for (String accession : dnaSequenceList.keySet()) { DNASequence contigSequence = dnaSequenceList.get(accession); ChromosomeSequence chromsomeSequence = new ChromosomeSequence(contigSequence.getSequenceAsString()); chromsomeSequence.setAccession(contigSequence.getAccession()); chromosomeSequenceList.put(accession, chromsomeSequence); String geneSequence = dnaSequence.getSequenceAsString(); String lcGeneSequence = geneSequence.toLowerCase(); String reverseGeneSequence = dnaSequence.getReverse().getSequenceAsString(); accession = id; contigDNASequence = dnaSequenceList.get(id); String contigSequence = contigDNASequence.getSequenceAsString().toLowerCase(); bioStart = contigSequence.indexOf(lcGeneSequence); if (bioStart != -1) {
seq = sequence.getSequence5PrimeTo3Prime().getSequenceAsString(); if (showExonUppercase) { StringBuilder sb = new StringBuilder(seq.toLowerCase());
seq = sequence.getSequence5PrimeTo3Prime().getSequenceAsString(); if (showExonUppercase) { StringBuilder sb = new StringBuilder(seq.toLowerCase());
logger.info("Coding Sequence: {}", codingSequence.getSequenceAsString()); logger.info("Sequence agreement error"); logger.info("CDS seq={}", testSequence);
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());