HpoAssociationParser { public Map<TermId,DiseaseToGeneAssociation> getDiseaseToAssociationsMap() { return this.diseaseToAssociationsMap; } HpoAssociationParser(String geneInfoPath,
                              String mim2geneMedgenPath,
                              String orphaToGenePath,
                              String phenotypeHpoaPath,
                              Ontology hpoOntology);  HpoAssociationParser(String geneInfoPath, String mim2geneMedgenPath, Ontology hpoOntology);  HpoAssociationParser(File geneInfoFile,
                              File mim2geneMedgenFile,
                              File orphaToGeneFile,
                              File phenotypeHpoaFile,
                              Ontology hpoOntology); Map<TermId,DiseaseToGeneAssociation> getDiseaseToAssociationsMap(); Map<TermId,String> getGeneIdToSymbolMap(); Multimap<TermId,TermId> getDiseaseToGeneIdMap(); Multimap<TermId,TermId> getGeneToDiseaseIdMap(); List<HpoGeneAnnotation> getPhenotypeToGene(); void setTermToGene(Multimap<TermId, TermId> phenotypeToDisease);  }
@Test void testHoltOram() { Map<TermId, DiseaseToGeneAssociation> diseasemap = parser.getDiseaseToAssociationsMap(); TermId holtOramId = TermId.of("OMIM:142900"); assertTrue(diseasemap.containsKey(holtOramId)); DiseaseToGeneAssociation holtOramAssociation = diseasemap.get(holtOramId); List<Gene> geneList = holtOramAssociation.getGeneList(); assertEquals(1, geneList.size()); Gene gene = geneList.get(0); TermId tbx5Id = TermId.of("NCBIGene:6910"); assertEquals(tbx5Id, gene.getId()); String symbol = "TBX5"; assertEquals(symbol, gene.getSymbol()); }
@Test void testAdamsOliver() { Map<TermId, DiseaseToGeneAssociation> diseasemap = parser.getDiseaseToAssociationsMap(); TermId adamsOliver1Id = TermId.of("OMIM:100300"); assertTrue(diseasemap.containsKey(adamsOliver1Id)); DiseaseToGeneAssociation holtOramAssociation = diseasemap.get(adamsOliver1Id); List<Gene> geneList = holtOramAssociation.getGeneList(); assertEquals(1, geneList.size()); Gene gene = geneList.get(0); TermId tbx5Id = TermId.of("NCBIGene:57514"); assertEquals(tbx5Id, gene.getId()); String symbol = "ARHGAP31"; assertEquals(symbol, gene.getSymbol()); }
@Test void testSusceptibilityGenes() { Map<TermId, DiseaseToGeneAssociation> diseasemap = parser.getDiseaseToAssociationsMap(); TermId familialHypercholesterolemia = TermId.of("OMIM:143890"); assertTrue(diseasemap.containsKey(familialHypercholesterolemia)); DiseaseToGeneAssociation hypercholesterolemiaAssociation = diseasemap.get(familialHypercholesterolemia); List<Gene> geneList = hypercholesterolemiaAssociation.getGeneList(); assertEquals(7, geneList.size()); Gene APOA2 = new Gene(TermId.of("NCBIGene:336"), "APOA2"); assertTrue(geneList.contains(APOA2)); Gene ITIH4 = new Gene(TermId.of("NCBIGene:3700"), "ITIH4"); assertTrue(geneList.contains(ITIH4)); Gene GHR = new Gene(TermId.of("NCBIGene:2690"), "GHR"); assertTrue(geneList.contains(GHR)); Gene PPP1R17 = new Gene(TermId.of("NCBIGene:10842"), "PPP1R17"); assertTrue(geneList.contains(PPP1R17)); Gene EPHX2 = new Gene(TermId.of("NCBIGene:2053"), "EPHX2"); assertTrue(geneList.contains(EPHX2)); Gene ABCA1 = new Gene(TermId.of("NCBIGene:19"), "ABCA1"); assertTrue(geneList.contains(ABCA1)); Gene LDLR = new Gene(TermId.of("NCBIGene:3949"), "LDLR"); assertTrue(geneList.contains(LDLR)); }