@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;
}
