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Alter PathogenicityData 'get' prefixed methods to remove the 'get' e.…
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…g. getPredictedPathogenicityScores() is now pathogenicityScores(), getPredictedScore(PathogenicitySource source) -> pathogenicityScore(PathogenicitySource source), getScore() -> pathogenicityScore()
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@julesjacobsen
julesjacobsen committed Feb 13, 2024
1 parent 12731b5 commit 099175c
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Showing 18 changed files with 102 additions and 102 deletions.
14 changes: 7 additions & 7 deletions ...java/org/monarchinitiative/exomiser/core/analysis/util/acmg/Acmg2015EvidenceAssigner.java
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Expand Up @@ -172,7 +172,7 @@ public AcmgEvidence assignVariantAcmgEvidence(VariantEvaluation variantEvaluatio
assignPP4(acmgEvidenceBuilder, compatibleDiseaseMatches);

PathogenicityData pathogenicityData = variantEvaluation.getPathogenicityData();
ClinVarData clinVarData = variantEvaluation.getPathogenicityData().getClinVarData();
ClinVarData clinVarData = variantEvaluation.getPathogenicityData().clinVarData();
if (!clinVarData.isEmpty()) {
// PP5 "Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation"
assignPP5(acmgEvidenceBuilder, clinVarData);
Expand Down Expand Up @@ -281,7 +281,7 @@ private void assignPM3orBP2(AcmgEvidence.Builder acmgEvidenceBuilder, VariantEva
if (contributingVariants.size() >= 2 && contributingVariants.contains(variantEvaluation)) {
for (VariantEvaluation otherVariant : contributingVariants) {
SampleGenotype otherVariantGenotype = otherVariant.getSampleGenotype(probandId);
ClinVarData otherClinVarData = otherVariant.getPathogenicityData().getClinVarData();
ClinVarData otherClinVarData = otherVariant.getPathogenicityData().clinVarData();
if (otherClinVarData.getPrimaryInterpretation() == ClinVarData.ClinSig.PATHOGENIC && !otherVariant.equals(variantEvaluation)) {
// X = this variant, P = other pathogenic variant
boolean inTrans = inTrans(thisVariantGenotype, otherVariantGenotype);
Expand Down Expand Up @@ -487,7 +487,7 @@ private void assignPP3orBP4(AcmgEvidence.Builder acmgEvidenceBuilder, Pathogenic
// classification and ClinGen recommendations for clinical use of PP3/BP4 criteria"
// https://www.biorxiv.org/content/10.1101/2022.03.17.484479v1
//
var revelScore = pathogenicityData.getPredictedScore(PathogenicitySource.REVEL);
var revelScore = pathogenicityData.pathogenicityScore(PathogenicitySource.REVEL);
if (revelScore != null) {
assignRevelBasedPP3BP4Classification(acmgEvidenceBuilder, revelScore);
} else {
Expand Down Expand Up @@ -538,18 +538,18 @@ else if (revel > 0.183f && revel <= 0.290f) {
private void assignEnsembleBasedPP3BP4Classification(AcmgEvidence.Builder acmgEvidenceBuilder, PathogenicityData pathogenicityData) {
int numBenign = 0;
int numPathogenic = 0;
List<PathogenicityScore> predictedPathogenicityScores = pathogenicityData.getPredictedPathogenicityScores();
for (PathogenicityScore pathogenicityScore : predictedPathogenicityScores) {
List<PathogenicityScore> pathogenicityScores = pathogenicityData.pathogenicityScores();
for (PathogenicityScore pathogenicityScore : pathogenicityScores) {
if (isPathogenic(pathogenicityScore)) {
numPathogenic++;
} else {
numBenign++;
}
}
if (predictedPathogenicityScores.size() > 1 && numPathogenic > numBenign) {
if (pathogenicityScores.size() > 1 && numPathogenic > numBenign) {
acmgEvidenceBuilder.add(PP3);
}
if (predictedPathogenicityScores.size() > 1 && numBenign > numPathogenic) {
if (pathogenicityScores.size() > 1 && numBenign > numPathogenic) {
acmgEvidenceBuilder.add(BP4);
}
}
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4 changes: 2 additions & 2 deletions ...core/src/main/java/org/monarchinitiative/exomiser/core/genome/VariantDataServiceImpl.java
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Expand Up @@ -147,7 +147,7 @@ public PathogenicityData getVariantPathogenicityData(Variant variant, Set<Pathog
}
for (CompletableFuture<PathogenicityData> pathogenicityDataCompletableFuture : futurePathData) {
PathogenicityData pathogenicityData = pathogenicityDataCompletableFuture.join();
allPathScores.addAll(pathogenicityData.getPredictedPathogenicityScores());
allPathScores.addAll(pathogenicityData.pathogenicityScores());
}
defaultPathogenicityData = futureDefaultData.join();
} else {
Expand All @@ -173,7 +173,7 @@ private boolean containsTabixSource(Set<PathogenicitySource> pathogenicitySource
}

private void addAllWantedScores(Set<PathogenicitySource> pathogenicitySources, PathogenicityData defaultPathogenicityData, List<PathogenicityScore> allPathScores) {
for (PathogenicityScore score : defaultPathogenicityData.getPredictedPathogenicityScores()) {
for (PathogenicityScore score : defaultPathogenicityData.pathogenicityScores()) {
if (pathogenicitySources.contains(score.getSource())) {
allPathScores.add(score);
}
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4 changes: 2 additions & 2 deletions exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/VariantEvaluation.java
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Expand Up @@ -379,8 +379,8 @@ public float getPathogenicityScore() {
if (whiteListed) {
return 1f;
}
float predictedScore = pathogenicityData.getScore();
float variantEffectScore = VariantEffectPathogenicityScore.getPathogenicityScoreOf(variantEffect);
float predictedScore = pathogenicityData.pathogenicityScore();
float variantEffectScore = VariantEffectPathogenicityScore.pathogenicityScoreOf(variantEffect);
if (this.isSymbolic()) {
// SvAnna scoring https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-022-01046-6/tables/1
// | element contains v
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2 changes: 1 addition & 1 deletion ...core/src/main/java/org/monarchinitiative/exomiser/core/model/frequency/FrequencyData.java
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Expand Up @@ -155,7 +155,7 @@ public boolean containsFrequencySource(FrequencySource frequencySource) {
}

@Nullable
public Frequency frequencyForSource(FrequencySource source) {
public Frequency frequency(FrequencySource source) {
int i = frequencySourceIndex(source);
return i < 0 ? null : frequency(i);
}
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16 changes: 8 additions & 8 deletions .../main/java/org/monarchinitiative/exomiser/core/model/pathogenicity/PathogenicityData.java
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Expand Up @@ -98,7 +98,7 @@ private PathogenicityData(ClinVarData clinVarData, Collection<PathogenicityScore
* @return a {@code ClinVarData} object
* @since 10.1.0
*/
public ClinVarData getClinVarData() {
public ClinVarData clinVarData() {
return clinVarData;
}

Expand All @@ -112,7 +112,7 @@ public boolean hasClinVarData() {
return !clinVarData.isEmpty();
}

public List<PathogenicityScore> getPredictedPathogenicityScores() {
public List<PathogenicityScore> pathogenicityScores() {
return new ArrayList<>(pathogenicityScores.values());
}

Expand All @@ -136,27 +136,27 @@ public boolean hasPredictedScore(PathogenicitySource pathogenicitySource) {
* @param pathogenicitySource
* @return
*/
public PathogenicityScore getPredictedScore(PathogenicitySource pathogenicitySource) {
public PathogenicityScore pathogenicityScore(PathogenicitySource pathogenicitySource) {
return pathogenicityScores.get(pathogenicitySource);
}

/**
* @return the predicted pathogenicity score for this data set. The score is ranked from 0 (non-pathogenic) to 1 (highly pathogenic)
*/
public float getScore() {
public float pathogenicityScore() {
if (pathogenicityScores.isEmpty()) {
return VariantEffectPathogenicityScore.NON_PATHOGENIC_SCORE;
}
return getPredictedPathScore();
return maxPredictedPathScore();
}

private float getPredictedPathScore() {
private float maxPredictedPathScore() {
// Once upon a time we used score-specific cutoffs. These are present in the score classes:
// Mutation Taster: >0.95 assumed pathogenic, prediction categories not shown
// Polyphen2 (HVAR): "D" (> 0.956,probably damaging), "P": [0.447-0.955], possibly damaging, and "B", <0.447, benign.
// SIFT: "D"<0.05, damaging and "T">0.05, tolerated
// TODO: re-implement this and add isPredictedPathogenic() to the PathogenicityScore
PathogenicityScore mostPathogenicPredictedScore = getMostPathogenicScore();
PathogenicityScore mostPathogenicPredictedScore = mostPathogenicScore();
if (mostPathogenicPredictedScore != null) {
// As of v12.0.0 scores are normalised internally so SIFT scores no longer need to be inverted here.
return mostPathogenicPredictedScore.getScore();
Expand All @@ -168,7 +168,7 @@ private float getPredictedPathScore() {
* @return The most pathogenic score or null if there are no predicted scores
*/
@Nullable
public PathogenicityScore getMostPathogenicScore() {
public PathogenicityScore mostPathogenicScore() {
// Add filter step using PathogenicityScore::isPredictedPathogenic?
// n.b. here min() is referring to the *first* element in a sorted list, rather than the minimum numeric value
// PathogenicityScore compareTo returns the most pathogenic first e.g. 1.0, 0.9, 0.8 ... which is the reverse of
Expand Down
2 changes: 1 addition & 1 deletion .../monarchinitiative/exomiser/core/model/pathogenicity/VariantEffectPathogenicityScore.java
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Expand Up @@ -84,7 +84,7 @@ private VariantEffectPathogenicityScore() {
//Uninstantiable. This class should be an enum, but then it doesn't code nicely :(
}

public static float getPathogenicityScoreOf(VariantEffect variantEffect) {
public static float pathogenicityScoreOf(VariantEffect variantEffect) {
switch (variantEffect) {
case SEQUENCE_VARIANT:
return NON_PATHOGENIC_SCORE;
Expand Down
6 changes: 3 additions & 3 deletions ...re/src/main/java/org/monarchinitiative/exomiser/core/writers/TsvVariantResultsWriter.java
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Expand Up @@ -163,7 +163,7 @@ private List<Object> buildVariantRecord(int rank, VariantEvaluation ve, GeneScor
fields.add(assignment.map(acmgAssignment -> acmgAssignment.disease().getDiseaseId()).orElse(""));
fields.add(assignment.map(acmgAssignment -> acmgAssignment.disease().getDiseaseName()).orElse(""));
PathogenicityData pathogenicityData = ve.getPathogenicityData();
ClinVarData clinVarData = pathogenicityData.getClinVarData();
ClinVarData clinVarData = pathogenicityData.clinVarData();
fields.add(clinVarData.getVariationId());
fields.add(clinVarData.getPrimaryInterpretation());
fields.add(clinVarData.starRating());
Expand All @@ -175,10 +175,10 @@ private List<Object> buildVariantRecord(int rank, VariantEvaluation ve, GeneScor
fields.add(maxFreq == null ? "" : maxFreq.source());
fields.add(maxFreq == null ? "" : maxFreq.frequency());
fields.add(toVcfFreqInfo(frequencyData.frequencies()));
PathogenicityScore maxPath = pathogenicityData.getMostPathogenicScore();
PathogenicityScore maxPath = pathogenicityData.mostPathogenicScore();
fields.add(maxPath == null ? "" : maxPath.getSource());
fields.add(maxPath == null ? "" : maxPath.getScore());
fields.add(toVcfPathInfo(pathogenicityData.getPredictedPathogenicityScores()));
fields.add(toVcfPathInfo(pathogenicityData.pathogenicityScores()));
return fields;
}

Expand Down
8 changes: 4 additions & 4 deletions exomiser-core/src/main/resources/templates/results.html
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Expand Up @@ -378,10 +378,10 @@ <h4>Variant Score: <b
<dd th:each="mostPathogenicScore: ${pathogenicityData.mostPathogenicScore}"
th:text="${#strings.prepend(mostPathogenicScore.score, 'Best Score: ')}">1.00
</dd>
<dd th:if="${#lists.isEmpty(pathogenicityData.predictedPathogenicityScores)}">No
<dd th:if="${#lists.isEmpty(pathogenicityData.pathogenicityScores)}">No
pathogenicity data
</dd>
<dd th:each="pathScore: ${pathogenicityData.predictedPathogenicityScores}"
<dd th:each="pathScore: ${pathogenicityData.pathogenicityScores}"
th:text="${pathScore}">Mutation Taster: 0.999 (P)
</dd>
</dl>
Expand Down Expand Up @@ -519,10 +519,10 @@ <h4>Variant Score: <b
<dd th:each="mostPathogenicScore: ${pathogenicityData.mostPathogenicScore}"
th:text="${#strings.prepend(mostPathogenicScore.score, 'Best Score: ')}">1.00
</dd>
<dd th:if="${#lists.isEmpty(pathogenicityData.predictedPathogenicityScores)}">No
<dd th:if="${#lists.isEmpty(pathogenicityData.pathogenicityScores)}">No
pathogenicity data
</dd>
<dd th:each="pathScore: ${pathogenicityData.predictedPathogenicityScores}"
<dd th:each="pathScore: ${pathogenicityData.pathogenicityScores}"
th:text="${pathScore}">Mutation Taster: 0.999 (P)
</dd>
</dl>
Expand Down
6 changes: 3 additions & 3 deletions ...core/src/test/java/org/monarchinitiative/exomiser/core/genome/TestVariantDataService.java
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Expand Up @@ -111,12 +111,12 @@ public FrequencyData getVariantFrequencyData(Variant variant, Set<FrequencySourc
public PathogenicityData getVariantPathogenicityData(Variant variant, Set<PathogenicitySource> pathogenicitySources) {
PathogenicityData pathData = expectedPathogenicityData.getOrDefault(variant, PathogenicityData.empty());

List<PathogenicityScore> wanted = pathData.getPredictedPathogenicityScores()
List<PathogenicityScore> wanted = pathData.pathogenicityScores()
.stream()
.filter(pathogenicity -> pathogenicitySources.contains(pathogenicity.getSource()))
.collect(Collectors.toList());
.toList();

return PathogenicityData.of(pathData.getClinVarData(), wanted);
return PathogenicityData.of(pathData.clinVarData(), wanted);
}

public static Builder builder() {
Expand Down
2 changes: 1 addition & 1 deletion .../src/test/java/org/monarchinitiative/exomiser/core/genome/VariantDataServiceImplTest.java
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Expand Up @@ -147,7 +147,7 @@ public void serviceReturnsSpecifiedPathogenicityDataForMissenseVariant() {
public void serviceReturnsCaddDataForMissenseVariant() {
variant = buildVariantOfType(VariantEffect.MISSENSE_VARIANT);
PathogenicityData result = instance.getVariantPathogenicityData(variant, EnumSet.of(PathogenicitySource.CADD));
assertThat(result, equalTo(PathogenicityData.of(PATH_CLINVAR_DATA, CADD_DATA.getPredictedScore(PathogenicitySource.CADD))));
assertThat(result, equalTo(PathogenicityData.of(PATH_CLINVAR_DATA, CADD_DATA.pathogenicityScore(PathogenicitySource.CADD))));
}

@Test
Expand Down
2 changes: 1 addition & 1 deletion ...c/test/java/org/monarchinitiative/exomiser/core/genome/VariantFactoryPerformanceTest.java
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Expand Up @@ -180,7 +180,7 @@ private Consumer<VariantEvaluation> printVariant() {
variantEvaluation.getTranscriptAnnotations().get(0).getHgvsCdna(),
variantEvaluation.getVariantScore(),
variantEvaluation.getFrequencyScore(), variantEvaluation.getFrequencyData().maxFreq(),
variantEvaluation.getPathogenicityScore(), variantEvaluation.getPathogenicityData().getPredictedPathogenicityScores()
variantEvaluation.getPathogenicityScore(), variantEvaluation.getPathogenicityData().pathogenicityScores()
);
}

Expand Down
2 changes: 1 addition & 1 deletion ...e/src/test/java/org/monarchinitiative/exomiser/core/genome/dao/ClinVarDaoMvStoreTest.java
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Expand Up @@ -287,7 +287,7 @@ void manualDataExplorer() {
if (pathogenicityData.isEmpty()) {
System.out.println("\t-");
} else {
pathogenicityData.getPredictedPathogenicityScores().forEach(path -> System.out.println("\t" + path));
pathogenicityData.pathogenicityScores().forEach(path -> System.out.println("\t" + path));
}
}

Expand Down
2 changes: 1 addition & 1 deletion .../src/test/java/org/monarchinitiative/exomiser/core/genome/dao/SvPathogenicityDaoTest.java
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Expand Up @@ -57,6 +57,6 @@ class SvPathogenicityDaoTest {
void getPathogenicityData(int chr, int start, int end, String alt, int changeLength, ClinVarData.ClinSig expected) {
Variant variant = TestFactory.variantBuilder(chr, start, end, "", alt, changeLength).build();
PathogenicityData result = instance.getPathogenicityData(variant);
assertThat(result.getClinVarData().getPrimaryInterpretation(), equalTo(expected));
assertThat(result.clinVarData().getPrimaryInterpretation(), equalTo(expected));
}
}
6 changes: 3 additions & 3 deletions ...r-core/src/test/java/org/monarchinitiative/exomiser/core/model/VariantEvaluationTest.java
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Expand Up @@ -379,7 +379,7 @@ public void testGetPathogenicityScoreNonMissenseVariantNoPredictions() {
VariantEffect type = VariantEffect.DOWNSTREAM_GENE_VARIANT;
instance = testVariantBuilder().variantEffect(type).build();

float expected = VariantEffectPathogenicityScore.getPathogenicityScoreOf(type);
float expected = VariantEffectPathogenicityScore.pathogenicityScoreOf(type);
assertThat(instance.getPathogenicityScore(), equalTo(expected));
}

Expand All @@ -389,15 +389,15 @@ public void testGetPathogenicityScoreNonMissenseVariantWithPredictions() {
PathogenicityData pathData = PathogenicityData.of(CaddScore.of(1f));
instance = testVariantBuilder().pathogenicityData(pathData).variantEffect(type).build();

assertThat(instance.getPathogenicityScore(), equalTo(pathData.getScore()));
assertThat(instance.getPathogenicityScore(), equalTo(pathData.pathogenicityScore()));
}

@Test
public void testGetPathogenicityScoreMissenseVariantNoPredictions() {
VariantEffect type = VariantEffect.MISSENSE_VARIANT;
instance = testVariantBuilder().variantEffect(type).build();

float expected = VariantEffectPathogenicityScore.getPathogenicityScoreOf(type);
float expected = VariantEffectPathogenicityScore.pathogenicityScoreOf(type);
assertThat(instance.getPathogenicityScore(), equalTo(expected));
}

Expand Down
14 changes: 7 additions & 7 deletions .../src/test/java/org/monarchinitiative/exomiser/core/model/frequency/FrequencyDataTest.java
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Expand Up @@ -114,37 +114,37 @@ public void testGetRsId() {

@Test
public void testGetNonExistentFrequency() {
assertThat(EMPTY_DATA.frequencyForSource(THOUSAND_GENOMES), equalTo(null));
assertThat(EMPTY_DATA.frequency(THOUSAND_GENOMES), equalTo(null));
}

@Test
public void testGetDbSnpMaf() {
assertThat(FREQUENCY_DATA.frequencyForSource(THOUSAND_GENOMES), equalTo(DBSNP_PASS));
assertThat(FREQUENCY_DATA.frequency(THOUSAND_GENOMES), equalTo(DBSNP_PASS));
}

@Test
public void testGetEspEaMaf() {
assertThat(FREQUENCY_DATA.frequencyForSource(ESP_EA), equalTo(ESP_EA_PASS));
assertThat(FREQUENCY_DATA.frequency(ESP_EA), equalTo(ESP_EA_PASS));
}

@Test
public void testGetEspAaMaf() {
assertThat(FREQUENCY_DATA.frequencyForSource(ESP_AA), equalTo(ESP_AA_PASS));
assertThat(FREQUENCY_DATA.frequency(ESP_AA), equalTo(ESP_AA_PASS));
}

@Test
public void testGetEspAllMaf() {
assertThat(FREQUENCY_DATA.frequencyForSource(ESP_ALL), equalTo(ESP_ALL_PASS));
assertThat(FREQUENCY_DATA.frequency(ESP_ALL), equalTo(ESP_ALL_PASS));
}

@Test
public void testGetFrequencyForUnavailableSource() {
assertThat(FREQUENCY_DATA.frequencyForSource(GNOMAD_E_NFE), equalTo(null));
assertThat(FREQUENCY_DATA.frequency(GNOMAD_E_NFE), equalTo(null));
}

@Test
public void testGetFrequencyForUnavailableSourceBefore() {
assertThat(FREQUENCY_DATA.frequencyForSource(UNKNOWN), equalTo(null));
assertThat(FREQUENCY_DATA.frequency(UNKNOWN), equalTo(null));
}

@Test
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