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Update to issues #501 & #473 - Include VariantEffect and geneSymbol a…
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…nnotations on ClinVarData at build time.
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@julesjacobsen
julesjacobsen committed Nov 15, 2023
1 parent bd6266b commit d69ba6c
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Showing 14 changed files with 531 additions and 145 deletions.
15 changes: 5 additions & 10 deletions ...c/main/java/org/monarchinitiative/exomiser/core/genome/JannovarSmallVariantAnnotator.java
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Expand Up @@ -31,14 +31,10 @@
import org.monarchinitiative.exomiser.core.model.TranscriptAnnotation;
import org.monarchinitiative.exomiser.core.model.VariantAnnotation;
import org.monarchinitiative.svart.GenomicVariant;
import org.monarchinitiative.svart.VariantType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.*;
import java.util.stream.Stream;

import static java.util.stream.Collectors.groupingBy;
Expand Down Expand Up @@ -127,16 +123,15 @@ private Stream<VariantAnnotations> splitAnnotationsByGene(VariantAnnotations var
return annotations.stream()
.collect(groupingBy(Annotation::getGeneSymbol))
.values().stream()
//.peek(annotationList -> annotationList.forEach(annotation -> logger.info("{}", toAnnotationString(annotation))))
//.peek(annotationList -> annotationList.forEach(annotation -> logger.info("{}", toAnnotationString(genomeVariant, annotation))))
.map(annos -> new VariantAnnotations(genomeVariant, annos));
}

private String toAnnotationString(VariantType variantType, SVAnnotation annotation) {
return variantType + ", " +
annotation.getVariant() + ", " +
private String toAnnotationString(GenomeVariant genomeVariant, Annotation annotation) {
return genomeVariant + ", " +
annotation.getTranscript().getGeneSymbol() + ", " +
annotation.getTranscript().getGeneID() + ", " +
annotation.getMostPathogenicVariantEffect() + ", " +
annotation.getMostPathogenicVarType() + ", " +
annotation.getPutativeImpact() + ", " +
annotation.getTranscript();
}
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128 changes: 94 additions & 34 deletions ...iser-core/src/main/java/org/monarchinitiative/exomiser/core/model/AlleleProtoAdaptor.java
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Expand Up @@ -21,13 +21,15 @@
package org.monarchinitiative.exomiser.core.model;

import com.google.common.collect.ImmutableMap;
import de.charite.compbio.jannovar.annotation.VariantEffect;
import org.monarchinitiative.exomiser.core.model.frequency.Frequency;
import org.monarchinitiative.exomiser.core.model.frequency.FrequencyData;
import org.monarchinitiative.exomiser.core.model.frequency.FrequencySource;
import org.monarchinitiative.exomiser.core.model.pathogenicity.ClinVarData;
import org.monarchinitiative.exomiser.core.model.pathogenicity.PathogenicityData;
import org.monarchinitiative.exomiser.core.model.pathogenicity.PathogenicityScore;
import org.monarchinitiative.exomiser.core.model.pathogenicity.PathogenicitySource;
import org.monarchinitiative.exomiser.core.proto.AlleleProto;
import org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey;
import org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties;
import org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar;
Expand Down Expand Up @@ -160,10 +162,13 @@ public static ClinVarData toClinVarData(ClinVar clinVar) {
}
ClinVarData.Builder builder = ClinVarData.builder();
builder.alleleId(clinVar.getAlleleId());
builder.variationId(clinVar.getVariationId());
builder.primaryInterpretation(toClinSig(clinVar.getPrimaryInterpretation()));
builder.secondaryInterpretations(toClinSigSet(clinVar.getSecondaryInterpretationsList()));
builder.includedAlleles(getToIncludedAlleles(clinVar.getIncludedAllelesMap()));
builder.reviewStatus(clinVar.getReviewStatus());
builder.geneSymbol(clinVar.getGeneSymbol());
builder.variantEffect(toVariantEffect(clinVar.getVariantEffect()));
return builder.build();
}

Expand Down Expand Up @@ -192,39 +197,94 @@ private static Set<ClinVarData.ClinSig> toClinSigSet(List<ClinVar.ClinSig> proto
}

private static ClinVarData.ClinSig toClinSig(ClinVar.ClinSig protoClinSig) {
switch (protoClinSig) {
case BENIGN:
return ClinVarData.ClinSig.BENIGN;
case BENIGN_OR_LIKELY_BENIGN:
return ClinVarData.ClinSig.BENIGN_OR_LIKELY_BENIGN;
case LIKELY_BENIGN:
return ClinVarData.ClinSig.LIKELY_BENIGN;
case UNCERTAIN_SIGNIFICANCE:
return ClinVarData.ClinSig.UNCERTAIN_SIGNIFICANCE;
case LIKELY_PATHOGENIC:
return ClinVarData.ClinSig.LIKELY_PATHOGENIC;
case PATHOGENIC_OR_LIKELY_PATHOGENIC:
return ClinVarData.ClinSig.PATHOGENIC_OR_LIKELY_PATHOGENIC;
case PATHOGENIC:
return ClinVarData.ClinSig.PATHOGENIC;
case CONFLICTING_PATHOGENICITY_INTERPRETATIONS:
return ClinVarData.ClinSig.CONFLICTING_PATHOGENICITY_INTERPRETATIONS;
case AFFECTS:
return ClinVarData.ClinSig.AFFECTS;
case ASSOCIATION:
return ClinVarData.ClinSig.ASSOCIATION;
case DRUG_RESPONSE:
return ClinVarData.ClinSig.DRUG_RESPONSE;
case OTHER:
return ClinVarData.ClinSig.OTHER;
case PROTECTIVE:
return ClinVarData.ClinSig.PROTECTIVE;
case RISK_FACTOR:
return ClinVarData.ClinSig.RISK_FACTOR;
case NOT_PROVIDED:
case UNRECOGNIZED:
default:
return ClinVarData.ClinSig.NOT_PROVIDED;
}
return switch (protoClinSig) {
case BENIGN -> ClinVarData.ClinSig.BENIGN;
case BENIGN_OR_LIKELY_BENIGN -> ClinVarData.ClinSig.BENIGN_OR_LIKELY_BENIGN;
case LIKELY_BENIGN -> ClinVarData.ClinSig.LIKELY_BENIGN;
case UNCERTAIN_SIGNIFICANCE -> ClinVarData.ClinSig.UNCERTAIN_SIGNIFICANCE;
case LIKELY_PATHOGENIC -> ClinVarData.ClinSig.LIKELY_PATHOGENIC;
case PATHOGENIC_OR_LIKELY_PATHOGENIC -> ClinVarData.ClinSig.PATHOGENIC_OR_LIKELY_PATHOGENIC;
case PATHOGENIC -> ClinVarData.ClinSig.PATHOGENIC;
case CONFLICTING_PATHOGENICITY_INTERPRETATIONS ->
ClinVarData.ClinSig.CONFLICTING_PATHOGENICITY_INTERPRETATIONS;
case AFFECTS -> ClinVarData.ClinSig.AFFECTS;
case ASSOCIATION -> ClinVarData.ClinSig.ASSOCIATION;
case DRUG_RESPONSE -> ClinVarData.ClinSig.DRUG_RESPONSE;
case OTHER -> ClinVarData.ClinSig.OTHER;
case PROTECTIVE -> ClinVarData.ClinSig.PROTECTIVE;
case RISK_FACTOR -> ClinVarData.ClinSig.RISK_FACTOR;
default -> ClinVarData.ClinSig.NOT_PROVIDED;
};
}

private static VariantEffect toVariantEffect(AlleleProto.VariantEffect clinVarVariantEffect) {
return switch (clinVarVariantEffect) {
case SEQUENCE_VARIANT -> VariantEffect.SEQUENCE_VARIANT;
case CHROMOSOME_NUMBER_VARIATION -> VariantEffect.CHROMOSOME_NUMBER_VARIATION;
case TRANSCRIPT_ABLATION -> VariantEffect.TRANSCRIPT_ABLATION;
case EXON_LOSS_VARIANT -> VariantEffect.EXON_LOSS_VARIANT;
case INVERSION -> VariantEffect.INVERSION;
case INSERTION -> VariantEffect.INSERTION;
case TRANSLOCATION -> VariantEffect.TRANSLOCATION;
case FRAMESHIFT_ELONGATION -> VariantEffect.FRAMESHIFT_ELONGATION;
case FRAMESHIFT_TRUNCATION -> VariantEffect.FRAMESHIFT_TRUNCATION;
case FRAMESHIFT_VARIANT -> VariantEffect.FRAMESHIFT_VARIANT;
case INTERNAL_FEATURE_ELONGATION -> VariantEffect.INTERNAL_FEATURE_ELONGATION;
case FEATURE_TRUNCATION -> VariantEffect.FEATURE_TRUNCATION;
case TRANSCRIPT_AMPLIFICATION -> VariantEffect.TRANSCRIPT_AMPLIFICATION;
case COPY_NUMBER_CHANGE -> VariantEffect.COPY_NUMBER_CHANGE;
case MNV -> VariantEffect.MNV;
case COMPLEX_SUBSTITUTION -> VariantEffect.COMPLEX_SUBSTITUTION;
case STOP_GAINED -> VariantEffect.STOP_GAINED;
case STOP_LOST -> VariantEffect.STOP_LOST;
case START_LOST -> VariantEffect.START_LOST;
case SPLICE_ACCEPTOR_VARIANT -> VariantEffect.SPLICE_ACCEPTOR_VARIANT;
case SPLICE_DONOR_VARIANT -> VariantEffect.SPLICE_DONOR_VARIANT;
case RARE_AMINO_ACID_VARIANT -> VariantEffect.RARE_AMINO_ACID_VARIANT;
case MISSENSE_VARIANT -> VariantEffect.MISSENSE_VARIANT;
case INFRAME_INSERTION -> VariantEffect.INFRAME_INSERTION;
case DISRUPTIVE_INFRAME_INSERTION -> VariantEffect.DISRUPTIVE_INFRAME_INSERTION;
case INFRAME_DELETION -> VariantEffect.INFRAME_DELETION;
case DISRUPTIVE_INFRAME_DELETION -> VariantEffect.DISRUPTIVE_INFRAME_DELETION;
case FIVE_PRIME_UTR_TRUNCATION -> VariantEffect.FIVE_PRIME_UTR_TRUNCATION;
case THREE_PRIME_UTR_TRUNCATION -> VariantEffect.THREE_PRIME_UTR_TRUNCATION;
case SPLICE_REGION_VARIANT -> VariantEffect.SPLICE_REGION_VARIANT;
case STOP_RETAINED_VARIANT -> VariantEffect.STOP_RETAINED_VARIANT;
case INITIATOR_CODON_VARIANT -> VariantEffect.INITIATOR_CODON_VARIANT;
case SYNONYMOUS_VARIANT -> VariantEffect.SYNONYMOUS_VARIANT;
case CODING_TRANSCRIPT_INTRON_VARIANT -> VariantEffect.CODING_TRANSCRIPT_INTRON_VARIANT;
case FIVE_PRIME_UTR_PREMATURE_START_CODON_GAIN_VARIANT ->
VariantEffect.FIVE_PRIME_UTR_PREMATURE_START_CODON_GAIN_VARIANT;
case FIVE_PRIME_UTR_EXON_VARIANT -> VariantEffect.FIVE_PRIME_UTR_EXON_VARIANT;
case THREE_PRIME_UTR_EXON_VARIANT -> VariantEffect.THREE_PRIME_UTR_EXON_VARIANT;
case FIVE_PRIME_UTR_INTRON_VARIANT -> VariantEffect.FIVE_PRIME_UTR_INTRON_VARIANT;
case THREE_PRIME_UTR_INTRON_VARIANT -> VariantEffect.THREE_PRIME_UTR_INTRON_VARIANT;
case NON_CODING_TRANSCRIPT_EXON_VARIANT -> VariantEffect.NON_CODING_TRANSCRIPT_EXON_VARIANT;
case NON_CODING_TRANSCRIPT_INTRON_VARIANT -> VariantEffect.NON_CODING_TRANSCRIPT_INTRON_VARIANT;
case DIRECT_TANDEM_DUPLICATION -> VariantEffect.DIRECT_TANDEM_DUPLICATION;
case MOBILE_ELEMENT_DELETION -> VariantEffect.MOBILE_ELEMENT_DELETION;
case MOBILE_ELEMENT_INSERTION -> VariantEffect.MOBILE_ELEMENT_INSERTION;
case UPSTREAM_GENE_VARIANT -> VariantEffect.UPSTREAM_GENE_VARIANT;
case DOWNSTREAM_GENE_VARIANT -> VariantEffect.DOWNSTREAM_GENE_VARIANT;
case INTERGENIC_VARIANT -> VariantEffect.INTERGENIC_VARIANT;
case TFBS_ABLATION -> VariantEffect.TFBS_ABLATION;
case TFBS_AMPLIFICATION -> VariantEffect.TFBS_AMPLIFICATION;
case TF_BINDING_SITE_VARIANT -> VariantEffect.TF_BINDING_SITE_VARIANT;
case REGULATORY_REGION_VARIANT -> VariantEffect.REGULATORY_REGION_VARIANT;
case REGULATORY_REGION_ABLATION -> VariantEffect.REGULATORY_REGION_ABLATION;
case REGULATORY_REGION_AMPLIFICATION -> VariantEffect.REGULATORY_REGION_AMPLIFICATION;
case CONSERVED_INTRON_VARIANT -> VariantEffect.CONSERVED_INTRON_VARIANT;
case INTRAGENIC_VARIANT -> VariantEffect.INTRAGENIC_VARIANT;
case CONSERVED_INTERGENIC_VARIANT -> VariantEffect.CONSERVED_INTERGENIC_VARIANT;
case STRUCTURAL_VARIANT -> VariantEffect.STRUCTURAL_VARIANT;
case CODING_SEQUENCE_VARIANT -> VariantEffect.CODING_SEQUENCE_VARIANT;
case INTRON_VARIANT -> VariantEffect.INTRON_VARIANT;
case EXON_VARIANT -> VariantEffect.EXON_VARIANT;
case SPLICING_VARIANT -> VariantEffect.SPLICING_VARIANT;
case MIRNA -> VariantEffect.MIRNA;
case CODING_TRANSCRIPT_VARIANT -> VariantEffect.CODING_TRANSCRIPT_VARIANT;
case NON_CODING_TRANSCRIPT_VARIANT -> VariantEffect.NON_CODING_TRANSCRIPT_VARIANT;
case UNRECOGNIZED -> VariantEffect.SEQUENCE_VARIANT;
};
}
}
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