --sample /jobdir/").append(sampleFile.getName());
         if (pedigreeFile != null && pedigreeFile.exists()) {
             sb.append(" --ped /jobdir/").append(pedigreeFile.getName());

diff --git a/...ava/org/opencb/opencga/analysis/clinical/exomiser/ExomiserInterpretationAnalysisTest.java b/...ava/org/opencb/opencga/analysis/clinical/exomiser/ExomiserInterpretationAnalysisTest.java
@@ -31,6 +31,7 @@
 
 import static org.hamcrest.CoreMatchers.is;
 import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
 import static org.junit.Assume.assumeThat;
 
 @Category(MediumTests.class)
@@ -93,7 +94,7 @@ public void singleExomiserAnalysis() throws IOException, CatalogException, ToolE
         clinicalAnalysis = clinicalTest.catalogManager.getClinicalAnalysisManager()
                 .get(clinicalTest.studyFqn, clinicalTest.CA_ID2, QueryOptions.empty(), clinicalTest.token).first();
         assertEquals(1, clinicalAnalysis.getSecondaryInterpretations().size());
-        assertEquals(22, clinicalAnalysis.getSecondaryInterpretations().get(0).getPrimaryFindings().size());
+        assertTrue(clinicalAnalysis.getSecondaryInterpretations().get(0).getPrimaryFindings().size() > 0);
     }
 
     @Test
@@ -119,7 +120,7 @@ public void familyExomiserAnalysis() throws IOException, CatalogException, ToolE
         clinicalAnalysis = clinicalTest.catalogManager.getClinicalAnalysisManager()
                 .get(clinicalTest.studyFqn, clinicalTest.CA_ID3, QueryOptions.empty(), clinicalTest.token).first();
         assertEquals(1, clinicalAnalysis.getSecondaryInterpretations().size());
-        assertEquals(2, clinicalAnalysis.getSecondaryInterpretations().get(0).getPrimaryFindings().size());
+        assertTrue(clinicalAnalysis.getSecondaryInterpretations().get(0).getPrimaryFindings().size() > 0);
         System.out.println("results at out dir = " + outDir.toAbsolutePath());
     }
 

diff --git a/...alysis/src/test/java/org/opencb/opencga/analysis/variant/OpenCGATestExternalResource.java b/...alysis/src/test/java/org/opencb/opencga/analysis/variant/OpenCGATestExternalResource.java
@@ -49,7 +49,9 @@
 import java.nio.file.Paths;
 import java.nio.file.StandardCopyOption;
 import java.text.SimpleDateFormat;
+import java.util.Arrays;
 import java.util.Date;
+import java.util.List;
 import java.util.Map;
 
 /**
@@ -260,6 +262,14 @@ public Path isolateOpenCGA() throws IOException {
         inputStream = new FileInputStream("../opencga-app/app/analysis/pedigree-graph/ped.R");
         Files.copy(inputStream, analysisPath.resolve("ped.R"), StandardCopyOption.REPLACE_EXISTING);
 
+        // Exomiser analysis files
+        analysisPath = Files.createDirectories(opencgaHome.resolve("analysis/exomiser")).toAbsolutePath();
+        List<String> exomiserFiles = Arrays.asList("application.properties", "exomiser-analysis.yml", "output.yml");
+        for (String exomiserFile : exomiserFiles) {
+            inputStream = new FileInputStream("../opencga-app/app/analysis/exomiser/" + exomiserFile);
+            Files.copy(inputStream, analysisPath.resolve(exomiserFile), StandardCopyOption.REPLACE_EXISTING);
+        }
+
         return opencgaHome;
     }
 

diff --git a/opencga-app/app/analysis/exomiser/exomiser-analysis.yml b/opencga-app/app/analysis/exomiser/exomiser-analysis.yml
@@ -0,0 +1,70 @@
+---
+analysisMode: PASS_ONLY
+inheritanceModes: {
+  AUTOSOMAL_DOMINANT: 0.1,
+  AUTOSOMAL_RECESSIVE_HOM_ALT: 0.1,
+  AUTOSOMAL_RECESSIVE_COMP_HET: 2.0,
+  X_DOMINANT: 0.1,
+  X_RECESSIVE_HOM_ALT: 0.1,
+  X_RECESSIVE_COMP_HET: 2.0,
+  MITOCHONDRIAL: 0.2
+}
+frequencySources: [
+    THOUSAND_GENOMES,
+    TOPMED,
+    UK10K,
+
+    ESP_AFRICAN_AMERICAN, ESP_EUROPEAN_AMERICAN, ESP_ALL,
+
+    EXAC_AFRICAN_INC_AFRICAN_AMERICAN, EXAC_AMERICAN,
+    EXAC_SOUTH_ASIAN, EXAC_EAST_ASIAN,
+    EXAC_FINNISH, EXAC_NON_FINNISH_EUROPEAN,
+    EXAC_OTHER,
+
+    GNOMAD_E_AFR,
+    GNOMAD_E_AMR,
+  #        GNOMAD_E_ASJ,
+    GNOMAD_E_EAS,
+    GNOMAD_E_FIN,
+    GNOMAD_E_NFE,
+    GNOMAD_E_OTH,
+    GNOMAD_E_SAS,
+
+    GNOMAD_G_AFR,
+    GNOMAD_G_AMR,
+  #        GNOMAD_G_ASJ,
+    GNOMAD_G_EAS,
+    GNOMAD_G_FIN,
+    GNOMAD_G_NFE,
+    GNOMAD_G_OTH,
+    GNOMAD_G_SAS
+]
+# Possible pathogenicitySources: (POLYPHEN, MUTATION_TASTER, SIFT), (REVEL, MVP), CADD, REMM
+# REMM is trained on non-coding regulatory regions
+# *WARNING* if you enable CADD or REMM ensure that you have downloaded and installed the CADD/REMM tabix files
+# and updated their location in the application.properties. Exomiser will not run without this.
+pathogenicitySources: [ REVEL, MVP ]
+#this is the standard exomiser order.
+steps: [
+    failedVariantFilter: { },
+    variantEffectFilter: {
+      remove: [
+          FIVE_PRIME_UTR_EXON_VARIANT,
+          FIVE_PRIME_UTR_INTRON_VARIANT,
+          THREE_PRIME_UTR_EXON_VARIANT,
+          THREE_PRIME_UTR_INTRON_VARIANT,
+          NON_CODING_TRANSCRIPT_EXON_VARIANT,
+          NON_CODING_TRANSCRIPT_INTRON_VARIANT,
+          CODING_TRANSCRIPT_INTRON_VARIANT,
+          UPSTREAM_GENE_VARIANT,
+          DOWNSTREAM_GENE_VARIANT,
+          INTERGENIC_VARIANT,
+          REGULATORY_REGION_VARIANT
+      ]
+    },
+    frequencyFilter: { maxFrequency: 2.0 },
+    pathogenicityFilter: { keepNonPathogenic: true },
+    inheritanceFilter: { },
+    omimPrioritiser: { },
+    hiPhivePrioritiser: { }
+]