String codons() {
char seq[] = chromoSequence.toCharArray();
char seqNew[] = chromoNewSequence.toCharArray();
codonsOld = "";
codonsNew = "";
int codonIdx = 0;
int i = 0;
int step = transcript.isStrandPlus() ? 1 : -1;
char codonOld[] = new char[3];
char codonNew[] = new char[3];
for (Exon ex : transcript.sortedStrand()) {
int start = ex.isStrandPlus() ? ex.getStart() : ex.getEnd();
for (i = start; ex.intersects(i); i += step, codonIdx = (codonIdx + 1) % 3) {
codonOld[codonIdx] = seq[i];
codonNew[codonIdx] = seqNew[i];
if (codonIdx == 2) addIfDiff(codonOld, codonNew);
}
}
for (; codonIdx != 0; i += step, codonIdx = (codonIdx + 1) % 3) {
codonOld[codonIdx] = 'N';
codonNew[codonIdx] = 'N';
if (codonIdx == 2) addIfDiff(codonOld, codonNew);
}
return codonsOld + "/" + codonsNew;
}
/**
* Find the last position where a nonsense mediated decay is supposed to occurr This is 50 bases
* (MND_BASES_BEFORE_LAST_JUNCTION bases) before the last exon-exon junction.
*
* @param tr
* @return
*/
public int lastNmdPos(Transcript tr) {
// ---
// Get last exon
// ---
int cdsEnd = tr.getCdsEnd();
int cdsStart = tr.getCdsStart();
Marker cds =
new Marker(
tr.getChromosome(),
Math.min(cdsStart, cdsEnd),
Math.max(cdsStart, cdsEnd),
tr.getStrand(),
""); // Create a cds marker
Exon lastExon = null;
int countCodingExons = 0;
for (Exon exon : tr.sortedStrand()) {
if (exon.intersects(cdsEnd)) lastExon = exon;
if (cds.intersects(exon)) countCodingExons++;
}
// Only one coding exon? => No NMD
// Note: I'm assuming that we should have a splice event in a coding part of the transcript for
// NMD to happen.
if (countCodingExons <= 1) return -1;
// Sanity check
if (lastExon == null)
throw new RuntimeException(
"Cannot find last coding exon for transcript '"
+ tr.getId()
+ "' (cdsEnd: "
+ cdsEnd
+ ")\n\t"
+ tr);
// ---
// Find that position of MND_BASES_BEFORE_LAST_JUNCTION before the last exon-exon junction
// ---
int lastExonJunction = tr.isStrandPlus() ? lastExon.getStart() : lastExon.getEnd();
int chrPos[] = tr.baseNumberCds2Pos();
int lastNmdPos = -1;
for (int cdsi = chrPos.length - 1; cdsi >= 0; cdsi--) {
if (chrPos[cdsi] == lastExonJunction) {
if (cdsi > MND_BASES_BEFORE_LAST_JUNCTION)
lastNmdPos = chrPos[cdsi - MND_BASES_BEFORE_LAST_JUNCTION - 1];
else return tr.isStrandPlus() ? 0 : Integer.MAX_VALUE; // Out of CDS range
return lastNmdPos;
}
}
throw new RuntimeException(
"Cannot find last exon junction position for transcript '" + tr.getId() + "'\n\t" + tr);
// return -1;
}