@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 //
;
}