Java tutorial
/* * Copyright 2015-2016 OpenCB * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package org.opencb.opencga.storage.hadoop.variant.converters.annotation; import org.apache.commons.lang.StringUtils; import org.apache.hadoop.hbase.client.Put; import org.opencb.biodata.models.variant.Variant; import org.opencb.biodata.models.variant.avro.*; import org.opencb.biodata.tools.variant.converters.Converter; import org.opencb.opencga.storage.hadoop.variant.GenomeHelper; import org.opencb.opencga.storage.hadoop.variant.converters.AbstractPhoenixConverter; import org.opencb.opencga.storage.hadoop.variant.index.phoenix.PhoenixHelper; import org.opencb.opencga.storage.hadoop.variant.index.phoenix.VariantPhoenixHelper; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import java.util.*; import static org.opencb.opencga.storage.hadoop.variant.index.phoenix.VariantPhoenixHelper.VariantColumn.*; /** * Created on 01/12/15. * * @author Jacobo Coll <jacobo167@gmail.com> */ public class VariantAnnotationToHBaseConverter extends AbstractPhoenixConverter implements Converter<VariantAnnotation, Map<PhoenixHelper.Column, ?>> { private final GenomeHelper genomeHelper; private boolean addFullAnnotation = true; public VariantAnnotationToHBaseConverter(GenomeHelper genomeHelper) { super(genomeHelper.getColumnFamily()); this.genomeHelper = genomeHelper; } private final Logger logger = LoggerFactory.getLogger(VariantAnnotationToHBaseConverter.class); @Override public Map<PhoenixHelper.Column, ?> convert(VariantAnnotation variantAnnotation) { HashMap<PhoenixHelper.Column, Object> map = new HashMap<>(); if (addFullAnnotation) { map.put(FULL_ANNOTATION, variantAnnotation.toString()); } Set<String> genes = new HashSet<>(); Set<String> transcripts = new HashSet<>(); Set<String> flags = new HashSet<>(); Set<Integer> so = new HashSet<>(); Set<String> biotype = new HashSet<>(); Set<Double> polyphen = new HashSet<>(); Set<Double> sift = new HashSet<>(); Set<String> polyphenDesc = new HashSet<>(); Set<String> siftDesc = new HashSet<>(); Set<String> geneTraitName = new HashSet<>(); Set<String> geneTraitId = new HashSet<>(); Set<String> hpo = new HashSet<>(); Set<String> drugs = new HashSet<>(); Set<String> proteinKeywords = new HashSet<>(); // Contains all the xrefs, and the id, the geneNames and transcripts Set<String> xrefs = new HashSet<>(); addNotNull(xrefs, variantAnnotation.getId()); for (ConsequenceType consequenceType : variantAnnotation.getConsequenceTypes()) { addNotNull(genes, consequenceType.getGeneName()); addNotNull(genes, consequenceType.getEnsemblGeneId()); addNotNull(transcripts, consequenceType.getEnsemblTranscriptId()); addNotNull(biotype, consequenceType.getBiotype()); addAllNotNull(flags, consequenceType.getTranscriptAnnotationFlags()); for (SequenceOntologyTerm sequenceOntologyTerm : consequenceType.getSequenceOntologyTerms()) { String accession = sequenceOntologyTerm.getAccession(); addNotNull(so, Integer.parseInt(accession.substring(3))); } if (consequenceType.getProteinVariantAnnotation() != null) { if (consequenceType.getProteinVariantAnnotation().getSubstitutionScores() != null) { for (Score score : consequenceType.getProteinVariantAnnotation().getSubstitutionScores()) { if (score.getSource().equalsIgnoreCase("sift")) { addNotNull(sift, score.getScore()); addNotNull(siftDesc, score.getDescription()); } else if (score.getSource().equalsIgnoreCase("polyphen")) { addNotNull(polyphen, score.getScore()); addNotNull(polyphenDesc, score.getDescription()); } } } if (consequenceType.getProteinVariantAnnotation().getKeywords() != null) { proteinKeywords.addAll(consequenceType.getProteinVariantAnnotation().getKeywords()); } addNotNull(xrefs, consequenceType.getProteinVariantAnnotation().getUniprotName()); addNotNull(xrefs, consequenceType.getProteinVariantAnnotation().getUniprotAccession()); addNotNull(xrefs, consequenceType.getProteinVariantAnnotation().getUniprotVariantId()); } } if (variantAnnotation.getVariantTraitAssociation() != null) { if (variantAnnotation.getVariantTraitAssociation().getCosmic() != null) { for (Cosmic cosmic : variantAnnotation.getVariantTraitAssociation().getCosmic()) { addNotNull(xrefs, cosmic.getMutationId()); } } if (variantAnnotation.getVariantTraitAssociation().getClinvar() != null) { for (ClinVar clinVar : variantAnnotation.getVariantTraitAssociation().getClinvar()) { addNotNull(xrefs, clinVar.getAccession()); } } } xrefs.addAll(genes); xrefs.addAll(transcripts); if (variantAnnotation.getXrefs() != null) { for (Xref xref : variantAnnotation.getXrefs()) { addNotNull(xrefs, xref.getId()); } } if (variantAnnotation.getGeneTraitAssociation() != null) { for (GeneTraitAssociation geneTrait : variantAnnotation.getGeneTraitAssociation()) { addNotNull(geneTraitName, geneTrait.getName()); addNotNull(geneTraitId, geneTrait.getId()); addNotNull(hpo, geneTrait.getHpo()); } } xrefs.addAll(hpo); if (variantAnnotation.getGeneDrugInteraction() != null) { for (GeneDrugInteraction drug : variantAnnotation.getGeneDrugInteraction()) { addNotNull(drugs, drug.getDrugName()); } } map.put(CHROMOSOME, variantAnnotation.getChromosome()); map.put(POSITION, variantAnnotation.getStart()); map.put(REFERENCE, variantAnnotation.getReference()); map.put(ALTERNATE, variantAnnotation.getAlternate()); map.put(GENES, genes); map.put(TRANSCRIPTS, transcripts); map.put(BIOTYPE, biotype); map.put(SO, so); map.put(POLYPHEN, sortProteinSubstitutionScores(polyphen)); map.put(POLYPHEN_DESC, polyphenDesc); map.put(SIFT, sortProteinSubstitutionScores(sift)); map.put(SIFT_DESC, siftDesc); map.put(TRANSCRIPTION_FLAGS, flags); map.put(GENE_TRAITS_ID, geneTraitId); map.put(PROTEIN_KEYWORDS, proteinKeywords); map.put(GENE_TRAITS_NAME, geneTraitName); map.put(HPO, hpo); map.put(DRUG, drugs); map.put(XREFS, xrefs); if (variantAnnotation.getConservation() != null) { for (Score score : variantAnnotation.getConservation()) { PhoenixHelper.Column column = VariantPhoenixHelper.getConservationScoreColumn(score.getSource()); map.put(column, score.getScore()); } } if (variantAnnotation.getPopulationFrequencies() != null) { for (PopulationFrequency pf : variantAnnotation.getPopulationFrequencies()) { PhoenixHelper.Column column = VariantPhoenixHelper.getPopulationFrequencyColumn(pf.getStudy(), pf.getPopulation()); map.put(column, Arrays.asList(pf.getRefAlleleFreq(), pf.getAltAlleleFreq())); } } if (variantAnnotation.getFunctionalScore() != null) { for (Score score : variantAnnotation.getFunctionalScore()) { PhoenixHelper.Column column = VariantPhoenixHelper.getFunctionalScoreColumn(score.getSource()); map.put(column, score.getScore()); } } VariantType variantType = Variant.inferType(variantAnnotation.getReference(), variantAnnotation.getAlternate(), variantAnnotation.getReference().length()); if (StringUtils.isNotBlank(variantAnnotation.getId())) { if (variantType.equals(VariantType.SNV)) { variantType = VariantType.SNP; } else if (variantType.equals(VariantType.MNV)) { variantType = VariantType.MNP; } } map.put(TYPE, variantType.toString()); return map; } Put buildPut(VariantAnnotation variantAnnotation, Map<PhoenixHelper.Column, ?> map) { byte[] bytesRowKey = genomeHelper.generateVariantRowKey(variantAnnotation.getChromosome(), variantAnnotation.getStart(), variantAnnotation.getReference(), variantAnnotation.getAlternate()); Put put = new Put(bytesRowKey); map.forEach((column, value) -> add(put, column, value)); return put; } private List<Double> sortProteinSubstitutionScores(Set<Double> scores) { List<Double> sorted = new ArrayList<>(scores.size()); Double min = scores.stream().min(Double::compareTo).orElse(-1.0); Double max = scores.stream().max(Double::compareTo).orElse(-1.0); if (min >= 0) { sorted.add(min); sorted.add(max); scores.remove(min); scores.remove(max); sorted.addAll(scores); } return sorted; } }