Esempio n. 1
0
  /**
   * Process a single {@link SequenceFile}
   *
   * @param sequenceFile file to process
   * @throws FileProcessorException if an error occurs while processing
   */
  private void processSingleFile(SequenceFile sequenceFile) throws FileProcessorException {
    Path fileToProcess = sequenceFile.getFile();
    AnalysisFastQC.AnalysisFastQCBuilder analysis =
        AnalysisFastQC.builder()
            .executionManagerAnalysisId(EXECUTION_MANAGER_ANALYSIS_ID)
            .description(
                messageSource.getMessage(
                    "fastqc.file.processor.analysis.description",
                    null,
                    LocaleContextHolder.getLocale()));
    try {
      uk.ac.babraham.FastQC.Sequence.SequenceFile fastQCSequenceFile =
          SequenceFactory.getSequenceFile(fileToProcess.toFile());
      BasicStats basicStats = new BasicStats();
      PerBaseQualityScores pbqs = new PerBaseQualityScores();
      PerSequenceQualityScores psqs = new PerSequenceQualityScores();
      OverRepresentedSeqs overRep = new OverRepresentedSeqs();
      QCModule[] moduleList = new QCModule[] {basicStats, pbqs, psqs, overRep};

      logger.debug("Launching FastQC analysis modules on all sequences.");
      while (fastQCSequenceFile.hasNext()) {
        Sequence sequence = fastQCSequenceFile.next();
        for (QCModule module : moduleList) {
          module.processSequence(sequence);
        }
      }

      logger.debug("Finished FastQC analysis modules.");
      handleBasicStats(basicStats, analysis);
      handlePerBaseQualityScores(pbqs, analysis);
      handlePerSequenceQualityScores(psqs, analysis);
      handleDuplicationLevel(overRep.duplicationLevelModule(), analysis);
      Set<OverrepresentedSequence> overrepresentedSequences =
          handleOverRepresentedSequences(overRep);

      logger.trace("Saving FastQC analysis.");
      analysis.overrepresentedSequences(overrepresentedSequences);

      sequenceFile.setFastQCAnalysis(analysis.build());

      sequenceFileRepository.save(sequenceFile);
    } catch (Exception e) {
      logger.error("FastQC failed to process the sequence file. Stack trace follows.", e);
      throw new FileProcessorException("FastQC failed to parse the sequence file.", e);
    }
  }
Esempio n. 2
0
  /**
   * Handle getting over represented sequences from fastqc.
   *
   * @param seqs overrepresented sequences.
   * @return a collection of {@link OverrepresentedSequence} corresponding to the FastQC {@link
   *     OverRepresentedSeqs}.
   */
  private Set<OverrepresentedSequence> handleOverRepresentedSequences(OverRepresentedSeqs seqs) {

    OverrepresentedSeq[] sequences = seqs.getOverrepresentedSequences();
    if (sequences == null) {
      return Collections.emptySet();
    }

    Set<OverrepresentedSequence> overrepresentedSequences = new HashSet<>(sequences.length);

    for (OverrepresentedSeq s : sequences) {
      String sequenceString = s.seq();
      int count = s.count();
      BigDecimal percent = BigDecimal.valueOf(s.percentage());
      String possibleSource = s.contaminantHit();

      overrepresentedSequences.add(
          new OverrepresentedSequence(sequenceString, count, percent, possibleSource));
    }
    return overrepresentedSequences;
  }