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Code to generate ontology annotated objects (e.g. HPO annotated patients)

License: GNU General Public License v3.0

Java 100.00%
hpo patients simulation phenotype hpo-annotated-patients phenotypes phenotyping phenotype-ontologies

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minimal example in groovy

Hello,

Thanks for the software - it was a bit difficult to get running, though. I thought I'd post this minimal Groovy example here, in case you'd like to include it in the README, or in case anyone else tries to run it and could use a hand. Also fixes a couple of issues/omissions from the Java version.

@Grapes([
  @GrabResolver(name='compbio', root='http://compbio.charite.de/tl_files/maven'),
  @Grab(group='annotation-simulation', module='annotation-simulation', version='0.0.1-SNAPSHOT'),
  @Grab(group='phenologizer', module='phenologizer', version='0.0.4-SNAPSHOT'),
  @GrabConfig(systemClassLoader=true)
])

import drseb.*
import ontologizer.ontology.*
import hpo.ItemId.ItemDatabase;
import groovy.json.*                                                                                                                          

// Parameters 
def ontologyFile = './hp.obo'
def annotationFile = './phenotype_annotation.tab'
def id = "114030";

// Generate patients
def simulator = new AnnotationSimulator(ontologyFile, annotationFile, OntologyProjectType.HPO);
def patients = simulator.simulatePatients(ItemDatabase.OMIM, id, 1000, 0.2, 0.4, 2, 10);

// Output
def json = JsonOutput.toJson(patients)
new File('patients.json').write(json)

println 'done'

javautil_pheno

@drseb where can I get it?

I get the error:

Exception in thread "main" java.lang.NoSuchMethodError: ontologizer.go.OBOParser.getDataVersion()Ljava/lang/String;
	at hpo.HpoDataProvider.parseOntology(HpoDataProvider.java:254)
	at hpo.HpoDataProvider.parseOntologyAndAssociations(HpoDataProvider.java:183)
	at drseb.AnnotationSimulator.<init>(AnnotationSimulator.java:42)
	at de.charite.compbio.exomiserbenchmark.Main.initialize(Main.java:117)
	at de.charite.compbio.exomiserbenchmark.Main.main(Main.java:94)

I think I do not use the latest version of javautil_pheno

seed

For debugging it is important that the simulator uses seeds to generate the exact same results if a seed is used!

like:

public AnnotationSimulator(ontologyFile, annotationFile, OntologyProjectType.HPO, seed); {
 this.seed = seed;
//etc
}
public AnnotationSimulator(ontologyFile, annotationFile, OntologyProjectType.HPO); {
AnnotationSimulator(ontologyFile, annotationFile, OntologyProjectType.HPO, new Random().nextInt())
}

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