for (String accession : dnaSequenceList.keySet()) { DNASequence contigSequence = dnaSequenceList.get(accession); ChromosomeSequence chromsomeSequence = new ChromosomeSequence(contigSequence.getSequenceAsString()); chromsomeSequence.setAccession(contigSequence.getAccession()); chromosomeSequenceList.put(accession, chromsomeSequence); GeneSequence geneSeq = chromosomeSequence.addGene(new AccessionID(geneaccession), bioStart, bioEnd, strand); geneSeq.addNote(note); geneSeq.setSource(uppercaseFastaFile.getName());
static public LinkedHashMap<String, GeneSequence> getGeneSequences(Collection<ChromosomeSequence> chromosomeSequences) throws Exception { LinkedHashMap<String, GeneSequence> geneSequenceHashMap = new LinkedHashMap<String, GeneSequence>(); for (ChromosomeSequence chromosomeSequence : chromosomeSequences) { for (GeneSequence geneSequence : chromosomeSequence.getGeneSequences().values()) { geneSequenceHashMap.put(geneSequence.getAccession().getID(), geneSequence); } } return geneSequenceHashMap; }
static public LinkedHashMap<String, ChromosomeSequence> getChromosomeSequenceFromDNASequence(LinkedHashMap<String, DNASequence> dnaSequenceList) { LinkedHashMap<String, ChromosomeSequence> chromosomeSequenceList = new LinkedHashMap<String, ChromosomeSequence>(); for (String key : dnaSequenceList.keySet()) { DNASequence dnaSequence = dnaSequenceList.get(key); ChromosomeSequence chromosomeSequence = new ChromosomeSequence(dnaSequence.getProxySequenceReader()); //we want the underlying sequence but don't need storage chromosomeSequence.setAccession(dnaSequence.getAccession()); chromosomeSequenceList.put(key, chromosomeSequence); } return chromosomeSequenceList; }
public static void main(String[] args) { try { ArrayList<GeneSequence> sequences = new ArrayList<GeneSequence>(); ChromosomeSequence seq1 = new ChromosomeSequence("ATATATATATATATATATATATATATATATATACGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCATATATATATATATATATATATACGCGCGCGCGCGCGCGCATATATATATATATATATATATATATATATATACGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCATATATATATATATATATATATACGCGCGCGCGCGCGCGC"); GeneSequence gene1 = seq1.addGene(new AccessionID("gene1"), 1, 20, Strand.POSITIVE); gene1.addExon(new AccessionID("t1_1_10"), 1, 10); gene1.addExon(new AccessionID("t1_12_15"), 12, 15); GeneSequence gene2 = seq1.addGene(new AccessionID("gene2"), 1, 20, Strand.NEGATIVE); gene2.addExon(new AccessionID("t2_1_10"), 1, 10); gene2.addExon(new AccessionID("t2_12_15"), 12, 15); sequences.add(gene1); sequences.add(gene2); FastaGeneWriter fastaWriter = new FastaGeneWriter(System.out, sequences, new GenericFastaHeaderFormat<GeneSequence, NucleotideCompound>(), true); fastaWriter.process(); } catch (Exception e) { logger.warn("Exception: ", e); } } }
geneSequence = seq.addGene(geneAccessionID, startCodonBegin, stopCodonEnd, strand); geneSequence.setSource(((Feature) feature).source()); } else {
String scaffold = geneSequence.getParentChromosomeSequence().getAccession().getID();
public static void main(String[] args) { try { ArrayList<GeneSequence> sequences = new ArrayList<GeneSequence>(); ChromosomeSequence seq1 = new ChromosomeSequence("ATATATATATATATATATATATATATATATATACGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCATATATATATATATATATATATACGCGCGCGCGCGCGCGCATATATATATATATATATATATATATATATATACGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCATATATATATATATATATATATACGCGCGCGCGCGCGCGC"); GeneSequence gene1 = seq1.addGene(new AccessionID("gene1"), 1, 20, Strand.POSITIVE); gene1.addExon(new AccessionID("t1_1_10"), 1, 10); gene1.addExon(new AccessionID("t1_12_15"), 12, 15); GeneSequence gene2 = seq1.addGene(new AccessionID("gene2"), 1, 20, Strand.NEGATIVE); gene2.addExon(new AccessionID("t2_1_10"), 1, 10); gene2.addExon(new AccessionID("t2_12_15"), 12, 15); sequences.add(gene1); sequences.add(gene2); FastaGeneWriter fastaWriter = new FastaGeneWriter(System.out, sequences, new GenericFastaHeaderFormat<GeneSequence, NucleotideCompound>(), true); fastaWriter.process(); } catch (Exception e) { logger.warn("Exception: ", e); } } }
geneSequence = seq.addGene(geneAccessionID, startCodonBegin, stopCodonEnd, strand); geneSequence.setSource(source);
geneSequence = seq.addGene(geneAccessionID, startCodonBegin, stopCodonEnd, strand); geneSequence.setSource(((Feature) feature).source()); } else {
static public LinkedHashMap<String, ProteinSequence> getProteinSequences(Collection<ChromosomeSequence> chromosomeSequences) throws Exception { LinkedHashMap<String, ProteinSequence> proteinSequenceHashMap = new LinkedHashMap<String, ProteinSequence>(); for (ChromosomeSequence dnaSequence : chromosomeSequences) { for (GeneSequence geneSequence : dnaSequence.getGeneSequences().values()) { for (TranscriptSequence transcriptSequence : geneSequence.getTranscripts().values()) { //TODO remove? // DNASequence dnaCodingSequence = transcriptSequence.getDNACodingSequence(); // logger.info("CDS={}", dnaCodingSequence.getSequenceAsString()); try { ProteinSequence proteinSequence = transcriptSequence.getProteinSequence(); // logger.info("{} {}", proteinSequence.getAccession().getID(), proteinSequence); if (proteinSequenceHashMap.containsKey(proteinSequence.getAccession().getID())) { throw new Exception("Duplicate protein sequence id=" + proteinSequence.getAccession().getID() + " found at Gene id=" + geneSequence.getAccession().getID()); } else { proteinSequenceHashMap.put(proteinSequence.getAccession().getID(), proteinSequence); } } catch (Exception e) { logger.error("Exception: ", e); } } } } return proteinSequenceHashMap; }
for (GeneSequence geneSequence : chromosomeSequence.getGeneSequences().values()) { gff3line = key + "\t" + geneSequence.getSource() + "\t" + "gene" + "\t" + geneSequence.getBioBegin() + "\t" + geneSequence.getBioEnd() + "\t"; Double score = geneSequence.getSequenceScore();