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)
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)
