@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; }
/** * Add into to a hash * * @param hits * @param marker * @param hit2add * @param showGeneDetails * @param compareTemplate */ void regionsAddHit( HashSet<String> hits, Marker hit2add, Marker marker, boolean showGeneDetails, boolean compareTemplate) { String hitStr = hit2add.getClass().getSimpleName(); if (compareTemplate) { Gene gene = (Gene) hit2add.findParent(Gene.class); if (gene != null) hitStr += (hit2add.isStrandPlus() == marker.isStrandPlus()) ? "_TEMPLATE_STRAND" : "_NON_TEMPLATE_STRAND"; } if (showGeneDetails && (hit2add instanceof Gene)) { Gene gene = (Gene) hit2add; hitStr += "[" + gene.getBioType() + ", " + gene.getGeneName() + ", " + (gene.isProteinCoding() ? "protein" : "not-protein") + "]"; } hits.add(hitStr); // Add marker name to the list }
public String toString(boolean useSeqOntology, boolean useHgvs) { // Get data to show String geneId = "", geneName = "", bioType = "", transcriptId = "", exonId = "", customId = ""; int exonRank = -1; if (marker != null) { // Gene Id, name and biotype Gene gene = getGene(); Transcript tr = getTranscript(); // CDS size info if (gene != null) { geneId = gene.getId(); geneName = gene.getGeneName(); bioType = getBiotype(); } // Update trId if (tr != null) transcriptId = tr.getId(); // Exon rank information Exon exon = getExon(); if (exon != null) { exonId = exon.getId(); exonRank = exon.getRank(); } // Regulation if (isRegulation()) bioType = ((Regulation) marker).getCellType(); } // Add seqChage's ID if (!variant.getId().isEmpty()) customId += variant.getId(); // Add custom markers if ((marker != null) && (marker instanceof Custom)) customId += (customId.isEmpty() ? "" : ";") + marker.getId(); // CDS length int cdsSize = getCdsLength(); String errWarn = error + (error.isEmpty() ? "" : "|") + warning; String aaChange = ""; if (useHgvs) aaChange = getHgvs(); else aaChange = ((aaRef.length() + aaAlt.length()) > 0 ? aaRef + "/" + aaAlt : ""); return errWarn // + "\t" + geneId // + "\t" + geneName // + "\t" + bioType // + "\t" + transcriptId // + "\t" + exonId // + "\t" + (exonRank >= 0 ? exonRank : "") // + "\t" + effect(false, false, false, useSeqOntology) // + "\t" + aaChange // + "\t" + ((codonsRef.length() + codonsAlt.length()) > 0 ? codonsRef + "/" + codonsAlt : "") // + "\t" + (codonNum >= 0 ? (codonNum + 1) : "") // + "\t" + (codonDegeneracy >= 0 ? codonDegeneracy + "" : "") // + "\t" + (cdsSize >= 0 ? cdsSize : "") // + "\t" + (codonsAroundOld.length() > 0 ? codonsAroundOld + " / " + codonsAroundNew : "") // + "\t" + (aasAroundOld.length() > 0 ? aasAroundOld + " / " + aasAroundNew : "") // + "\t" + customId // ; }