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Fixed support for newer Gencode GTF versions #8351

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merged 5 commits into from
Jun 28, 2023
Merged

Fixed support for newer Gencode GTF versions #8351

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ef97ae6
checkpoint of work, still need to finish tests and update testing
jamesemery Jun 6, 2023
939961a
refactoring the enums and fixing the downstream breaks that resulted …
jamesemery Jun 7, 2023
09a2be8
cleanup
jamesemery Jun 7, 2023
125aa5a
responded to comments and removed the AnonomyousOptionalField string …
jamesemery Jun 27, 2023
a7f9733
removing commented statements
jamesemery Jun 27, 2023
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5 changes: 3 additions & 2 deletions src/main/java/org/broadinstitute/hellbender/tools/funcotator/TranscriptSelectionMode.java
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
package org.broadinstitute.hellbender.tools.funcotator;

import org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation;
import org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGTFFieldConstants;
import org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature;

import java.util.Comparator;
Expand Down Expand Up @@ -246,8 +247,8 @@ public ComparatorByProteinCodingStatus(){}
@Override
public int compare( final GencodeFuncotation a, final GencodeFuncotation b ) {
// Is it protein coding?
final boolean isAProteinCoding = GencodeGtfFeature.KnownGeneBiotype.PROTEIN_CODING.toString().equals(a.getGeneTranscriptType());
final boolean isBProteinCoding = GencodeGtfFeature.KnownGeneBiotype.PROTEIN_CODING.toString().equals(b.getGeneTranscriptType());
final boolean isAProteinCoding = GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString().equals(a.getGeneTranscriptType());
final boolean isBProteinCoding = GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString().equals(b.getGeneTranscriptType());
if ( isAProteinCoding != isBProteinCoding ) {
if ( isAProteinCoding ) {
return -1;
Expand Down
9 changes: 5 additions & 4 deletions ...rg/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotation.java
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Expand Up @@ -7,6 +7,7 @@
import org.broadinstitute.hellbender.tools.funcotator.Funcotation;
import org.broadinstitute.hellbender.tools.funcotator.metadata.FuncotationMetadata;
import org.broadinstitute.hellbender.tools.funcotator.vcfOutput.VcfOutputRenderer;
import org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGTFFieldConstants;
import org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfGeneFeature;

import java.util.Arrays;
Expand Down Expand Up @@ -74,7 +75,7 @@ public class GencodeFuncotation implements Funcotation {

// These are included because they help determine the transcript selection
private Integer locusLevel;
private GencodeGtfGeneFeature.FeatureTag apprisRank;
private GencodeGTFFieldConstants.FeatureTag apprisRank;
private Integer transcriptLength;
private String version;
private String geneTranscriptType;
Expand Down Expand Up @@ -378,7 +379,7 @@ public boolean equals(final Object o) {
if (transcriptLength != null ? !transcriptLength.equals(that.transcriptLength) : that.transcriptLength != null)
return false;
if (version != null ? !version.equals(that.version) : that.version != null) return false;
if (geneTranscriptType != that.geneTranscriptType) return false;
if (geneTranscriptType != that.geneTranscriptType) return false; //TODO this is a problem string equality comparison.... it breaks tests to fix it though...
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if (hugoSymbolSerializedOverride != null ? !hugoSymbolSerializedOverride.equals(that.hugoSymbolSerializedOverride) : that.hugoSymbolSerializedOverride != null)
return false;
if (ncbiBuildSerializedOverride != null ? !ncbiBuildSerializedOverride.equals(that.ncbiBuildSerializedOverride) : that.ncbiBuildSerializedOverride != null)
Expand Down Expand Up @@ -660,11 +661,11 @@ public void setLocusLevel(final Integer locusLevel) {
this.locusLevel = locusLevel;
}

public GencodeGtfGeneFeature.FeatureTag getApprisRank() {
public GencodeGTFFieldConstants.FeatureTag getApprisRank() {
return apprisRank;
}

public void setApprisRank(final GencodeGtfGeneFeature.FeatureTag apprisRank) {
public void setApprisRank(final GencodeGTFFieldConstants.FeatureTag apprisRank) {
this.apprisRank = apprisRank;
}

Expand Down
5 changes: 3 additions & 2 deletions ...dinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationBuilder.java
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Expand Up @@ -5,6 +5,7 @@
import htsjdk.variant.variantcontext.Allele;
import org.broadinstitute.hellbender.exceptions.GATKException;
import org.broadinstitute.hellbender.tools.funcotator.metadata.FuncotationMetadataUtils;
import org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGTFFieldConstants;
import org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfGeneFeature;

import java.util.ArrayList;
Expand Down Expand Up @@ -260,10 +261,10 @@ public GencodeFuncotationBuilder setLocusLevel( final Integer locusLevel ) {

/**
* Set the Appris Rank in the {@link GencodeFuncotation}.
* @param apprisRank The {@link GencodeGtfGeneFeature.FeatureTag} containing the Appris Rank for the {@link GencodeFuncotation}.
* @param apprisRank The {@link GencodeGTFFieldConstants.FeatureTag} containing the Appris Rank for the {@link GencodeFuncotation}.
* @return {@code this} {@link GencodeFuncotationBuilder}
*/
public GencodeFuncotationBuilder setApprisRank( final GencodeGtfGeneFeature.FeatureTag apprisRank ) {
public GencodeFuncotationBuilder setApprisRank( final GencodeGTFFieldConstants.FeatureTag apprisRank ) {
gencodeFuncotation.setApprisRank( apprisRank );
return this;
}
Expand Down
62 changes: 29 additions & 33 deletions ...dinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactory.java
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Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,7 @@
import java.util.regex.Pattern;
import java.util.stream.Collectors;

import static org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag.*;
import static org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGTFFieldConstants.FeatureTag.*;

/**
* A factory to create {@link GencodeFuncotation}s.
Expand Down Expand Up @@ -111,24 +111,22 @@ public class GencodeFuncotationFactory extends DataSourceFuncotationFactory {
/**
* List of valid Appris Ranks used for sorting funcotations to get the "best" one.z
*/
private static final HashSet<GencodeGtfGeneFeature.FeatureTag> apprisRanks = new HashSet<>(
Arrays.asList(
APPRIS_PRINCIPAL,
APPRIS_PRINCIPAL_1,
APPRIS_PRINCIPAL_2,
APPRIS_PRINCIPAL_3,
APPRIS_PRINCIPAL_4,
APPRIS_PRINCIPAL_5,
APPRIS_ALTERNATIVE_1,
APPRIS_ALTERNATIVE_2,
APPRIS_CANDIDATE_HIGHEST_SCORE,
APPRIS_CANDIDATE_LONGEST_CCDS,
APPRIS_CANDIDATE_CCDS,
APPRIS_CANDIDATE_LONGEST_SEQ,
APPRIS_CANDIDATE_LONGEST,
APPRIS_CANDIDATE
)
);
private static final LinkedHashMap<String, GencodeGTFFieldConstants.FeatureTag> apprisRanks = new LinkedHashMap<>() {{
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put(APPRIS_PRINCIPAL.toString(), APPRIS_PRINCIPAL);
put(APPRIS_PRINCIPAL_1.toString(), APPRIS_PRINCIPAL_1);
put(APPRIS_PRINCIPAL_2.toString(), APPRIS_PRINCIPAL_2);
put(APPRIS_PRINCIPAL_3.toString(), APPRIS_PRINCIPAL_3);
put(APPRIS_PRINCIPAL_4.toString(), APPRIS_PRINCIPAL_4);
put(APPRIS_PRINCIPAL_5.toString(), APPRIS_PRINCIPAL_5);
put(APPRIS_ALTERNATIVE_1.toString(), APPRIS_ALTERNATIVE_1);
put(APPRIS_ALTERNATIVE_2.toString(), APPRIS_ALTERNATIVE_2);
put(APPRIS_CANDIDATE_HIGHEST_SCORE.toString(), APPRIS_CANDIDATE_HIGHEST_SCORE);
put(APPRIS_CANDIDATE_LONGEST_CCDS.toString(), APPRIS_CANDIDATE_LONGEST_CCDS);
put(APPRIS_CANDIDATE_CCDS.toString(), APPRIS_CANDIDATE_CCDS);
put(APPRIS_CANDIDATE_LONGEST_SEQ.toString(), APPRIS_CANDIDATE_LONGEST_SEQ);
put(APPRIS_CANDIDATE_LONGEST.toString(), APPRIS_CANDIDATE_LONGEST);
put(APPRIS_CANDIDATE.toString(), APPRIS_CANDIDATE);
}};

/**
* The set of {@link GencodeFuncotation.VariantClassification} types that are valid for coding regions.
Expand Down Expand Up @@ -946,8 +944,7 @@ private static boolean isBasic(final GencodeGtfTranscriptFeature transcript) {
// Check if this transcript has the `basic` tag:
return transcript.getOptionalFields().stream()
.filter( f -> f.getName().equals("tag") )
.filter( f -> f.getValue() instanceof GencodeGtfFeature.FeatureTag )
.filter( f -> f.getValue().equals(GencodeGtfFeature.FeatureTag.BASIC) )
.filter( f -> f.getValue().equals(GencodeGTFFieldConstants.FeatureTag.BASIC.toString()) )
.count() > 0;
}

Expand Down Expand Up @@ -1079,7 +1076,7 @@ private GencodeFuncotation createExonFuncotation(final VariantContext variant,

// Before we get started, check to see if this is a non-protein-coding feature.
// If it is, we must handle it differently:
if ( GencodeGtfFeature.KnownGeneBiotype.PROTEIN_CODING.toString().equals(transcript.getGeneType()) ) {
if ( GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString().equals(transcript.getGeneType()) ) {
return createCodingRegionFuncotationForProteinCodingFeature(variant, altAllele, reference, transcript, exon);
}
else {
Expand Down Expand Up @@ -1700,7 +1697,7 @@ private GencodeFuncotation createIntronFuncotation(final VariantContext variant,
gencodeFuncotationBuilder.setReferenceContext(referenceBases.getBaseString(Strand.POSITIVE));

// Set the VariantClassification:
if ( GencodeGtfFeature.KnownGeneBiotype.PROTEIN_CODING.toString().equals(transcript.getGeneType()) ) {
if ( GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString().equals(transcript.getGeneType()) ) {
gencodeFuncotationBuilder.setVariantClassification(GencodeFuncotation.VariantClassification.INTRON);
}
else {
Expand Down Expand Up @@ -2708,19 +2705,18 @@ else if (altAllele.length() < refAllele.length()) {

/**
* Get the Appris Rank from the given {@link GencodeGtfGeneFeature}.
* Appris ranks are specified as annotations using {@link org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.FeatureTag}s.
* Appris ranks are specified as annotations using {@link GencodeGTFFieldConstants.FeatureTag}s.
* @param gtfFeature The {@link GencodeGtfTranscriptFeature} from which to get the Appris Rank.
* @return The highest Appris Rank found in the given {@code gtfFeature}; if no Appris Rank exists, {@code null}.
*/
@VisibleForTesting
static GencodeGtfFeature.FeatureTag getApprisRank( final GencodeGtfTranscriptFeature gtfFeature ) {
static GencodeGTFFieldConstants.FeatureTag getApprisRank(final GencodeGtfTranscriptFeature gtfFeature ) {

// Get our appris tag(s) if it/they exist(s):
final List<GencodeGtfFeature.FeatureTag> gtfApprisTags = gtfFeature.getOptionalFields().stream()
// Get the Appris Rank tags and convert them to Sortable Enums:
final List<GencodeGTFFieldConstants.FeatureTag> gtfApprisTags = gtfFeature.getOptionalFields().stream()
.filter( f -> f.getName().equals("tag") )
.filter( f -> f.getValue() instanceof GencodeGtfFeature.FeatureTag )
.filter( f -> apprisRanks.contains( f.getValue() ) )
.map( f -> (GencodeGtfFeature.FeatureTag)f.getValue() ).collect(Collectors.toList());
.filter( f -> apprisRanks.containsKey( f.getValue() ) )
.map( f -> apprisRanks.get(f.getValue()) ).collect(Collectors.toList());

if ( gtfApprisTags.isEmpty() ) {
return null;
Expand All @@ -2737,16 +2733,16 @@ else if ( gtfApprisTags.size() == 1 ) {

/**
* Converts a given GeneTranscriptType {@link String} to a {@link org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation.VariantClassification}.
* Assumes the given {@code type} is not {@link GencodeGtfFeature.KnownGeneBiotype#PROTEIN_CODING}.
* Assumes the given {@code type} is not {@link GencodeGTFFieldConstants.KnownGeneBiotype#PROTEIN_CODING}.
* If no type can be assessed, returns {@code null}.
* @param type A {@link String} representing a GeneTranscriptType to convert to a {@link org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation.VariantClassification}.
* @return A {@link org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation.VariantClassification} representing the given GeneTranscriptType {@link String}, or {@code null}.
*/
private static GencodeFuncotation.VariantClassification convertGeneTranscriptTypeToVariantClassification (final String type ) {

//TODO: This all needs to be fixed so there is a 1:1 mapping of GencodeGtfFeature.KnownGeneBiotype->VariantClassification - Issue #4405
if (GencodeGtfFeature.KnownGeneBiotype.LINCRNA.toString().equals(type) ||
GencodeGtfFeature.KnownGeneBiotype.MACRO_LNCRNA.toString().equals(type)) {
if (GencodeGTFFieldConstants.KnownGeneBiotype.LINCRNA.toString().equals(type) ||
GencodeGTFFieldConstants.KnownGeneBiotype.MACRO_LNCRNA.toString().equals(type)) {
return GencodeFuncotation.VariantClassification.LINCRNA;
}
return GencodeFuncotation.VariantClassification.RNA;
Expand Down
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