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app: update protein manager and DB adaptor to retreive protein substi…
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…tution predictions (sift, polyphen, revel and alphamissense), #TASK-TASK-5421, #TASK-5388
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@jtarraga
jtarraga committed Jan 12, 2024
1 parent bbabc8d commit a4bbb37
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Showing 2 changed files with 43 additions and 74 deletions.
98 changes: 43 additions & 55 deletions cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/ProteinMongoDBAdaptor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -18,11 +18,13 @@

import com.mongodb.BasicDBList;
import com.mongodb.client.model.Filters;
import com.mongodb.client.model.Projections;
import org.apache.commons.collections4.CollectionUtils;
import org.apache.commons.lang3.StringUtils;
import org.bson.Document;
import org.bson.conversions.Bson;
import org.opencb.biodata.formats.protein.uniprot.v202003jaxb.Entry;
import org.opencb.biodata.models.core.ProteinSubstitutionPrediction;
import org.opencb.biodata.models.core.ProteinSubstitutionPredictionScore;
import org.opencb.biodata.models.variant.avro.ProteinFeature;
import org.opencb.biodata.models.variant.avro.ProteinVariantAnnotation;
import org.opencb.biodata.models.variant.avro.Score;
Expand All @@ -34,7 +36,7 @@
import org.opencb.cellbase.core.result.CellBaseDataResult;
import org.opencb.cellbase.lib.iterator.CellBaseIterator;
import org.opencb.cellbase.lib.iterator.CellBaseMongoDBIterator;
import org.opencb.cellbase.lib.variant.VariantAnnotationUtils;
import org.opencb.commons.datastore.core.DataResult;
import org.opencb.commons.datastore.core.Query;
import org.opencb.commons.datastore.core.QueryOptions;
import org.opencb.commons.datastore.core.QueryParam;
Expand Down Expand Up @@ -90,69 +92,55 @@ private void init() {
logger.debug("ProteinMongoDBAdaptor: in 'constructor'");

mongoDBCollectionByRelease = buildCollectionByReleaseMap("protein");
proteinSubstitutionMongoDBCollectionByRelease = buildCollectionByReleaseMap("protein_functional_prediction");
proteinSubstitutionMongoDBCollectionByRelease = buildCollectionByReleaseMap("protein_substitution_predictions");
}

public CellBaseDataResult<Score> getSubstitutionScores(TranscriptQuery query, Integer position, String aa) throws CellBaseException {
CellBaseDataResult result = null;
public CellBaseDataResult<Score> getSubstitutionScores(TranscriptQuery query, Integer aaPosition, String aa) throws CellBaseException {
long dbTimeStart = System.currentTimeMillis();
Map<String, Score> scoreSet = new HashMap<>();

// transcriptId, aaPosition, aaAlternate are needed for this collection
if (query.getTranscriptsId() != null && query.getTranscriptsId().get(0) != null && aaPosition != null
&& StringUtils.isNotEmpty(aa)) {

// Ensembl transcript id is needed for this collection
if (query.getTranscriptsId() != null && query.getTranscriptsId().get(0) != null) {
String transcriptId = query.getTranscriptsId().get(0).split("\\.")[0];
Bson transcript = Filters.eq("transcriptId", transcriptId);
MongoDBCollection mongoDBCollection = getCollectionByRelease(proteinSubstitutionMongoDBCollectionByRelease,
query.getDataRelease());

String aaShortName = null;
// If position and aa change are provided we create a 'projection' to return only the required data from the database
if (position != null) {
String projectionString = "aaPositions." + position;

// If aa change is provided we only return that information
if (StringUtils.isNotEmpty(aa)) {
aaShortName = aaShortNameMap.get(aa.toUpperCase());
projectionString += "." + aaShortName;
}

// Projection is used to minimize the returned data
Bson positionProjection = Projections.include(projectionString);
result = new CellBaseDataResult<>(mongoDBCollection.find(transcript, positionProjection, query.toQueryOptions()));
} else {
// Return the whole transcript data
result = new CellBaseDataResult<>(mongoDBCollection.find(transcript, query.toQueryOptions()));
}

if (result != null && !result.getResults().isEmpty()) {
Document document = (Document) result.getResults().get(0);
Document aaPositionsDocument = (Document) document.get("aaPositions");

// Position or aa change were not provided, returning whole transcript data
if (position == null || position == -1 || aaShortName == null) {
// Return only the inner Document, not the whole document projected
result.setResults(Collections.singletonList(aaPositionsDocument));
// Position and aa were provided, return only corresponding Score objects
} else {
List<Score> scoreList = null;
if (result.getNumResults() == 1 && aaPositionsDocument != null) {
scoreList = new ArrayList<>(NUM_PROTEIN_SUBSTITUTION_SCORE_METHODS);
Document positionDocument = (Document) aaPositionsDocument.get(Integer.toString(position));
Document aaDocument = (Document) positionDocument.get(aaShortName);
if (aaDocument.get("ss") != null) {
scoreList.add(new Score(Double.parseDouble("" + aaDocument.get("ss")),
"sift", VariantAnnotationUtils.SIFT_DESCRIPTIONS.get(aaDocument.get("se"))));
}
if (aaDocument.get("ps") != null) {
scoreList.add(new Score(Double.parseDouble("" + aaDocument.get("ps")),
"polyphen", VariantAnnotationUtils.POLYPHEN_DESCRIPTIONS.get(aaDocument.get("pe"))));
List<Bson> andBsonList = new ArrayList<>();
// Sanity check, protein substitution predictions do not contain the transcript ID version
String transcriptId = query.getTranscriptsId().get(0).split("\\.")[0];
andBsonList.add(Filters.eq("transcriptId", transcriptId));
andBsonList.add(Filters.eq("aaPosition", aaPosition));
String aaAlternate = aaShortNameMap.get(aa.toUpperCase());
andBsonList.add(Filters.eq("scores.aaAlternate", aaAlternate));
Bson bson = Filters.and(andBsonList);

System.out.println("transcriptId = " + transcriptId + ", aaPosition = " + aaPosition + ", aa = " + aa + ", aaAlternate = "
+ aaAlternate);

DataResult<ProteinSubstitutionPrediction> predictions = mongoDBCollection.find(bson, null, ProteinSubstitutionPrediction.class,
new QueryOptions());

if (predictions != null && CollectionUtils.isNotEmpty(predictions.getResults())) {
for (ProteinSubstitutionPrediction prediction : predictions.getResults()) {
for (ProteinSubstitutionPredictionScore predictionScore : prediction.getScores()) {
System.out.println("predictionScore = " + predictionScore.toString());
if (StringUtils.isNotEmpty(predictionScore.getAaAlternate()) && StringUtils.isNotEmpty(aaAlternate)
&& predictionScore.getAaAlternate().equals(aaAlternate)) {
String key = prediction.getSource() + ":" + predictionScore.getScore() + ":" + predictionScore.getEffect();
if (!scoreSet.containsKey(key)) {
Score score = new Score(predictionScore.getScore(), prediction.getSource(), predictionScore.getEffect());
scoreSet.put(key, score);
}
}
}
result.setResults(scoreList);
}
}
}
// Return null if no transcript id is provided
return result;

int dbTime = Long.valueOf(System.currentTimeMillis() - dbTimeStart).intValue();
return new CellBaseDataResult<>("getSubstitutionScores", dbTime, new ArrayList<>(), scoreSet.size(),
new ArrayList<>(scoreSet.values()), scoreSet.size());
}

// public CellBaseDataResult<Score> getSubstitutionScores(Query query, QueryOptions options) {
Expand Down Expand Up @@ -231,12 +219,12 @@ public CellBaseDataResult<ProteinVariantAnnotation> getVariantAnnotation(String
// Stop_gain/lost variants do not have SIFT/POLYPHEN scores
// System.out.println("aaReference = " + aaReference);
// System.out.println("aaAlternate = " + aaAlternate);
if (!aaAlternate.equals("STOP") && !aaReference.equals("STOP")) {
// if (!aaAlternate.equals("STOP") && !aaReference.equals("STOP")) {
TranscriptQuery query = new TranscriptQuery();
query.setTranscriptsId(Collections.singletonList(ensemblTranscriptId));
query.setDataRelease(dataRelease);
proteinVariantAnnotation.setSubstitutionScores(getSubstitutionScores(query, position, aaAlternate).getResults());
}
// }

CellBaseDataResult proteinVariantData;
String shortAlternativeAa = aaShortNameMap.get(aaAlternate);
Expand Down
19 changes: 0 additions & 19 deletions cellbase-lib/src/main/java/org/opencb/cellbase/lib/managers/ProteinManager.java
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Original file line number Diff line number Diff line change
Expand Up @@ -18,9 +18,7 @@

import com.fasterxml.jackson.core.JsonProcessingException;
import org.opencb.biodata.formats.protein.uniprot.v202003jaxb.Entry;
import org.opencb.biodata.models.core.MissenseVariantFunctionalScore;
import org.opencb.biodata.models.core.Transcript;
import org.opencb.biodata.models.core.TranscriptMissenseVariantFunctionalScore;
import org.opencb.biodata.models.variant.Variant;
import org.opencb.biodata.models.variant.avro.ProteinVariantAnnotation;
import org.opencb.biodata.models.variant.avro.Score;
Expand Down Expand Up @@ -105,30 +103,13 @@ public CellBaseDataResult<ProteinVariantAnnotation> getVariantAnnotation(Variant
int dataRelease) throws CellBaseException {
CellBaseDataResult<ProteinVariantAnnotation> proteinVariantAnnotation = proteinDBAdaptor.getVariantAnnotation(ensemblTranscriptId,
aaPosition, aaReference, aaAlternate, options, dataRelease);
CellBaseDataResult<TranscriptMissenseVariantFunctionalScore> revelResults =
missenseVariationFunctionalScoreMongoDBAdaptor.getScores(
variant.getChromosome(), variant.getStart(), variant.getReference(), variant.getAlternate(),
aaReference, aaAlternate, dataRelease);
if (proteinVariantAnnotation.getResults() != null && revelResults.getResults() != null) {
if (proteinVariantAnnotation.getResults().get(0).getSubstitutionScores() == null) {
proteinVariantAnnotation.getResults().get(0).setSubstitutionScores(new ArrayList<>());
}
proteinVariantAnnotation.getResults().get(0).getSubstitutionScores().add(
new Score(revelResults.first().getScore(), "revel", ""));
}
return proteinVariantAnnotation;
}

public CellBaseDataResult<Object> getProteinSubstitutionRawData(List<String> transcriptIds, CellBaseQueryOptions options,
int dataRelease) throws CellBaseException {
return proteinDBAdaptor.getProteinSubstitutionRawData(transcriptIds, options, dataRelease);
}

public CellBaseDataResult<MissenseVariantFunctionalScore> getMissenseVariantFunctionalScores(String chromosome, List<Integer> positions,
CellBaseQueryOptions options,
int dataRelease) throws CellBaseException {
return missenseVariationFunctionalScoreMongoDBAdaptor.getScores(chromosome, positions, options, dataRelease);
}
}


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