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, "+", "+",
"Experiment_1", "1", True)
experiment_1 = FusionDetectionExperiment("Experiment_1")
experiment_1.add_fusion(fusion_1)
experiment_1.annotate_genes(genes)
fusion_2 = Fusion("chr1", "chr1", 85000, 15000, "+", "+",
"Experiment_2", "2", True)
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_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, "+", "-",
"Experiment_1", 3, True)
fusion_2 = Fusion("chr1", "chr1", 15000, 85000, "-", "+",
"Experiment_2", 4, True)
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, "+", "+",
"Experiment_AB1", "1", True)
fusion_AB2 = Fusion("chr1", "chr1", 15000, 85000, "-", "-",
"Experiment_AB2", "2", True)
fusion_AB3 = Fusion("chr1", "chr1", 15000, 85000, "+", "-",
"Experiment_AB3", "3", True)
fusion_AB4 = Fusion("chr1", "chr1", 15000, 85000, "-", "+",
"Experiment_AB4", "4", True)
fusion_BA1 = Fusion("chr1", "chr1", 85000, 15000, "+", "+",
"Experiment_BA1", "5", True)
fusion_BA2 = Fusion("chr1", "chr1", 85000, 15000, "-", "-",
"Experiment_BA2", "6", True)
fusion_BA3 = Fusion("chr1", "chr1", 85000, 15000, "+", "-",
"Experiment_BA3", "7", True)
fusion_BA4 = Fusion("chr1", "chr1", 85000, 15000, "-", "+",
"Experiment_BA4", "8", True)
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)
