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)