protected int setCdsAndProteinPosition(int cdnaVariantPosition, int firstCdsPhase, int cdnaCodingStart) { if (cdnaVariantPosition != -1) { // cdnaVariantStart may be null if variantEnd falls in an intron if (transcript.unconfirmedStart()) { cdnaCodingStart -= ((3 - firstCdsPhase) % 3); } int cdsVariantStart = cdnaVariantPosition - cdnaCodingStart + 1; consequenceType.setCdsPosition(cdsVariantStart); // First place where protein variant annotation is added to the Consequence type, // must create the ProteinVariantAnnotation object ProteinVariantAnnotation proteinVariantAnnotation = new ProteinVariantAnnotation(); proteinVariantAnnotation.setPosition(((cdsVariantStart - 1) / 3) + 1); consequenceType.setProteinVariantAnnotation(proteinVariantAnnotation); } return cdnaCodingStart; }
protected int setCdsAndProteinPosition(int cdnaVariantPosition, int firstCdsPhase, int cdnaCodingStart) { if (cdnaVariantPosition != -1) { // cdnaVariantStart may be null if variantEnd falls in an intron if (transcript.unconfirmedStart()) { cdnaCodingStart -= ((3 - firstCdsPhase) % 3); } int cdsVariantStart = cdnaVariantPosition - cdnaCodingStart + 1; consequenceType.setCdsPosition(cdsVariantStart); // First place where protein variant annotation is added to the Consequence type, // must create the ProteinVariantAnnotation object ProteinVariantAnnotation proteinVariantAnnotation = new ProteinVariantAnnotation(); proteinVariantAnnotation.setPosition(((cdsVariantStart - 1) / 3) + 1); consequenceType.setProteinVariantAnnotation(proteinVariantAnnotation); } return cdnaCodingStart; }
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 } }
proteinVariantAnnotation.setPosition(position); proteinVariantAnnotation.setReference(aaReference); proteinVariantAnnotation.setAlternate(aaAlternate);
proteinVariantAnnotation.setPosition(position); proteinVariantAnnotation.setReference(aaReference); proteinVariantAnnotation.setAlternate(aaAlternate);
if (StringUtils.isNotEmpty(fields[13])) { try { protVarAnnotation.setPosition(Integer.parseInt(fields[13])); } catch (NumberFormatException e) { logger.warn("Parsing position: " + e.getMessage());
proteinVariantAnnotation.setPosition(((cdsVariantStart - 1) / 3) + 1); consequenceType.setProteinVariantAnnotation(proteinVariantAnnotation);
proteinVariantAnnotation.setPosition(((cdsVariantStart - 1) / 3) + 1); consequenceType.setProteinVariantAnnotation(proteinVariantAnnotation);
proteinVariantAnnotation.setPosition(((cdsVariantStart - 1) / 3) + 1); consequenceType.setProteinVariantAnnotation(proteinVariantAnnotation);
proteinVariantAnnotation.setPosition(((cdsVariantStart - 1) / 3) + 1); consequenceType.setProteinVariantAnnotation(proteinVariantAnnotation);