@Override
protected Void doInBackground() throws Exception {
int count = 0;
String sep = "\t";
try {
PrintWriter writer = new PrintWriter(file);
writer.write("Feature_Number" + sep);
writer.write("Location" + sep);
writer.write("Gene_name" + sep);
writer.write("Gene_accession" + sep);
writer.write("Gene_Location" + sep);
writer.write("distance_to_tss" + "\n");
for (Region r : feature.getRegions()) {
Peak peak = (Peak) r;
String chrom = peak.chrom;
if (geneData.hasKey(chrom)) {
int index = geneData.getNCList(chrom).getOverlapIndex(peak);
Vector<Region> preGenes = new Vector<Region>();
Vector<Region> nearGenes;
Vector<Region> postGenes = new Vector<Region>();
if (index > 0) {
preGenes = geneData.getNCList(chrom).getRegionsAt(index - 1);
}
nearGenes = geneData.getNCList(chrom).getRegionsAt(index);
if (index + 1 < geneData.getNCList(chrom).size()) {
postGenes = geneData.getNCList(chrom).getRegionsAt(index + 1);
}
nearGenes.addAll(preGenes);
nearGenes.addAll(postGenes);
Gene nearestGene = null;
long min_dist = Long.MAX_VALUE;
for (Region testPeak : nearGenes) {
// print(testPeak.getClass().toString());
Gene g = (Gene) testPeak;
long dist = getDistToTss(peak, g);
if (dist < min_dist) {
min_dist = dist;
nearestGene = (Gene) testPeak;
}
} // end for, each close gene.
writer.write(count + sep);
writer.write(peak.getLocationString() + sep);
writer.write(nearestGene.getName() + sep);
writer.write(nearestGene.getAccession() + sep);
writer.write(nearestGene.getLocationString() + sep);
writer.write(min_dist + "\n");
} // end if, has same chromosome key
++count;
} // end for, each peak region
writer.close();
} catch (Exception ex) {
ex.printStackTrace();
}
return null;
}
