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v4.10.0 - Add additional properties to annotations #586

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340f8c6
add unit test to check for additional properties for phased MNVs. add…
julie-sullivan May 11, 2022
756e8a9
better function name, remove extra method
julie-sullivan May 11, 2022
85c0c30
remove redundant statement
julie-sullivan May 11, 2022
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2 changes: 1 addition & 1 deletion cellbase-app/pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
<parent>
<groupId>org.opencb.cellbase</groupId>
<artifactId>cellbase</artifactId>
<version>4.9.8</version>
<version>4.10.0-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

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26 changes: 0 additions & 26 deletions cellbase-app/src/main/java/org/opencb/cellbase/app/transform/Main.java
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This file was deleted.

73 changes: 64 additions & 9 deletions ...-app/src/main/java/org/opencb/cellbase/app/transform/clinical/variant/ClinVarIndexer.java
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Expand Up @@ -66,6 +66,8 @@ public class ClinVarIndexer extends ClinicalIndexer {
private int numberGermlineRecords = 0;
private int numberNoDiseaseTrait = 0;
private int numberMultipleInheritanceModels = 0;
private static final String RCVIDS = "rcvIds";
private static final String SCVIDS = "scvIds";
private static final Set<ModeOfInheritance> DOMINANT_TERM_SET
= new HashSet<>(Arrays.asList(ModeOfInheritance.monoallelic,
ModeOfInheritance.monoallelic_maternally_imprinted,
Expand Down Expand Up @@ -213,7 +215,7 @@ private boolean updateRocksDB(AlleleLocationData alleleLocationData, PublicSetTy
String mateVariantString, Map<String, EFO> traitsToEfoTermsMap)
throws RocksDBException, IOException {

// More than one variant being returned from the normalisatio process would mean it's and MNV which has been
// More than one variant being returned from the normalisation process would mean it's and MNV which has been
// decomposed
List<String> normalisedVariantStringList = getNormalisedVariantString(
alleleLocationData.getSequenceLocation().getChromosome(),
Expand All @@ -232,32 +234,42 @@ private boolean updateRocksDB(AlleleLocationData alleleLocationData, PublicSetTy
clinicalHaplotypeString = StringUtils.join(normalisedVariantStringList, HAPLOTYPE_STRING_SEPARATOR);
}

// get VCV ID
String vcvId = getVcvId(publicSet);

// parse RCVs
String accession = publicSet.getReferenceClinVarAssertion().getClinVarAccession().getAcc();
String rcvAccession = publicSet.getReferenceClinVarAssertion().getClinVarAccession().getAcc();
String clinicalSignficanceDescription = publicSet.getReferenceClinVarAssertion()
.getClinicalSignificance()
.getDescription();
String reviewStatusName = publicSet.getReferenceClinVarAssertion().getClinicalSignificance()
.getReviewStatus().name();
List<ObservationSet> getObservedIn = publicSet.getReferenceClinVarAssertion().getObservedIn();
addNewEntries(variantAnnotation, publicSet, alleleLocationData.getAlleleId(), mateVariantString,
clinicalHaplotypeString, traitsToEfoTermsMap, accession, clinicalSignficanceDescription,
reviewStatusName, getObservedIn);
clinicalHaplotypeString, traitsToEfoTermsMap, rcvAccession, clinicalSignficanceDescription,
reviewStatusName, getObservedIn, vcvId);

List<String> scvAccessions = new ArrayList<>();

// parse SCVs
for (MeasureTraitType measureTraitType : publicSet.getClinVarAssertion()) {
accession = measureTraitType.getClinVarAccession().getAcc();
String scvAccession = measureTraitType.getClinVarAccession().getAcc();
clinicalSignficanceDescription
= StringUtils.join(measureTraitType.getClinicalSignificance().getDescription(),
CLINICAL_SIGNIFICANCE_SEPARATOR);

reviewStatusName = getReviewStatusIfPresent(measureTraitType);
getObservedIn = measureTraitType.getObservedIn();
addNewEntries(variantAnnotation, publicSet, alleleLocationData.getAlleleId(), mateVariantString,
clinicalHaplotypeString, traitsToEfoTermsMap, accession, clinicalSignficanceDescription,
reviewStatusName, getObservedIn);
clinicalHaplotypeString, traitsToEfoTermsMap, scvAccession, clinicalSignficanceDescription,
reviewStatusName, getObservedIn, vcvId);
scvAccessions.add(scvAccession);
}

if (StringUtils.isNotEmpty(vcvId)) {
// add SCVs and RCVs to VCV entry
addAdditionalProperties(variantAnnotation, vcvId, rcvAccession, scvAccessions);
}
rdb.put(normalisedVariantString.getBytes(), jsonObjectWriter.writeValueAsBytes(variantAnnotation));
}
return true;
Expand All @@ -266,6 +278,46 @@ private boolean updateRocksDB(AlleleLocationData alleleLocationData, PublicSetTy
return false;
}

private String getVcvId(PublicSetType publicSet) {
if (publicSet.getReferenceClinVarAssertion() == null || publicSet.getReferenceClinVarAssertion().getMeasureSet() == null
|| publicSet.getReferenceClinVarAssertion().getMeasureSet().getID() == null) {
return null;
}
return publicSet.getReferenceClinVarAssertion().getMeasureSet().getID().toString();
}

private void addAdditionalProperties(VariantAnnotation variantAnnotation, String vcvId, String rcvAccession,
List<String> scvAccessions) {
List<Property> properties = getTraitAssociation(variantAnnotation, vcvId).getAdditionalProperties();
boolean hasRCVIds = false;
boolean hasSCVIds = false;
for (Property property : properties) {
if (RCVIDS.equals(property.getName())) {
hasRCVIds = true;
property.setValue(property.getValue() + "," + rcvAccession);
}
if (SCVIDS.equals(property.getName())) {
hasSCVIds = true;
property.setValue(property.getValue() + "," + String.join(",", scvAccessions));
}
}
if (!hasRCVIds) {
properties.add(new Property(null, RCVIDS, rcvAccession));
}
if (!hasSCVIds) {
properties.add(new Property(null, SCVIDS, String.join(",", scvAccessions)));
}
}

private EvidenceEntry getTraitAssociation(VariantAnnotation variantAnnotation, String vcvId) {
for (EvidenceEntry evidenceEntry: variantAnnotation.getTraitAssociation()) {
if (vcvId.equals(evidenceEntry.getId())) {
return evidenceEntry;
}
}
return null;
}

private String getReviewStatusIfPresent(MeasureTraitType measureTraitType) {
if (measureTraitType.getClinicalSignificance().getReviewStatus() != null) {
return measureTraitType.getClinicalSignificance().getReviewStatus().name();
Expand Down Expand Up @@ -355,10 +407,13 @@ private void addNewEntries(VariantAnnotation variantAnnotation, PublicSetType pu
String mateVariantString, String clinicalHaplotypeString,
Map<String, EFO> traitsToEfoTermsMap, String accession,
String clinicalSignficanceDescription, String reviewStatusName,
List<ObservationSet> getObservedIn)
List<ObservationSet> getObservedIn, String vcvId)
throws JsonProcessingException {

List<Property> additionalProperties = new ArrayList<>(3);
List<Property> additionalProperties = new ArrayList<>();
if (StringUtils.isNotEmpty(vcvId)) {
additionalProperties.add(new Property(null, "vcvIds", vcvId));
}
EvidenceSource evidenceSource = new EvidenceSource(EtlCommons.CLINVAR_DATA, null, null);
// String accession = publicSet.getReferenceClinVarAssertion().getClinVarAccession().getAcc();

Expand Down
25 changes: 25 additions & 0 deletions ...st/java/org/opencb/cellbase/app/transform/clinical/variant/ClinicalVariantParserTest.java
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Expand Up @@ -63,6 +63,8 @@ private void initGrch38() throws Exception {
(new ClinicalVariantParser(clinicalVariantFolder, true, genomeSequenceFilePath, "GRCh38", serializer)).parse();
}



@Test
public void testUnexpectedAccession() throws Exception {
cleanUp();
Expand All @@ -80,8 +82,31 @@ public void testUnexpectedAccession() throws Exception {
assertEquals("G", variant.getReference());
assertEquals("A", variant.getAlternate());

// variant should have list of SCVs and RCVs and VCVs
EvidenceEntry evidenceEntry = getEvidenceEntryByAccession(variant, "RCV000007529");
assertEquals(4, evidenceEntry.getAdditionalProperties().size());
assertEquals("7109", getValueByName(evidenceEntry, "vcvIds"));

evidenceEntry = getEvidenceEntryByAccession(variant, "SCV000053488");
assertEquals(4, evidenceEntry.getAdditionalProperties().size());
assertEquals("7109", getValueByName(evidenceEntry, "vcvIds"));

evidenceEntry = getEvidenceEntryByAccession(variant, "7109");
assertEquals(4, evidenceEntry.getAdditionalProperties().size());
assertEquals("RCV000007529", getValueByName(evidenceEntry, "rcvIds"));
assertEquals("SCV000053488", getValueByName(evidenceEntry, "scvIds"));
}

private String getValueByName(EvidenceEntry evidenceEntry, String name) {
for (Property property : evidenceEntry.getAdditionalProperties()) {
if (property.getName().equals(name)) {
return property.getValue();
}
}
return null;
}


@Test
public void testReallyLongVariant() throws Exception {
cleanUp();
Expand Down
2 changes: 1 addition & 1 deletion cellbase-client/pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
<parent>
<groupId>org.opencb.cellbase</groupId>
<artifactId>cellbase</artifactId>
<version>4.9.8</version>
<version>4.10.0-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

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2 changes: 1 addition & 1 deletion cellbase-core/pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
<parent>
<groupId>org.opencb.cellbase</groupId>
<artifactId>cellbase</artifactId>
<version>4.9.8</version>
<version>4.10.0-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

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16 changes: 9 additions & 7 deletions ...rc/main/java/org/opencb/cellbase/core/variant/annotation/VariantAnnotationCalculator.java
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Expand Up @@ -697,7 +697,8 @@ private void adjustPhasedConsequenceTypes(Object[] variantArray) {
consequenceType3.setSequenceOntologyTerms(soTerms);

// Flag these transcripts as already updated for this variant
flagTranscriptAnnotationUpdated(variant2, consequenceType1.getEnsemblTranscriptId());
flagTranscriptAnnotationUpdated(variant2, consequenceType1.getEnsemblTranscriptId(),
Arrays.asList(variant0, variant1));

variant2DisplayCTNeedsUpdate = true;

Expand Down Expand Up @@ -745,8 +746,8 @@ private void adjustPhasedConsequenceTypes(Object[] variantArray) {
consequenceType2.setSequenceOntologyTerms(soTerms);

// Flag these transcripts as already updated for this variant
flagTranscriptAnnotationUpdated(variant0, consequenceType1.getEnsemblTranscriptId());
flagTranscriptAnnotationUpdated(variant1, consequenceType1.getEnsemblTranscriptId());
flagTranscriptAnnotationUpdated(variant0, consequenceType1.getEnsemblTranscriptId(), Arrays.asList((variant1)));
flagTranscriptAnnotationUpdated(variant1, consequenceType1.getEnsemblTranscriptId(), Arrays.asList((variant0)));

variant0DisplayCTNeedsUpdate = true;
variant1DisplayCTNeedsUpdate = true;
Expand All @@ -771,24 +772,25 @@ private void adjustPhasedConsequenceTypes(Object[] variantArray) {
}
}

private void flagTranscriptAnnotationUpdated(Variant variant, String ensemblTranscriptId) {
private void flagTranscriptAnnotationUpdated(Variant variant, String ensemblTranscriptId, List<Variant> phasedVariants) {
Map<String, AdditionalAttribute> additionalAttributesMap = variant.getAnnotation().getAdditionalAttributes();
if (additionalAttributesMap == null) {
additionalAttributesMap = new HashMap<>();
AdditionalAttribute additionalAttribute = new AdditionalAttribute();
Map<String, String> transcriptsSet = new HashMap<>();
transcriptsSet.put(ensemblTranscriptId, null);
transcriptsSet.put(ensemblTranscriptId, VariantAnnotationUtils.buildVariantIds(phasedVariants));
additionalAttribute.setAttribute(transcriptsSet);
additionalAttributesMap.put("phasedTranscripts", additionalAttribute);
variant.getAnnotation().setAdditionalAttributes(additionalAttributesMap);
} else if (additionalAttributesMap.get("phasedTranscripts") == null) {
AdditionalAttribute additionalAttribute = new AdditionalAttribute();
Map<String, String> transcriptsSet = new HashMap<>();
transcriptsSet.put(ensemblTranscriptId, null);
transcriptsSet.put(ensemblTranscriptId, VariantAnnotationUtils.buildVariantIds(phasedVariants));
additionalAttribute.setAttribute(transcriptsSet);
additionalAttributesMap.put("phasedTranscripts", additionalAttribute);
} else {
additionalAttributesMap.get("phasedTranscripts").getAttribute().put(ensemblTranscriptId, null);
additionalAttributesMap.get("phasedTranscripts").getAttribute().put(ensemblTranscriptId,
VariantAnnotationUtils.buildVariantIds(phasedVariants));
}
}

Expand Down
23 changes: 22 additions & 1 deletion ...ore/src/main/java/org/opencb/cellbase/core/variant/annotation/VariantAnnotationUtils.java
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Expand Up @@ -601,12 +601,33 @@ public static SequenceOntologyTerm newSequenceOntologyTerm(String name) throws S
return new SequenceOntologyTerm(ConsequenceTypeMappings.getSoAccessionString(name), name);
}

public static String buildVariantId(Variant variant) {
if (variant == null) {
return null;
}
return buildVariantId(variant.getChromosome(), variant.getStart(), variant.getReference(), variant.getAlternate());
}

public static String buildVariantIds(List<Variant> variants) {
StringBuilder variantIds = new StringBuilder();
for (Variant variant : variants) {
if (variant == null) {
continue;
}
variantIds.append(buildVariantId(variant.getChromosome(), variant.getStart(), variant.getReference(), variant.getAlternate()));
}
if (variantIds == null) {
return null;
}
return variantIds.toString();
}

public static String buildVariantId(String chromosome, int start, String reference, String alternate) {
StringBuilder stringBuilder = new StringBuilder();

appendChromosome(chromosome, stringBuilder)
.append(SEPARATOR_CHAR)
.append(StringUtils.leftPad(Integer.toString(start), 10, " "))
.append(start)
.append(SEPARATOR_CHAR);

// if (reference.length() > Variant.SV_THRESHOLD) {
Expand Down
2 changes: 1 addition & 1 deletion cellbase-lib/pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
<parent>
<groupId>org.opencb.cellbase</groupId>
<artifactId>cellbase</artifactId>
<version>4.9.8</version>
<version>4.10.0-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

Expand Down
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