private void parseRemainingFields(ConsequenceType consequenceType, String[] lineFields) { consequenceType.setEnsemblGeneId(lineFields[3]); // fill Ensembl gene id consequenceType.setEnsemblTranscriptId(lineFields[4]); // fill Ensembl transcript id ProteinVariantAnnotation proteinVariantAnnotation = new ProteinVariantAnnotation(); if(!lineFields[7].equals("-")) { consequenceType.setCdnaPosition(parseStringInterval(lineFields[7])); // fill cdna position } if(!lineFields[8].equals("-")) { consequenceType.setCdsPosition(parseStringInterval(lineFields[8])); // fill cds position } if(!lineFields[9].equals("-")) { proteinVariantAnnotation.setPosition(parseStringInterval(lineFields[9])); // fill aa position } if(!lineFields[10].equals("-")) { String parts[] = lineFields[10].split("/"); if(parts.length == 2) { proteinVariantAnnotation.setReference(parts[0]); // fill aa change proteinVariantAnnotation.setAlternate(parts[1]); // fill aa change } } consequenceType.setProteinVariantAnnotation(proteinVariantAnnotation); consequenceType.setCodon(lineFields[11]); // fill codon change if(!lineFields[6].equals("") && !lineFields.equals("-")) { // VEP may leave this field empty consequenceType.setSequenceOntologyTerms( getSequenceOntologyTerms(Arrays.asList(lineFields[6].split(",")))); // fill so terms // consequenceType.setSoTermsFromSoNames(Arrays.asList(lineFields[6].split(","))); // fill so terms } }
consequenceType.setEnsemblTranscriptId(fields[1]); consequenceType.setBiotype(fields[2]); consequenceType.setEnsemblGeneId(""); consequenceType.setGeneName(""); consequenceType.setEnsemblTranscriptId(""); consequenceType.setSequenceOntologyTerms(Collections.singletonList(sequenceOntologyTerm)); consequenceTypes.add(consequenceType);
consequenceType.setGeneName(gene.getName()); consequenceType.setEnsemblGeneId(gene.getId()); consequenceType.setEnsemblTranscriptId(transcript.getId()); consequenceType.setStrand(transcript.getStrand()); consequenceType.setBiotype(transcript.getBiotype());
consequenceType.setGeneName(gene.getName()); consequenceType.setEnsemblGeneId(gene.getId()); consequenceType.setEnsemblTranscriptId(transcript.getId()); consequenceType.setStrand(transcript.getStrand()); consequenceType.setBiotype(transcript.getBiotype());
consequenceType.setGeneName(gene.getName()); consequenceType.setEnsemblGeneId(gene.getId()); consequenceType.setEnsemblTranscriptId(transcript.getId()); consequenceType.setStrand(transcript.getStrand()); consequenceType.setBiotype(transcript.getBiotype());
consequenceType.setGeneName(gene.getName()); consequenceType.setEnsemblGeneId(gene.getId()); consequenceType.setEnsemblTranscriptId(transcript.getId()); consequenceType.setStrand(transcript.getStrand()); consequenceType.setBiotype(transcript.getBiotype());
consequenceType.setGeneName(gene.getName()); consequenceType.setEnsemblGeneId(gene.getId()); consequenceType.setEnsemblTranscriptId(transcript.getId()); consequenceType.setStrand(transcript.getStrand()); consequenceType.setBiotype(transcript.getBiotype());
consequenceType.setGeneName(gene.getName()); consequenceType.setEnsemblGeneId(gene.getId()); consequenceType.setEnsemblTranscriptId(transcript.getId()); consequenceType.setStrand(transcript.getStrand()); consequenceType.setBiotype(transcript.getBiotype());
consequenceType.setGeneName(gene.getName()); consequenceType.setEnsemblGeneId(gene.getId()); consequenceType.setEnsemblTranscriptId(transcript.getId()); consequenceType.setStrand(transcript.getStrand()); consequenceType.setBiotype(transcript.getBiotype());
consequenceType.setGeneName(gene.getName()); consequenceType.setEnsemblGeneId(gene.getId()); consequenceType.setEnsemblTranscriptId(transcript.getId()); consequenceType.setStrand(transcript.getStrand()); consequenceType.setBiotype(transcript.getBiotype());
consequenceType.setGeneName(gene.getName()); consequenceType.setEnsemblGeneId(gene.getId()); consequenceType.setEnsemblTranscriptId(transcript.getId()); consequenceType.setStrand(transcript.getStrand()); consequenceType.setBiotype(transcript.getBiotype());
consequenceType.setGeneName(gene.getName()); consequenceType.setEnsemblGeneId(gene.getId()); consequenceType.setEnsemblTranscriptId(transcript.getId()); consequenceType.setStrand(transcript.getStrand()); consequenceType.setBiotype(transcript.getBiotype());
consequenceType.setGeneName(gene.getName()); consequenceType.setEnsemblGeneId(gene.getId()); consequenceType.setEnsemblTranscriptId(transcript.getId()); consequenceType.setStrand(transcript.getStrand()); consequenceType.setBiotype(transcript.getBiotype());
consequenceType.setGeneName(gene.getName()); consequenceType.setEnsemblGeneId(gene.getId()); consequenceType.setEnsemblTranscriptId(transcript.getId()); consequenceType.setStrand(transcript.getStrand()); consequenceType.setBiotype(transcript.getBiotype());
consequenceType.setGeneName(gene.getName()); consequenceType.setEnsemblGeneId(gene.getId()); consequenceType.setEnsemblTranscriptId(transcript.getId()); consequenceType.setStrand(transcript.getStrand()); consequenceType.setBiotype(transcript.getBiotype());
consequenceType.setGeneName(gene.getName()); consequenceType.setEnsemblGeneId(gene.getId()); consequenceType.setEnsemblTranscriptId(transcript.getId()); consequenceType.setStrand(transcript.getStrand()); consequenceType.setBiotype(transcript.getBiotype());