/** Check proteins using all possible codon tables */
void checkCodonTables() {
if (verbose) Timer.showStdErr("Comparing Proteins...");
createTrByChromo(); // Create lists of transcripts by chromosome
// For each chromosome...
for (Chromosome chromo : genome) {
String chr = chromo.getId();
// Check against each codon table
for (CodonTable codonTable : CodonTables.getInstance()) {
setCodonTable(chromo, codonTable);
proteinCompare(chr, false, false);
}
}
if (verbose) Timer.showStdErr("done");
}
/** Set codon table for a given chromosome */
void setCodonTable(Chromosome chromo, CodonTable codonTable) {
CodonTables.getInstance().set(genome, chromo, codonTable); // Set codon tables
// Reset all protein translations for this chromosome
for (Transcript tr : trByChromo.get(chromo.getId())) tr.resetCache();
}
/** Compare list of proteins */
double proteinCompare(String chr, boolean addTotals, boolean updateTranscriptAaCheck) {
List<Transcript> trList = null;
// No chromosome name specified? => Use all transcripts
if (chr == null) {
trList = new ArrayList<Transcript>();
for (Gene g : genome.getGenes()) for (Transcript tr : g) trList.add(tr);
} else trList = trByChromo.get(chr);
// No transcripts in the list? We are done
if (trList.isEmpty()) return 0;
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.out.print((chr != null ? chr : "") + "\t");
}
// Check each transcript
int countNotFound = 0, countOk = 0, countErrors = 0;
for (Transcript tr : trList) {
char status = ' ';
String protein = tr.protein();
String proteinReference = proteinByTrId.get(tr.getId());
if (proteinReference == null) {
if (tr.isProteinCoding()) {
status = '.';
if (debug)
System.err.println("\nWARNING:Cannot find Protein for transcript " + tr.getId());
}
} else if (equals(protein, proteinReference)) {
status = '+';
} else {
status = '*';
if (debug || storeAlignments || onlyOneError) {
protein = proteinFormat(protein);
proteinReference = proteinFormat(proteinReference);
SmithWaterman sw = new SmithWaterman(protein, proteinReference);
if (Math.max(protein.length(), proteinReference.length()) < SnpEffCmdCds.MAX_ALIGN_LENGTH)
sw.align();
if (storeAlignments) alignmentByTrId.put(tr.getId(), sw);
int maxScore = Math.min(protein.length(), proteinReference.length());
int score = sw.getAlignmentScore();
if (debug || onlyOneError) {
System.err.println(
"\nERROR: Proteins do not match for transcript "
+ tr.getId() //
+ "\tStrand:"
+ (tr.isStrandPlus() ? "+" : "-") //
+ "\tExons: "
+ tr.numChilds() //
+ "\n" //
+ String.format(
"\tSnpEff protein (%6d) : '%s'\n", protein.length(), protein) //
+ String.format(
"\tReference protein (%6d) : '%s'\n",
proteinReference.length(), proteinReference) //
+ "\tAlignment (Snpeff protein vs Reference protein)." //
+ "\tScore: "
+ score //
+ "\tMax. possible score: "
+ maxScore //
+ "\tDiff: "
+ (maxScore - score) //
+ "\n"
+ sw //
);
System.err.println("Transcript details:\n" + tr);
}
}
if (onlyOneError) {
System.err.println("Transcript details:\n" + tr);
throw new RuntimeException("DIE");
}
}
// Update counters
boolean ok = false;
switch (status) {
case '.':
countNotFound++;
break;
case '+':
countOk++;
ok = true;
break;
case '*':
countErrors++;
break;
case ' ':
break;
default:
throw new RuntimeException("Unknown status '" + status + "'");
}
// Update transcript status
if (ok && updateTranscriptAaCheck) tr.setAaCheck(true);
// Show a mark
if (verbose && (status != ' ')) {
System.out.print(status);
i++;
if (i % 100 == 0) System.out.print("\n\t");
}
}
// Relative error rate
double errorRate = ((double) countErrors) / ((double) (countErrors + countOk));
if (verbose) System.out.println("\n");
System.out.println(
"\tProtein check:" //
+ "\t"
+ genome.getVersion() //
+ (chr != null ? "\tChromosome: " + chr : "") //
+ (chr != null
? "\tCodon table: " + CodonTables.getInstance().getTable(genome, chr).getName()
: "") //
+ "\tOK: "
+ countOk //
+ "\tNot found: "
+ countNotFound //
+ "\tErrors: "
+ countErrors //
+ "\tError percentage: "
+ (100 * errorRate)
+ "%" //
);
// Add to totals
if (addTotals) {
totalNotFound += countNotFound;
totalOk += countOk;
totalErrors += countErrors;
}
return errorRate;
}