Merge pull request #661 from awab-ahmed/fix-long-mnv-bug

Fix long mnv bug
opencb · Aug 31, 2023 · b73ac42 · b73ac42
2 parents 3624baf + 34b6b01
commit b73ac42
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Showing 10 changed files with 69 additions and 8 deletions.
diff --git a/cellbase-app/pom.xml b/cellbase-app/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.cellbase</groupId>
         <artifactId>cellbase</artifactId>
-        <version>4.12.3</version>
+        <version>4.12.4</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/cellbase-client/pom.xml b/cellbase-client/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.cellbase</groupId>
         <artifactId>cellbase</artifactId>
-        <version>4.12.3</version>
+        <version>4.12.4</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/cellbase-core/pom.xml b/cellbase-core/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.cellbase</groupId>
         <artifactId>cellbase</artifactId>
-        <version>4.12.3</version>
+        <version>4.12.4</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/...rc/main/java/org/opencb/cellbase/core/variant/annotation/VariantAnnotationCalculator.java b/...rc/main/java/org/opencb/cellbase/core/variant/annotation/VariantAnnotationCalculator.java
@@ -1102,6 +1102,10 @@ private ConsequenceTypeCalculator getConsequenceTypeCalculator(Variant variant)
             case BREAKEND:
                 return new ConsequenceTypeBNDCalculator();
             default:
+                logger.error("There is no ConsequenceTypeCalculator for variant %s of type %s",
+                        variant,
+                        VariantAnnotationUtils.getVariantType(variant)
+                );
                 throw new UnsupportedURLVariantFormat();
         }
     }

diff --git a/...ore/src/main/java/org/opencb/cellbase/core/variant/annotation/VariantAnnotationUtils.java b/...ore/src/main/java/org/opencb/cellbase/core/variant/annotation/VariantAnnotationUtils.java
@@ -5,6 +5,8 @@
 import org.opencb.biodata.models.variant.annotation.ConsequenceTypeMappings;
 import org.opencb.biodata.models.variant.annotation.exceptions.SOTermNotAvailableException;
 import org.opencb.biodata.models.variant.avro.*;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import java.util.*;
 
@@ -146,6 +148,8 @@ public class VariantAnnotationUtils {
 
     public static final String MT = "MT";
     public static final String UNKNOWN_AMINOACID = "X";
+    private static final int MAX_MNV_THRESHOLD = 1000;
+    private static Logger logger = LoggerFactory.getLogger(VariantAnnotationUtils.class);
 
     static {
 
@@ -670,6 +674,12 @@ public static VariantType getVariantType(Variant variant) throws UnsupportedURLV
             } else {
                 return VariantType.MNV;
             }
+        } else if (!variant.isSymbolic() && variant.getReference().length() > 1 && variant.getAlternate().length() > 1) {
+            if (variant.getReference().length() <= MAX_MNV_THRESHOLD && variant.getAlternate().length() <= MAX_MNV_THRESHOLD) {
+                return VariantType.MNV;
+            } else {
+                logger.warn("Provided alleles for variant are too long to be considered an MNV: %s", variant);
+            }
         }
         return variant.getType();
 //        return getVariantType(variant.getReferenceStart(), variant.getAlternate());

diff --git a/cellbase-lib/pom.xml b/cellbase-lib/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.cellbase</groupId>
         <artifactId>cellbase</artifactId>
-        <version>4.12.3</version>
+        <version>4.12.4</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/VariantAnnotationCalculatorTest.java b/cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/VariantAnnotationCalculatorTest.java
@@ -20,6 +20,7 @@
 import com.fasterxml.jackson.databind.MapperFeature;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.fasterxml.jackson.databind.ObjectReader;
+import org.apache.commons.lang3.StringUtils;
 import org.hamcrest.CoreMatchers;
 import org.junit.Before;
 import org.junit.Test;
@@ -28,6 +29,7 @@
 import org.opencb.biodata.models.variant.avro.*;
 import org.opencb.cellbase.core.variant.AnnotationBasedPhasedQueryManager;
 import org.opencb.cellbase.core.variant.annotation.VariantAnnotationCalculator;
+import org.opencb.cellbase.core.variant.annotation.UnsupportedURLVariantFormat;
 import org.opencb.cellbase.lib.GenericMongoDBAdaptorTest;
 import org.opencb.commons.datastore.core.QueryOptions;
 import org.opencb.commons.datastore.core.QueryResult;
@@ -40,7 +42,6 @@
 
 import static org.junit.Assert.*;
 
-
 public class VariantAnnotationCalculatorTest extends GenericMongoDBAdaptorTest {
 
     ObjectMapper jsonObjectMapper;
@@ -2379,7 +2380,53 @@ public void testSpliceAnnotation() throws Exception {
                                 "splice_acceptor_variant"))
         );
     }
+    @Test
+    public void testLongMNVConsequenceTypes() throws Exception {
+        Variant variant = new  Variant("22", 17668822, "TCTCTACTAAAAATACAAAAAATTAGCCAGGCGTGGTGGCAGGTGCCTGTAGTAC", "CC");
+        QueryOptions queryOptions = new QueryOptions("useCache", false);
+        queryOptions.put("include", "consequenceType");
+        queryOptions.put("skipDecompose", true);
+        QueryResult<VariantAnnotation> queryResult = variantAnnotationCalculator
+                .getAnnotationByVariant(variant, queryOptions);
+        List<ConsequenceType> consequenceTypeList  = queryResult.getResult().get(0).getConsequenceTypes();
+        assertFalse(consequenceTypeList.isEmpty());
+        String sequenceOntologyTerms = getSequenceOntologyTerms("ENST00000399839", consequenceTypeList);
+        assertEquals("[{\"accession\": \"SO:0001627\", \"name\": \"intron_variant\"}]", sequenceOntologyTerms);
+
+        // Deletion instead of MNV produces feature_truncation in addition to intron_variant
+        variant = new  Variant("22", 17668822, "TCTCTACTAAAAATACAAAAAATTAGCCAGGCGTGGTGGCAGGTGCCTGTAGTAC", "");
+        queryResult = variantAnnotationCalculator
+                .getAnnotationByVariant(variant, queryOptions);
+        consequenceTypeList  = queryResult.getResult().get(0).getConsequenceTypes();
+        assertFalse(consequenceTypeList.isEmpty());
+        sequenceOntologyTerms = getSequenceOntologyTerms("ENST00000399839", consequenceTypeList);
+        assertEquals("[{\"accession\": \"SO:0001906\", \"name\": \"feature_truncation\"}, {\"accession\": \"SO:0001627\", \"name\": \"intron_variant\"}]", sequenceOntologyTerms);
+    }
 
+    @Test(expected = UnsupportedURLVariantFormat.class)
+    public void testLongMNVConsequenceTypesFailsForAboveThresholdLength() throws Exception {
+        QueryOptions queryOptions = new QueryOptions("useCache", false);
+        queryOptions.put("include", "consequenceType");
+        queryOptions.put("skipDecompose", true);
+        // Very long MNV > MAX_MNV_THRESHOLD should return no consequence type
+        String alt = "C" + StringUtils.repeat('A', 1001);
+        Variant aboveThresholdVariant = new  Variant("22", 17668822, "TCTCTACTAAAAATACAAAAAATTAGCCAGGCGTGGTGGCAGGTGCCTGTAGTAC",alt);
+        QueryResult<VariantAnnotation> queryResult = variantAnnotationCalculator
+                .getAnnotationByVariant(aboveThresholdVariant, queryOptions);
+        List<ConsequenceType> consequenceTypeList  = queryResult.getResult().get(0).getConsequenceTypes();
+        assertTrue(consequenceTypeList.isEmpty());
+        // Very long MNV > MAX_MNV_THRESHOLD throws UnsupportedURLVariantFormat
+        variantAnnotationCalculator.getAllConsequenceTypesByVariant(aboveThresholdVariant, queryOptions);
+    }
+
+    public String getSequenceOntologyTerms(String transcriptID, List<ConsequenceType> consequenceTypeList){
+        for (ConsequenceType consequenceType : consequenceTypeList) {
+            if (consequenceType.getEnsemblTranscriptId().equals("ENST00000399839")){
+                return consequenceType.getSequenceOntologyTerms().toString();
+            };
+        }
+        return null;
+    }
     private <T> void assertObjectListEquals(String expectedConsequenceTypeJson, List<T> actualList,
                                             Class<T> clazz) throws IOException {
         ObjectReader reader = jsonObjectMapper

diff --git a/cellbase-server/pom.xml b/cellbase-server/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.cellbase</groupId>
         <artifactId>cellbase</artifactId>
-        <version>4.12.3</version>
+        <version>4.12.4</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/cellbase-test/pom.xml b/cellbase-test/pom.xml
@@ -22,7 +22,7 @@
 
     <groupId>org.opencb.cellbase</groupId>
     <artifactId>cellbase-test</artifactId>
-    <version>4.12.3</version>
+    <version>4.12.4</version>
     <packaging>pom</packaging>
 
     <dependencies>

diff --git a/pom.xml b/pom.xml
@@ -6,7 +6,7 @@
 
     <groupId>org.opencb.cellbase</groupId>
     <artifactId>cellbase</artifactId>
-    <version>4.12.3</version>
+    <version>4.12.4</version>
     <packaging>pom</packaging>
 
     <name>CellBase project</name>