tools: update clinical variant creators, #189

opencb · Sep 2, 2020 · 7efc592 · 7efc592
1 parent 426ec38
commit 7efc592
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Showing 4 changed files with 49 additions and 56 deletions.
diff --git a/biodata-tools/src/main/java/org/opencb/biodata/tools/clinical/ClinicalVariantCreator.java b/biodata-tools/src/main/java/org/opencb/biodata/tools/clinical/ClinicalVariantCreator.java
@@ -23,10 +23,10 @@
 import org.apache.commons.collections.MapUtils;
 import org.apache.commons.lang.StringUtils;
 import org.opencb.biodata.models.clinical.ClinicalProperty;
+import org.opencb.biodata.models.clinical.ClinicalProperty.ModeOfInheritance;
 import org.opencb.biodata.models.clinical.Disorder;
 import org.opencb.biodata.models.clinical.Phenotype;
 import org.opencb.biodata.models.clinical.interpretation.*;
-import org.opencb.biodata.models.clinical.ClinicalProperty.ModeOfInheritance;
 import org.opencb.biodata.models.clinical.interpretation.exceptions.InterpretationAnalysisException;
 import org.opencb.biodata.models.variant.Variant;
 import org.opencb.biodata.models.variant.avro.ConsequenceType;
@@ -126,8 +126,8 @@ public List<ClinicalVariant> createSecondaryFindings(List<Variant> variants) {
 
             // If we have clinical variant evidences, then we have to create the clinical variant
             if (CollectionUtils.isNotEmpty(clinicalVariantEvidences)) {
-                ClinicalVariant clinicalVariant = new ClinicalVariant(variant.getImpl(), 0, new ArrayList<>(),
-                        Collections.emptyList(), ClinicalVariant.Status.NOT_REVIEWED, Collections.emptyMap());
+                ClinicalVariant clinicalVariant = new ClinicalVariant(variant.getImpl(), Collections.emptyList(), Collections.emptyList(),
+                        Collections.emptyList(), "", ClinicalVariant.Status.NOT_REVIEWED, Collections.emptyMap());
                 clinicalVariant.setEvidences(clinicalVariantEvidences);
 
                 // Add variant to the list
@@ -198,16 +198,15 @@ protected Map<String, Map<String, ClinicalProperty.ModeOfInheritance>> getGeneTo
         return idToPanelMoiMap;
     }
 
-    protected ClinicalVariantEvidence createClinicalVariantEvidence(List<SequenceOntologyTerm> consequenceTypes,
-                                                                    GenomicFeature genomicFeature, String panelId, ModeOfInheritance moi,
+    protected ClinicalVariantEvidence createClinicalVariantEvidence(GenomicFeature genomicFeature, String panelId, ModeOfInheritance moi,
                                                                     Penetrance penetrance, String tier, Variant variant) {
         ClinicalVariantEvidence clinicalVariantEvidence = new ClinicalVariantEvidence();
 
-        // Consequence types
-        if (CollectionUtils.isNotEmpty(consequenceTypes)) {
-            // Set consequence type
-            clinicalVariantEvidence.setConsequenceTypes(consequenceTypes);
-        }
+//        // Consequence types
+//        if (CollectionUtils.isNotEmpty(consequenceTypes)) {
+//            // Set consequence type
+//            clinicalVariantEvidence.setConsequenceTypes(consequenceTypes);
+//        }
 
         // Genomic feature
         if (genomicFeature != null) {
@@ -323,22 +322,23 @@ protected List<ClinicalVariantEvidence> createClinicalVariantEvidences(String ti
         if (ct != null) {
             soTerms = getSOTerms(ct, includeSoTerms);
 
-            genomicFeature = new GenomicFeature(ct.getEnsemblGeneId(), "GENE", ct.getEnsemblTranscriptId(), ct.getGeneName(), null);
+            genomicFeature = new GenomicFeature(ct.getEnsemblGeneId(), "GENE", ct.getEnsemblTranscriptId(), ct.getGeneName(), soTerms,
+                    null);
         }
 
         if (CollectionUtils.isNotEmpty(panelIds)) {
             for (String panelId : panelIds) {
-                ClinicalVariantEvidence clinicalVariantEvidence = createClinicalVariantEvidence(soTerms, genomicFeature, panelId,
-                        modeOfInheritance, penetrance, tier, variant);
+                ClinicalVariantEvidence clinicalVariantEvidence = createClinicalVariantEvidence(genomicFeature, panelId, modeOfInheritance,
+                        penetrance, tier, variant);
                 if (clinicalVariantEvidence != null) {
                     clinicalVariantEvidences.add(clinicalVariantEvidence);
                 }
             }
         } else {
             // We report events without panels, e.g., actionable variants (tier 3)
             if (CollectionUtils.isNotEmpty(soTerms)) {
-                ClinicalVariantEvidence clinicalVariantEvidence = createClinicalVariantEvidence(soTerms, genomicFeature, null,
-                        modeOfInheritance, penetrance, tier, variant);
+                ClinicalVariantEvidence clinicalVariantEvidence = createClinicalVariantEvidence(genomicFeature, null, modeOfInheritance,
+                        penetrance, tier, variant);
                 if (clinicalVariantEvidence != null) {
                     clinicalVariantEvidences.add(clinicalVariantEvidence);
                 }

diff --git a/...-tools/src/main/java/org/opencb/biodata/tools/clinical/DefaultClinicalVariantCreator.java b/...-tools/src/main/java/org/opencb/biodata/tools/clinical/DefaultClinicalVariantCreator.java
@@ -24,19 +24,17 @@
 import org.opencb.biodata.models.clinical.ClinicalProperty;
 import org.opencb.biodata.models.clinical.ClinicalProperty.ModeOfInheritance;
 import org.opencb.biodata.models.clinical.ClinicalProperty.Penetrance;
+import org.opencb.biodata.models.clinical.Disorder;
+import org.opencb.biodata.models.clinical.interpretation.ClinicalVariant;
 import org.opencb.biodata.models.clinical.interpretation.ClinicalVariantEvidence;
 import org.opencb.biodata.models.clinical.interpretation.DiseasePanel;
-import org.opencb.biodata.models.clinical.interpretation.ClinicalVariant;
-import org.opencb.biodata.models.clinical.Disorder;
 import org.opencb.biodata.models.variant.Variant;
 import org.opencb.biodata.models.variant.avro.ConsequenceType;
 
 import java.util.*;
 import java.util.stream.Collectors;
 
-import static org.opencb.biodata.models.clinical.interpretation.VariantClassification.TIER_1;
-import static org.opencb.biodata.models.clinical.interpretation.VariantClassification.TIER_2;
-import static org.opencb.biodata.models.clinical.interpretation.VariantClassification.UNTIERED;
+import static org.opencb.biodata.models.clinical.interpretation.VariantClassification.*;
 
 public class DefaultClinicalVariantCreator extends ClinicalVariantCreator {
 
@@ -126,8 +124,8 @@ public List<ClinicalVariant> create(List<Variant> variants) {
 
             // Create a clinical variant only if we have evidences
             if (CollectionUtils.isNotEmpty(clinicalVariantEvidences)) {
-                ClinicalVariant clinicalVariant = new ClinicalVariant(variant.getImpl(), 0, new ArrayList<>(),
-                        Collections.emptyList(), ClinicalVariant.Status.NOT_REVIEWED, Collections.emptyMap());
+                ClinicalVariant clinicalVariant = new ClinicalVariant(variant.getImpl(), Collections.emptyList(), Collections.emptyList(),
+                        Collections.emptyList(), "", ClinicalVariant.Status.NOT_REVIEWED, Collections.emptyMap());
                 clinicalVariant.setEvidences(clinicalVariantEvidences);
 
                 // Add variant to the list

diff --git a/...ata-tools/src/main/java/org/opencb/biodata/tools/clinical/TeamClinicalVariantCreator.java b/...ata-tools/src/main/java/org/opencb/biodata/tools/clinical/TeamClinicalVariantCreator.java
@@ -123,8 +123,8 @@ public List<ClinicalVariant> create(List<Variant> variants) throws Interpretatio
 
             // If we have clinical variant evidences, then we have to create the clinical variant
             if (CollectionUtils.isNotEmpty(clinicalVariantEvidences)) {
-                ClinicalVariant clinicalVariant = new ClinicalVariant(variant.getImpl(), 0, new ArrayList<>(),
-                        Collections.emptyList(), ClinicalVariant.Status.NOT_REVIEWED, Collections.emptyMap());
+                ClinicalVariant clinicalVariant = new ClinicalVariant(variant.getImpl(), Collections.emptyList(), Collections.emptyList(),
+                        Collections.emptyList(), "", ClinicalVariant.Status.NOT_REVIEWED, Collections.emptyMap());
                 clinicalVariant.setEvidences(clinicalVariantEvidences);
 
                 // Add variant to the list