def test_04(self): """ Check the duplication removal - simple test; 2 identical fusions but checking presevation of the gene names from different annotations """ args = CLI(['-m','subset','--no-strand-specific-matching','-s','']) gene_1_hg18 = Gene("gene_1", False) gene_1_hg19 = Gene("gene_1", False) gene_2_hg18 = Gene("gene_2", False) gene_2_hg19 = Gene("gene_2", False) fusion_hg18 = Fusion("chr1","chr2",15000,20000,"+","+","Experiment","",True) fusion_hg19 = Fusion("chr1","chr2",15500,20500,"+","+","Experiment","",True) fusion_hg18.annotate_genes_left([gene_1_hg18]) fusion_hg19.annotate_genes_left([gene_1_hg19]) fusion_hg18.annotate_genes_right([gene_2_hg18]) fusion_hg19.annotate_genes_right([gene_2_hg19]) experiment = FusionDetectionExperiment("Experiment_1") experiment.genes_spanning_left_junction = [True] experiment.genes_spanning_right_junction = [True] experiment.add_fusion(fusion_hg18) experiment.add_fusion(fusion_hg19) self.assertEqual(len(experiment), 2) experiment.remove_duplicates(args) self.assertEqual(len(experiment), 1) for fusion in experiment: self.assertEqual(len(fusion.annotated_genes_left), 2)