@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;
}
