def test_01(self): """ #1: break1 break2 | | [ --- Gene A --- ] [ --- Gene B --- ] #2: break1 break2 | | [ --- Gene B --- ] [ --- Gene A --- ] """ args_on = CLI(['--acceptor-donor-order-specific-matching','-f','summary','-s','']) args_off = CLI(['-f','summary','-s','']) gene_A = Gene("A", False) gene_B = Gene("B", False) genes = GeneAnnotation("hg19") genes.add_annotation(gene_A,"1",10000,20000) genes.add_annotation(gene_B,"1",80000,90000) fusion_1 = Fusion("chr1","chr1",15000,85000,None,None,"+","+","Experiment_1") fusion_1.add_location({'left':[fusion_1.get_left_chromosome(), fusion_1.get_left_break_position()], 'right':[fusion_1.get_right_chromosome(), fusion_1.get_right_break_position()], 'id':1, 'dataset':fusion_1.dataset_name }) experiment_1 = FusionDetectionExperiment("Experiment_1") experiment_1.add_fusion(fusion_1) experiment_1.annotate_genes(genes) fusion_2 = Fusion("chr1","chr1",85000,15000,None,None,"+","+","Experiment_2") fusion_2.add_location({ 'left':[fusion_2.get_left_chromosome(), fusion_2.get_left_break_position()], 'right':[fusion_2.get_right_chromosome(), fusion_2.get_right_break_position()], 'id':2, 'dataset':fusion_2.dataset_name }) experiment_2 = FusionDetectionExperiment("Experiment_2") experiment_2.add_fusion(fusion_2) experiment_2.annotate_genes(genes) self.assertEqual(len(fusion_1.annotated_genes_left) , 1) self.assertEqual(len(fusion_2.annotated_genes_left) , 1) self.assertEqual( fusion_1.acceptor_donor_direction , AD_DIRECTION_FORWARD ) self.assertEqual( fusion_2.acceptor_donor_direction , AD_DIRECTION_REVERSE ) overlapping_complex = OverlapComplex() overlapping_complex.add_experiment(experiment_1) overlapping_complex.add_experiment(experiment_2) overlap = overlapping_complex.overlay_fusions(True,False,args_on) self.assertEqual(len(overlap[0]), 0) overlapping_complex = OverlapComplex() overlapping_complex.add_experiment(experiment_1) overlapping_complex.add_experiment(experiment_2) overlap = overlapping_complex.overlay_fusions(True,False,args_off) self.assertEqual(len(overlap[0]), 1)
def test_01(self): fusion_1 = Fusion("chr1","chrX",15000,15000,None,None,"-","+","Experiment_1") fusion_1.add_location({'left':[fusion_1.get_left_chromosome(), fusion_1.get_left_break_position()], 'right':[fusion_1.get_right_chromosome(), fusion_1.get_right_break_position()], 'id':1, 'dataset':fusion_1.dataset_name }) self.assertEqual( fusion_1.left_break_position , 15000 ) self.assertEqual( fusion_1.right_break_position , 15000 ) self.assertEqual( fusion_1.left_strand , STRAND_REVERSE ) self.assertEqual( fusion_1.right_strand , STRAND_FORWARD )
def test_04(self): """ #1: --> <-- break1 break2 | | [ --- Gene A --- ] [ --- Gene B --- ] #2: <-- --> break1 break2 | | [ --- Gene A --- ] [ --- Gene B --- ] Ensure the strand of the merged fusion is not set! """ gene_A = Gene("A", False) gene_B = Gene("B", False) genes = GeneAnnotation("hg19") genes.add_annotation(gene_A,"1",10000,20000) genes.add_annotation(gene_B,"1",80000,90000) fusion_1 = Fusion("chr1","chr1",15000,85000,None,None,"+","-","Experiment_1") fusion_1.add_location({'left':[fusion_1.get_left_chromosome(), fusion_1.get_left_break_position()], 'right':[fusion_1.get_right_chromosome(), fusion_1.get_right_break_position()], 'id':3, 'dataset':fusion_1.dataset_name }) fusion_2 = Fusion("chr1","chr1",15000,85000,None,None,"-","+","Experiment_2") fusion_2.add_location({'left':[fusion_2.get_left_chromosome(), fusion_2.get_left_break_position()], 'right':[fusion_2.get_right_chromosome(), fusion_2.get_right_break_position()], 'id':4, 'dataset':fusion_2.dataset_name }) experiment_1 = FusionDetectionExperiment("Experiment_1") experiment_1.add_fusion(fusion_1) experiment_1.annotate_genes(genes) experiment_2 = FusionDetectionExperiment("Experiment_2") experiment_2.add_fusion(fusion_2) experiment_2.annotate_genes(genes) args = CLI(['-f','summary','--no-strand-specific-matching','-s','']) overlapping_complex = OverlapComplex() overlapping_complex.add_experiment(experiment_1) overlapping_complex.add_experiment(experiment_2) overlap = overlapping_complex.overlay_fusions(True,False,args) self.assertEqual(overlap[0][0].left_strand, None) self.assertEqual(overlap[0][0].right_strand, None) args = CLI(['-f','summary','--no-strand-specific-matching','-s','']) overlapping_complex = OverlapComplex() overlapping_complex.add_experiment(experiment_1) overlapping_complex.add_experiment(experiment_1) overlap = overlapping_complex.overlay_fusions(True,False,args) self.assertNotEqual(overlap[0][0].left_strand, None) self.assertNotEqual(overlap[0][0].right_strand, None) args = CLI(['-f','summary','--no-strand-specific-matching','-s','']) overlapping_complex = OverlapComplex() overlapping_complex.add_experiment(experiment_2) overlapping_complex.add_experiment(experiment_2) overlap = overlapping_complex.overlay_fusions(True,False,args) self.assertNotEqual(overlap[0][0].left_strand, None) self.assertNotEqual(overlap[0][0].right_strand, None)
def test_03(self): """ #AB1: --> --> break1 break2 | | [ --- Gene A --- ] [ --- Gene B --- ] #AB2: <-- <-- break1 break2 | | [ --- Gene A --- ] [ --- Gene B --- ] #AB3: --> <-- break1 break2 | | [ --- Gene A --- ] [ --- Gene B --- ] #AB4: <-- --> break1 break2 | | [ --- Gene A --- ] [ --- Gene B --- ] #BA1: --> --> break1 break2 | | [ --- Gene B --- ] [ --- Gene A --- ] #BA2: <-- <-- break1 break2 | | [ --- Gene B --- ] [ --- Gene A --- ] #BA3: --> <-- break1 break2 | | [ --- Gene B --- ] [ --- Gene A --- ] #BA4: <-- --> break1 break2 | | [ --- Gene B --- ] [ --- Gene A --- ] """ gene_A = Gene("A", False) gene_B = Gene("B", False) genes = GeneAnnotation("hg19") genes.add_annotation(gene_A,"1",10000,20000) genes.add_annotation(gene_B,"1",80000,90000) fusion_AB1 = Fusion("chr1","chr1",15000,85000,None,None,"+","+","Experiment_AB1") fusion_AB1.add_location({'left':[fusion_AB1.get_left_chromosome(), fusion_AB1.get_left_break_position()], 'right':[fusion_AB1.get_right_chromosome(), fusion_AB1.get_right_break_position()], 'id':1, 'dataset':fusion_AB1.dataset_name }) fusion_AB2 = Fusion("chr1","chr1",15000,85000,None,None,"-","-","Experiment_AB2") fusion_AB2.add_location({'left':[fusion_AB2.get_left_chromosome(), fusion_AB2.get_left_break_position()], 'right':[fusion_AB2.get_right_chromosome(), fusion_AB2.get_right_break_position()], 'id':2, 'dataset':fusion_AB2.dataset_name }) fusion_AB3 = Fusion("chr1","chr1",15000,85000,None,None,"+","-","Experiment_AB3") fusion_AB3.add_location({'left':[fusion_AB3.get_left_chromosome(), fusion_AB3.get_left_break_position()], 'right':[fusion_AB3.get_right_chromosome(), fusion_AB3.get_right_break_position()], 'id':3, 'dataset':fusion_AB3.dataset_name }) fusion_AB4 = Fusion("chr1","chr1",15000,85000,None,None,"-","+","Experiment_AB4") fusion_AB4.add_location({'left':[fusion_AB4.get_left_chromosome(), fusion_AB4.get_left_break_position()], 'right':[fusion_AB4.get_right_chromosome(), fusion_AB4.get_right_break_position()], 'id':4, 'dataset':fusion_AB4.dataset_name }) fusion_BA1 = Fusion("chr1","chr1",85000,15000,None,None,"+","+","Experiment_BA1") fusion_BA1.add_location({'left':[fusion_BA1.get_left_chromosome(), fusion_BA1.get_left_break_position()], 'right':[fusion_BA1.get_right_chromosome(), fusion_BA1.get_right_break_position()], 'id':5, 'dataset':fusion_BA1.dataset_name }) fusion_BA2 = Fusion("chr1","chr1",85000,15000,None,None,"-","-","Experiment_BA2") fusion_BA2.add_location({'left':[fusion_BA2.get_left_chromosome(), fusion_BA2.get_left_break_position()], 'right':[fusion_BA2.get_right_chromosome(), fusion_BA2.get_right_break_position()], 'id':6, 'dataset':fusion_BA2.dataset_name }) fusion_BA3 = Fusion("chr1","chr1",85000,15000,None,None,"+","-","Experiment_BA3") fusion_BA3.add_location({'left':[fusion_BA3.get_left_chromosome(), fusion_BA3.get_left_break_position()], 'right':[fusion_BA3.get_right_chromosome(), fusion_BA3.get_right_break_position()], 'id':7, 'dataset':fusion_BA3.dataset_name }) fusion_BA4 = Fusion("chr1","chr1",85000,15000,None,None,"-","+","Experiment_BA4") fusion_BA4.add_location({'left':[fusion_BA4.get_left_chromosome(), fusion_BA4.get_left_break_position()], 'right':[fusion_BA4.get_right_chromosome(), fusion_BA4.get_right_break_position()], 'id':8, 'dataset':fusion_BA4.dataset_name }) experiments = {'AB':[],'BA':[]} experiments['AB'].append(FusionDetectionExperiment("Experiment_AB1")) experiments['AB'][0].add_fusion(fusion_AB1) experiments['AB'][0].annotate_genes(genes) experiments['AB'].append(FusionDetectionExperiment("Experiment_AB2")) experiments['AB'][1].add_fusion(fusion_AB2) experiments['AB'][1].annotate_genes(genes) experiments['AB'].append(FusionDetectionExperiment("Experiment_AB3")) experiments['AB'][2].add_fusion(fusion_AB3) experiments['AB'][2].annotate_genes(genes) experiments['AB'].append(FusionDetectionExperiment("Experiment_AB4")) experiments['AB'][3].add_fusion(fusion_AB4) experiments['AB'][3].annotate_genes(genes) experiments['BA'].append(FusionDetectionExperiment("Experiment_BA1")) experiments['BA'][0].add_fusion(fusion_BA1) experiments['BA'][0].annotate_genes(genes) experiments['BA'].append(FusionDetectionExperiment("Experiment_BA2")) experiments['BA'][1].add_fusion(fusion_BA2) experiments['BA'][1].annotate_genes(genes) # Swap 3 and 4 - to match "-" , "+" and AB <-> BA experiments['BA'].append(FusionDetectionExperiment("Experiment_BA4")) experiments['BA'][2].add_fusion(fusion_BA4) experiments['BA'][2].annotate_genes(genes) experiments['BA'].append(FusionDetectionExperiment("Experiment_BA3")) experiments['BA'][3].add_fusion(fusion_BA3) experiments['BA'][3].annotate_genes(genes) # No strict settings - everything should match with everything args = CLI(['-f','summary','--no-strand-specific-matching','-s','']) for ad_direction_1 in experiments.keys(): for breakpoint_strand_1 in range(len(experiments[ad_direction_1])): for ad_direction_2 in experiments.keys(): for breakpoint_strand_2 in range(len(experiments[ad_direction_2])): overlapping_complex = OverlapComplex() overlapping_complex.add_experiment(experiments[ad_direction_1][breakpoint_strand_1]) overlapping_complex.add_experiment(experiments[ad_direction_2][breakpoint_strand_2]) overlap = overlapping_complex.overlay_fusions(True,False,args) self.assertEqual(len(overlap[0]), 1) if(ad_direction_1 == ad_direction_2): self.assertNotEqual(overlap[0][0].acceptor_donor_direction, None) else: self.assertEqual(overlap[0][0].acceptor_donor_direction, None) # No strict settings - everything should match with everything args = CLI(['-f','summary','--strand-specific-matching','-s','']) for ad_direction_1 in experiments.keys(): for breakpoint_strand_1 in range(len(experiments[ad_direction_1])): for ad_direction_2 in experiments.keys(): for breakpoint_strand_2 in range(len(experiments[ad_direction_2])): overlapping_complex = OverlapComplex() overlapping_complex.add_experiment(experiments[ad_direction_1][breakpoint_strand_1]) overlapping_complex.add_experiment(experiments[ad_direction_2][breakpoint_strand_2]) overlap = overlapping_complex.overlay_fusions(True,False,args) if(breakpoint_strand_1 == breakpoint_strand_2): self.assertEqual(len(overlap[0]), 1) else: self.assertEqual(len(overlap[0]), 0) # No strict settings - everything should match with everything args = CLI(['-f','summary','--no-strand-specific-matching','--acceptor-donor-order-specific-matching','-s','']) for ad_direction_1 in experiments.keys(): for breakpoint_strand_1 in range(len(experiments[ad_direction_1])): for ad_direction_2 in experiments.keys(): for breakpoint_strand_2 in range(len(experiments[ad_direction_2])): overlapping_complex = OverlapComplex() overlapping_complex.add_experiment(experiments[ad_direction_1][breakpoint_strand_1]) overlapping_complex.add_experiment(experiments[ad_direction_2][breakpoint_strand_2]) overlap = overlapping_complex.overlay_fusions(True,False,args) if(ad_direction_1 == ad_direction_2): self.assertEqual(len(overlap[0]), 1) else: self.assertEqual(len(overlap[0]), 0) # No strict settings - everything should match with everything args = CLI(['-f','summary','--strand-specific-matching','--acceptor-donor-order-specific-matching','-s','']) for ad_direction_1 in experiments.keys(): for breakpoint_strand_1 in range(len(experiments[ad_direction_1])): for ad_direction_2 in experiments.keys(): for breakpoint_strand_2 in range(len(experiments[ad_direction_2])): overlapping_complex = OverlapComplex() overlapping_complex.add_experiment(experiments[ad_direction_1][breakpoint_strand_1]) overlapping_complex.add_experiment(experiments[ad_direction_2][breakpoint_strand_2]) overlap = overlapping_complex.overlay_fusions(True,False,args) if (breakpoint_strand_1 == breakpoint_strand_2) and (ad_direction_1 == ad_direction_2): self.assertEqual(len(overlap[0]), 1) else: self.assertEqual(len(overlap[0]), 0)