@Override public boolean run() { for (Gene g : config.getSnpEffectPredictor().getGenome().getGenes()) { // System.out.println(g.getGeneName()); for (Transcript tr : g) { if (!tr.isProteinCoding()) continue; if (tr.introns().size() < 2) continue; // System.out.println("\t" + tr.getId()); for (Intron i : tr.introns()) { int pos = i.getStart() + (int) (Math.random() * (i.size() - 2)) + 1; String line = i.getChromosomeName() + "\t" + pos + "\t.\tA\tT\t.\t.\tAC=1;GENE=" + g.getGeneName() + ";TR=" + tr.getId() + ";INTRON=" + i.getRank(); System.out.println(line); sb.append(line + "\n"); } } } Gpr.toFile(Gpr.HOME + "/introns_test.vcf", sb); return true; }
/** * Name of the regions hit by a marker * * @param marker * @param showGeneDetails * @param compareTemplate * @param id : Only use genes or transcripts matching this ID * @return */ public Set<String> regions( Marker marker, boolean showGeneDetails, boolean compareTemplate, String id) { if (Config.get().isErrorOnMissingChromo() && isChromosomeMissing(marker)) throw new RuntimeEOFException("Chromosome missing for marker: " + marker); boolean hitChromo = false; HashSet<String> hits = new HashSet<String>(); Markers intersects = query(marker); if (intersects.size() > 0) { for (Marker markerInt : intersects) { if (markerInt instanceof Chromosome) { hitChromo = true; // OK (we have to hit a chromosome, otherwise it's an error hits.add(markerInt.getClass().getSimpleName()); // Add marker name to the list } else if (markerInt instanceof Gene) { // Analyze Genes Gene gene = (Gene) markerInt; regionsAddHit(hits, gene, marker, showGeneDetails, compareTemplate); // For all transcripts... for (Transcript tr : gene) { if ((id == null) || gene.getId().equals(id) || tr.getId().equals(id)) { // Mathes ID? (...or no ID to match) // Does it intersect this transcript? if (tr.intersects(marker)) { regionsAddHit(hits, tr, marker, showGeneDetails, compareTemplate); // Does it intersect a UTR? for (Utr utr : tr.getUtrs()) if (utr.intersects(marker)) regionsAddHit(hits, utr, marker, showGeneDetails, compareTemplate); // Does it intersect an exon? for (Exon ex : tr) if (ex.intersects(marker)) regionsAddHit(hits, ex, marker, showGeneDetails, compareTemplate); // Does it intersect an intron? for (Intron intron : tr.introns()) if (intron.intersects(marker)) regionsAddHit(hits, intron, marker, showGeneDetails, compareTemplate); } } } } else { // No ID to match? if (id == null) regionsAddHit(hits, markerInt, marker, showGeneDetails, compareTemplate); else { // Is ID from transcript? Transcript tr = (Transcript) markerInt.findParent(Transcript.class); if ((tr != null) && (tr.getId().equals(id))) { regionsAddHit( hits, markerInt, marker, showGeneDetails, compareTemplate); // Transcript ID matches => count } else { // Is ID from gene? Gene gene = (Gene) markerInt.findParent(Gene.class); if ((gene != null) && (gene.getId().equals(id))) regionsAddHit( hits, markerInt, marker, showGeneDetails, compareTemplate); // Gene ID matches => count } } } } } if (!hitChromo) throw new RuntimeException("ERROR: Out of chromosome range. " + marker); return hits; }