void analyze(int i, int pos, String ref, String mnp) {
String codons = codons();
Variant seqChange = new Variant(chromosome, pos, ref + "", mnp + "", "");
// ---
// Calculate effects
// ---
VariantEffects effects = snpEffectPredictor.variantEffect(seqChange);
// Show
VariantEffect effect = null;
if (effects.size() > 1) { // Usually there is only one effect
for (VariantEffect ce : effects) {
if ((ce.getEffectType() != EffectType.SPLICE_SITE_ACCEPTOR) //
&& (ce.getEffectType() != EffectType.SPLICE_SITE_DONOR) //
&& (ce.getEffectType() != EffectType.INTRON) //
&& (ce.getEffectType() != EffectType.INTERGENIC) //
) //
effect = ce;
}
} else effect = effects.get();
if (effect != null) {
String effStr = effect.effect(true, true, true, false);
if (codons.length() > 1) {
String codonsExp[] = codons.split("/");
boolean error =
(!codonsExp[0].toUpperCase().equals(effect.getCodonsRef().toUpperCase()) //
|| !codonsExp[1].toUpperCase().equals(effect.getCodonsAlt().toUpperCase()));
if (error || debug) {
Gpr.debug(
"Fatal error:" //
+ "\n\tPos : "
+ pos //
+ "\n\tSeqChange : "
+ seqChange
+ (seqChange.isStrandPlus() ? "+" : "-") //
+ "\n\tCodon (exp) : "
+ codons //
+ "\n\tCodon (pred) : "
+ effect.getCodonsRef().toUpperCase()
+ "/"
+ effect.getCodonsAlt().toUpperCase() //
+ "\n\tEffect (pred) : "
+ effStr //
+ "\n\tEffect (pred) : "
+ effect //
+ "\n\tGene : "
+ gene //
+ "\n\tChromo : "
+ chromoSequence //
);
}
/** Error? Dump so we can debug... */
if (error) {
System.err.println("Error. Dumping data");
Save save = new Save();
save.snpEffectPredictor = snpEffectPredictor;
save.chromoSequence = chromoSequence;
save.chromoNewSequence = chromoNewSequence;
save.ref = ref;
save.pos = pos;
save.mnp = mnp;
String outFile = "/tmp/sep_" + i + "_" + pos + ".bin";
Gpr.toFileSerialize(outFile, save);
throw new RuntimeException("Codons do not match!\n\tData dumped: '" + outFile + "'");
}
}
}
}
