/** * Create and return a new {@link DNASequence} with quality scores from the specified * FASTQ formatted sequence. The quality scores are stored in a {@link QualityFeature} * with a type <code>"qualityScores"</code> the same length as the sequence. * * @param fastq FASTQ formatted sequence, must not be null * @return a new {@link DNASequence} with quality scores from the specified FASTQ formatted sequence * @throws CompoundNotFoundException if DNA sequence in fastq contains unrecognised compounds */ public static DNASequence createDNASequenceWithQualityScores(final Fastq fastq) throws CompoundNotFoundException { DNASequence sequence = createDNASequence(fastq); sequence.addFeature(1, sequence.getLength(), createQualityScores(fastq)); return sequence; }
/** * Create and return a new {@link DNASequence} with quality scores and error probabilities from the * specified FASTQ formatted sequence. The quality scores are stored in a {@link QualityFeature} * with a type <code>"qualityScores"</code> the same length as the sequence and the error * probabilities are stored in a {@link QuantityFeature} with a type <code>"errorProbabilities"</code> * the same length as the sequence. * * @param fastq FASTQ formatted sequence, must not be null * @return a new {@link DNASequence} with quality scores and error probabilities from the specified * FASTQ formatted sequence * @throws CompoundNotFoundException if DNA sequence in fastq contains unrecognised compounds */ public static DNASequence createDNASequenceWithQualityScoresAndErrorProbabilities(final Fastq fastq) throws CompoundNotFoundException { DNASequence sequence = createDNASequence(fastq); sequence.addFeature(1, sequence.getLength(), createQualityScores(fastq)); sequence.addFeature(1, sequence.getLength(), createErrorProbabilities(fastq)); return sequence; }
/** * Create and return a new {@link DNASequence} with error probabilities from the specified * FASTQ formatted sequence. The error probabilities are stored in a {@link QuantityFeature} * with a type <code>"errorProbabilities"</code> the same length as the sequence. * * @param fastq FASTQ formatted sequence, must not be null * @return a new {@link DNASequence} with error probabilities from the specified FASTQ formatted sequence * @throws CompoundNotFoundException if DNA sequence in fastq contains unrecognised compounds */ public static DNASequence createDNASequenceWithErrorProbabilities(final Fastq fastq) throws CompoundNotFoundException { DNASequence sequence = createDNASequence(fastq); sequence.addFeature(1, sequence.getLength(), createErrorProbabilities(fastq)); return sequence; }
genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence); dnaSequence.setAccession(new AccessionID("NM_001126")); logger.info("Sequence ({},{})={}...", dnaSequence.getAccession(), dnaSequence.getLength(), dnaSequence.getSequenceAsString().substring(0, 10)); logger.info("Keywords: {}", genbankDNAReader.getKeyWords()); logger.info("DatabaseReferences: {}", genbankDNAReader.getDatabaseReferences()); dnaSequence = new DNASequence(genbankDNAReader); genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence); logger.info("Sequence ({},{})={}...", dnaSequence.getAccession(), dnaSequence.getLength(), dnaSequence.getSequenceAsString().substring(0, 10)); logger.info("Keywords: {}", genbankDNAReader.getKeyWords()); logger.info("DatabaseReferences: {}", genbankDNAReader.getDatabaseReferences()); dnaSequence = new DNASequence(genbankDNAReader); genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence); logger.info("Sequence ({},{})={}...", dnaSequence.getAccession(), dnaSequence.getLength(), dnaSequence.getSequenceAsString().substring(0, 10)); logger.info("Keywords: {}", genbankDNAReader.getKeyWords()); logger.info("DatabaseReferences: {}", genbankDNAReader.getDatabaseReferences()); dnaSequence = new DNASequence(genbankDNAReader); genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence); logger.info("Sequence ({},{})={}...", dnaSequence.getAccession(), dnaSequence.getLength(), dnaSequence.getSequenceAsString().substring(0, 10)); logger.info("Keywords: {}", genbankDNAReader.getKeyWords()); logger.info("DatabaseReferences: {}", genbankDNAReader.getDatabaseReferences()); dnaSequence = new DNASequence(genbankDNAReader); genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence); logger.info("Sequence ({},{})={}...", dnaSequence.getAccession(), dnaSequence.getLength(), dnaSequence.getSequenceAsString().substring(0, 10)); logger.info("Keywords: {}", genbankDNAReader.getKeyWords()); logger.info("DatabaseReferences: {}", genbankDNAReader.getDatabaseReferences());
genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence); dnaSequence.setAccession(new AccessionID("NM_001126")); logger.info("Sequence ({},{})={}...", dnaSequence.getAccession(), dnaSequence.getLength(), dnaSequence.getSequenceAsString().substring(0, 10)); logger.info("Keywords: {}", genbankDNAReader.getKeyWords()); logger.info("DatabaseReferences: {}", genbankDNAReader.getDatabaseReferences()); dnaSequence = new DNASequence(genbankDNAReader); genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence); logger.info("Sequence ({},{})={}...", dnaSequence.getAccession(), dnaSequence.getLength(), dnaSequence.getSequenceAsString().substring(0, 10)); logger.info("Keywords: {}", genbankDNAReader.getKeyWords()); logger.info("DatabaseReferences: {}", genbankDNAReader.getDatabaseReferences()); dnaSequence = new DNASequence(genbankDNAReader); genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence); logger.info("Sequence ({},{})={}...", dnaSequence.getAccession(), dnaSequence.getLength(), dnaSequence.getSequenceAsString().substring(0, 10)); logger.info("Keywords: {}", genbankDNAReader.getKeyWords()); logger.info("DatabaseReferences: {}", genbankDNAReader.getDatabaseReferences()); dnaSequence = new DNASequence(genbankDNAReader); genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence); logger.info("Sequence ({},{})={}...", dnaSequence.getAccession(), dnaSequence.getLength(), dnaSequence.getSequenceAsString().substring(0, 10)); logger.info("Keywords: {}", genbankDNAReader.getKeyWords()); logger.info("DatabaseReferences: {}", genbankDNAReader.getDatabaseReferences()); dnaSequence = new DNASequence(genbankDNAReader); genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence); logger.info("Sequence ({},{})={}...", dnaSequence.getAccession(), dnaSequence.getLength(), dnaSequence.getSequenceAsString().substring(0, 10)); logger.info("Keywords: {}", genbankDNAReader.getKeyWords()); logger.info("DatabaseReferences: {}", genbankDNAReader.getDatabaseReferences());