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Merge pull request #92 from apriltuesday/EVA-2479
EVA-2479 - Consume ENA sequence report
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src/main/java/uk/ac/ebi/eva/contigalias/datasource/ENAAssemblyDataSource.java
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| /* | ||
| * Copyright 2021 EMBL - European Bioinformatics Institute | ||
| * | ||
| * 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. | ||
| */ | ||
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|
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| package uk.ac.ebi.eva.contigalias.datasource; | ||
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| import org.springframework.beans.factory.annotation.Autowired; | ||
| import org.springframework.stereotype.Repository; | ||
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| import uk.ac.ebi.eva.contigalias.dus.ENAAssemblyReportReader; | ||
| import uk.ac.ebi.eva.contigalias.dus.ENAAssemblyReportReaderFactory; | ||
| import uk.ac.ebi.eva.contigalias.dus.ENABrowser; | ||
| import uk.ac.ebi.eva.contigalias.dus.ENABrowserFactory; | ||
| import uk.ac.ebi.eva.contigalias.entities.AssemblyEntity; | ||
| import uk.ac.ebi.eva.contigalias.entities.ChromosomeEntity; | ||
| import uk.ac.ebi.eva.contigalias.entities.ScaffoldEntity; | ||
| import uk.ac.ebi.eva.contigalias.entities.SequenceEntity; | ||
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| import java.io.IOException; | ||
| import java.io.InputStream; | ||
| import java.util.HashMap; | ||
| import java.util.List; | ||
| import java.util.Map; | ||
| import java.util.Optional; | ||
| import java.util.stream.Stream; | ||
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| @Repository("ENADataSource") | ||
| public class ENAAssemblyDataSource implements AssemblyDataSource { | ||
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| private final ENABrowserFactory factory; | ||
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| private final ENAAssemblyReportReaderFactory readerFactory; | ||
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| @Autowired | ||
| public ENAAssemblyDataSource(ENABrowserFactory factory, | ||
| ENAAssemblyReportReaderFactory readerFactory) { | ||
| this.factory = factory; | ||
| this.readerFactory = readerFactory; | ||
| } | ||
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| @Override | ||
| public Optional<AssemblyEntity> getAssemblyByAccession(String accession) throws IOException { | ||
| ENABrowser enaBrowser = factory.build(); | ||
| enaBrowser.connect(); | ||
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| AssemblyEntity assemblyEntity; | ||
| try (InputStream stream = enaBrowser.getAssemblyReportInputStream(accession)) { | ||
| ENAAssemblyReportReader reader = readerFactory.build(stream); | ||
| assemblyEntity = reader.getAssemblyEntity(); | ||
| } finally { | ||
| enaBrowser.disconnect(); | ||
| } | ||
| return Optional.of(assemblyEntity); | ||
| } | ||
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| /** | ||
| * Adds ENA sequence names to chromosomes and scaffolds in an assembly. Will modify the AssemblyEntity in-place. | ||
| * | ||
| * @param optional {@link AssemblyEntity} to add ENA sequence names to | ||
| * @throws IOException Passes IOException thrown by {@link #getAssemblyByAccession(String)} | ||
| */ | ||
| public void addENASequenceNamesToAssembly(Optional<AssemblyEntity> optional) throws IOException { | ||
| if (optional.isPresent()) { | ||
| AssemblyEntity targetAssembly = optional.get(); | ||
| if (!hasAllEnaSequenceNames(targetAssembly)) { | ||
| String genbank = targetAssembly.getGenbank(); | ||
| Optional<AssemblyEntity> enaAssembly = getAssemblyByAccession(genbank); | ||
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| if (enaAssembly.isPresent()) { | ||
| AssemblyEntity sourceAssembly = enaAssembly.get(); | ||
| addENASequenceNames(sourceAssembly.getChromosomes(), targetAssembly.getChromosomes()); | ||
| addENASequenceNames(sourceAssembly.getScaffolds(), targetAssembly.getScaffolds()); | ||
| } | ||
| } | ||
| } | ||
| } | ||
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| public boolean hasAllEnaSequenceNames(AssemblyEntity assembly) { | ||
| List<ChromosomeEntity> chromosomes = assembly.getChromosomes(); | ||
| List<ScaffoldEntity> scaffolds = assembly.getScaffolds(); | ||
| return Stream.concat(chromosomes.stream(), scaffolds.stream()) | ||
| .allMatch(sequence -> sequence.getEnaSequenceName() != null); | ||
| } | ||
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| private void addENASequenceNames( | ||
| List<? extends SequenceEntity> sourceSequences, List<? extends SequenceEntity> targetSequences) { | ||
| Map<String, SequenceEntity> genbankToSequenceEntity = new HashMap<>(); | ||
| for (SequenceEntity targetSeq : targetSequences) { | ||
| genbankToSequenceEntity.put(targetSeq.getGenbank(), targetSeq); | ||
| } | ||
| for (SequenceEntity sourceSeq : sourceSequences) { | ||
| String sourceGenbank = sourceSeq.getGenbank(); | ||
| if (genbankToSequenceEntity.containsKey(sourceGenbank)) { | ||
| genbankToSequenceEntity.get(sourceGenbank).setEnaSequenceName(sourceSeq.getEnaSequenceName()); | ||
| } else { | ||
| genbankToSequenceEntity.put(sourceGenbank, sourceSeq); | ||
| } | ||
| } | ||
| } | ||
| } |
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