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Take a look at the LIRICAL SimulateVcf class, e;g;
Phenopacket pp = ...//
if (pp.getDiseasesCount() != 1) {
System.err.println("[ERROR] to run this simulation a phenoopacket must have exactly one disease diagnosis");
System.err.println("[ERROR] " + pp.getSubject().getId() + " had " + pp.getDiseasesCount());
return; // skip to next Phenopacket
}
Disease diagnosis = pp.getDiseases(0);
simulatedDisease = diagnosis.getTerm().getId(); // should be an ID such as OMIM:600102
@pnrobinson
Could you add me to your phenopacket repo?
Now we can call Phenomiser with multiple query lists. The app optimizes the query sequence so to avoid repeated IO. Entry point is:
Phenomiser/phenomiser-core/src/main/java/org/jax/Phenomiser.java
Line 114 in 27c8307
It can also output the rank of the target disease if you provide one:
Phenomiser/phenomiser-core/src/main/java/org/jax/Phenomiser.java
Lines 145 to 146 in 27c8307
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