/**
* Gather data from transcript
*
* @param isoformRef
* @param aaStart
* @param aaEnd
* @param sequence
* @param subSeq
* @return
*/
TranscriptData transcriptData(
String isoformRef, int aaStart, int aaEnd, String sequence, String subSeq) {
String trId = trIdByUniqueName.get(isoformRef);
TranscriptData trData = new TranscriptData();
if (trId != null) {
Transcript tr = trById.get(trId);
if (tr != null) {
trData.tr = tr;
String protein = tr.protein();
// Remove trailing stop codon ('*')
if (!protein.isEmpty() && (protein.charAt(protein.length() - 1) == '*'))
protein = protein.substring(0, protein.length() - 1);
// Sanity check: Do protein sequences match?
if (protein.equals(sequence)) {
proteinOk.add(trId);
if ((aaStart >= 0) && (aaEnd >= aaStart)) {
// Try to map to chromosome position
int cdsBase2Pos[] = tr.cdsBaseNumber2ChrPos();
int codonStart = aaStart * 3;
int codonEnd = (aaEnd + 1) * 3 - 1;
if (tr.isStrandPlus()) {
trData.chrPosStart = cdsBase2Pos[codonStart];
trData.chrPosEnd = cdsBase2Pos[codonEnd];
} else {
trData.chrPosStart = cdsBase2Pos[codonEnd];
trData.chrPosEnd = cdsBase2Pos[codonStart];
}
trData.chrName = tr.getChromosomeName();
// More sanity checks
trData.codon = tr.cds().substring(codonStart, codonEnd + 1);
trData.aa = CodonTables.getInstance().aa(trData.codon, genome, trData.chrName);
if (!subSeq.equals(trData.aa))
Timer.showStdErr(
"WARNING: AA differ: " //
+ "\tUniqueName"
+ isoformRef //
+ "\tEnsembl ID: "
+ trId //
+ "\tEnsembl AA: "
+ trData.aa //
+ "\tNextProt AA:"
+ subSeq //
+ "\n");
else trData.ok = true; // All sanity checks passed
}
} else {
if (!proteinDifferences.contains(trId))
Timer.showStdErr(
"WARNING: Protein sequences differ: " //
+ "\tUniqueName"
+ isoformRef //
+ "\tEnsembl ID: "
+ trId //
+ "\n\tEnsembl ("
+ protein.length()
+ "): "
+ protein //
+ "\n\tNextProt ("
+ sequence.length()
+ "): "
+ sequence //
+ "\n");
proteinDifferences.add(trId);
}
}
}
return trData;
}
/** Compare all CDS */
double cdsCompare() {
int i = 1;
if (verbose) {
// Show labels
System.err.println("\tLabels:");
System.err.println("\t\t'+' : OK");
System.err.println("\t\t'.' : Missing");
System.err.println("\t\t'*' : Error");
System.err.print("\t");
}
// Compare all genes
for (Gene gint : config.getGenome().getGenes())
for (Transcript tint : gint) {
String cds = tint.cds().toUpperCase();
String mRna = tint.mRna().toUpperCase();
String cdsReference = cdsByTrId.get(tint.getId());
if (cdsReference != null) cdsReference = cdsReference.toUpperCase();
if (cdsReference == null) {
if (debug)
System.err.println(
"\nWARNING:Cannot find reference CDS for transcript '" + tint.getId() + "'");
else if (verbose) System.out.print('.');
totalNotFound++;
} else if (cds.isEmpty()) {
if (debug)
System.err.println("\nWARNING:Empty CDS for transcript '" + tint.getId() + "'");
else if (verbose) System.out.print('.');
totalNotFound++;
} else if (cds.equals(cdsReference)) {
totalOk++;
if (verbose) System.out.print('+');
// Sanity check: Start and stop codons
if ((cds != null) && (cds.length() >= 3)) {
CodonTable ctable =
CodonTables.getInstance().getTable(config.getGenome(), tint.getChromosomeName());
// Check start codon
String startCodon = cds.substring(0, 3);
if (!ctable.isStart(startCodon)) {
if (debug)
System.err.println(
"\nWARNING: CDS for transcript '"
+ tint.getId()
+ "' does not start with a start codon:\t"
+ startCodon
+ "\t"
+ cds);
totalWarnings++;
}
// Check stop codon
String stopCodon = cds.substring(cds.length() - 3, cds.length());
if (!ctable.isStop(stopCodon)) {
if (debug)
System.err.println(
"\nWARNING: CDS for transcript '"
+ tint.getId()
+ "' does not end with a stop codon:\t"
+ stopCodon
+ "\t"
+ cds);
totalWarnings++;
}
}
} else if (mRna.equals(cdsReference)) { // May be the file has mRNA instead of CDS?
totalOk++;
if (verbose) System.out.print('+');
} else if ((mRna.length()
< cdsReference
.length()) // CDS longer than mRNA? May be it is actually an mRNA + poly-A tail
// (instead of a CDS)
&& cdsReference
.substring(mRna.length())
.replace('A', ' ')
.trim()
.isEmpty() // May be it is an mRNA and it has a ploy-A tail added
&& cdsReference.substring(0, mRna.length()).equals(mRna) // Compare cutting poly-A tail
) {
// OK, it was a mRNA + polyA
totalOk++;
if (verbose) System.out.print('+');
} else if ((mRna.length() > cdsReference.length()) // PolyA in the reference?
&& mRna.substring(cdsReference.length()).replace('A', ' ').trim().isEmpty() //
&& mRna.substring(0, cdsReference.length()).equals(mRna) //
) {
// OK, it was a mRNA + polyA
totalOk++;
if (verbose) System.out.print('+');
} else {
if (debug || onlyOneError) {
// Create a string indicating differences
String diffMrna = SnpEffCmdProtein.diffStr(mRna, cdsReference);
int diffMrnaCount = SnpEffCmdProtein.diffCount(mRna, cdsReference);
String diffCds = SnpEffCmdProtein.diffStr(cds, cdsReference);
int diffCdsCount = SnpEffCmdProtein.diffCount(cds, cdsReference);
System.err.println(
"\nERROR:CDS do not match for transcript "
+ tint.getId()
+ "\tStrand:"
+ tint.getStrand()
+ "\tExons: "
+ tint.numChilds());
if (diffMrnaCount < diffCdsCount) {
System.err.println(
String.format("\tsnpEff mRNA (%6d) : '%s'", mRna.length(), mRna.toLowerCase()));
System.err.println(
String.format("\tdiff (%6d) : '%s'", diffMrnaCount, diffMrna));
} else {
System.err.println(
String.format("\tsnpEff CDS (%6d) : '%s'", cds.length(), cds.toLowerCase()));
System.err.println(
String.format("\tdiff (%6d) : '%s'", diffCdsCount, diffCds));
}
System.err.println(
String.format(
"\tReference (%6d) : '%s'",
cdsReference.length(), cdsReference.toLowerCase()));
System.err.println("Transcript details:\n" + tint);
if (onlyOneError) {
System.err.println("Transcript details:\n" + tint);
throw new RuntimeException("DIE");
}
} else if (verbose) System.out.print('*');
totalErrors++;
}
// Show a mark
if (verbose && (i % 100 == 0)) System.out.print("\n\t");
i++;
}
double perc = ((double) totalErrors) / ((double) (totalErrors + totalOk));
System.out.println(
"\n\tCDS check:\t"
+ config.getGenome().getVersion()
+ "\tOK: "
+ totalOk
+ "\tWarnings: "
+ totalWarnings
+ "\tNot found: "
+ totalNotFound
+ "\tErrors: "
+ totalErrors
+ "\tError percentage: "
+ (100 * perc)
+ "%");
return perc;
}
