def test_03(self):
"""
Check the duplication removal - simple test; 2 identical fusions
"""
args = CLI(['-m','subset','--no-strand-specific-matching','-s',''])
fusion_1 = Fusion("chr1","chr2",15000,20000,"+","+","Experiment","",True)
fusion_2 = Fusion("chr1","chr2",15000,20000,"+","+","Experiment","",True)
experiment = FusionDetectionExperiment("Experiment_1")
experiment.add_fusion(fusion_1)
experiment.add_fusion(fusion_2)
self.assertEqual(len(experiment), 2)
genes = ParseBED("tests/data/test_FusionDetectionExperiment.TestFusionDetectionExperiment.test_03.bed","hg18", 200000)
experiment.annotate_genes(genes)
experiment.remove_duplicates(args)
self.assertEqual(len(experiment), 1)
for fusion in experiment:
self.assertEqual(len(fusion.annotated_genes_left), 1)
self.assertEqual(len(fusion.annotated_genes_right), 1)
def test_08(self):
"""
Check the duplication removal - 2 fusions where one is missing
annotations -> one should be lost because it isn't gene
spanning
"""
args = CLI(['-m','subset','--no-strand-specific-matching','-s',''])
fusion_1 = Fusion("chr1","chr2",15000,20000,"+","+","Experiment","",True)
fusion_2 = Fusion("chr1","chr2",15000,30000,"+","+","Experiment","",True)
experiment = FusionDetectionExperiment("Experiment_1")
experiment.add_fusion(fusion_1)
experiment.add_fusion(fusion_2)
self.assertEqual(len(experiment), 2)
genes = ParseBED("tests/data/test_FusionDetectionExperiment.TestFusionDetectionExperiment.test_08.bed","hg18", 200000)
experiment.annotate_genes(genes)
experiment.remove_duplicates(args)
self.assertEqual(len(experiment), 1)
for fusion in experiment:
self.assertEqual(len(fusion.annotated_genes_left), 1)
self.assertEqual(len(fusion.annotated_genes_right), 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_08(self):
"""
Check the duplication removal - 2 fusions where one is missing
annotations -> one should be lost because it isn't gene
spanning
"""
args = CLI(['-m','subset','--no-strand-specific-matching','-s',''])
fusion_1 = Fusion("chr1","chr2",15000,20000,"+","+","Experiment","",True)
fusion_2 = Fusion("chr1","chr2",15000,30000,"+","+","Experiment","",True)
experiment = FusionDetectionExperiment("Experiment_1")
experiment.add_fusion(fusion_1)
experiment.add_fusion(fusion_2)
self.assertEqual(len(experiment), 2)
genes = ParseBED("tests/data/test_FusionDetectionExperiment.TestFusionDetectionExperiment.test_08.bed","hg18", 200000)
experiment.annotate_genes(genes)
experiment.remove_duplicates(args)
self.assertEqual(len(experiment), 1)
for fusion in experiment:
self.assertEqual(len(fusion.annotated_genes_left), 1)
self.assertEqual(len(fusion.annotated_genes_right), 1)
def test_05(self):
"""
Check the duplication removal - 2 fusions; one has two
overlapping left genes, the other only one, and for right is
vice versa. The 1 gene is always a subset of the others 2 genes
and must therefore be treated as identical annotations
"""
args = CLI(['-m','subset','--no-strand-specific-matching','-s',''])
fusion_1 = Fusion("chr1","chr2",15000,20050,"+","+","Experiment","",True)#(1A):(2A,2B)
fusion_2 = Fusion("chr1","chr2",15050,20000,"+","+","Experiment","",True)#(1A,1B):(2A)
experiment = FusionDetectionExperiment("Experiment_1")
experiment.add_fusion(fusion_1)
experiment.add_fusion(fusion_2)
self.assertEqual(len(experiment), 2)
genes = ParseBED("tests/data/test_FusionDetectionExperiment.TestFusionDetectionExperiment.test_05.bed","hg18", 200000)
experiment.annotate_genes(genes)
experiment.remove_duplicates(args)
self.assertEqual(len(experiment), 1)
for fusion in experiment:
self.assertEqual(len(fusion.annotated_genes_left), 1) # subset = (1A)
self.assertEqual(len(fusion.annotated_genes_right), 1) # subset = (2A)
def test_03(self):
"""
Check the duplication removal - simple test; 2 identical fusions
"""
args = CLI(['-m','subset','--no-strand-specific-matching','-s',''])
fusion_1 = Fusion("chr1","chr2",15000,20000,"+","+","Experiment","",True)
fusion_2 = Fusion("chr1","chr2",15000,20000,"+","+","Experiment","",True)
experiment = FusionDetectionExperiment("Experiment_1")
experiment.add_fusion(fusion_1)
experiment.add_fusion(fusion_2)
self.assertEqual(len(experiment), 2)
genes = ParseBED("tests/data/test_FusionDetectionExperiment.TestFusionDetectionExperiment.test_03.bed","hg18", 200000)
experiment.annotate_genes(genes)
experiment.remove_duplicates(args)
self.assertEqual(len(experiment), 1)
for fusion in experiment:
self.assertEqual(len(fusion.annotated_genes_left), 1)
self.assertEqual(len(fusion.annotated_genes_right), 1)
def test_05(self):
"""
Check the duplication removal - 2 fusions; one has two
overlapping left genes, the other only one, and for right is
vice versa. The 1 gene is always a subset of the others 2 genes
and must therefore be treated as identical annotations
"""
args = CLI(['-m','subset','--no-strand-specific-matching','-s',''])
fusion_1 = Fusion("chr1","chr2",15000,20050,"+","+","Experiment","",True)#(1A):(2A,2B)
fusion_2 = Fusion("chr1","chr2",15050,20000,"+","+","Experiment","",True)#(1A,1B):(2A)
experiment = FusionDetectionExperiment("Experiment_1")
experiment.add_fusion(fusion_1)
experiment.add_fusion(fusion_2)
self.assertEqual(len(experiment), 2)
genes = ParseBED("tests/data/test_FusionDetectionExperiment.TestFusionDetectionExperiment.test_05.bed","hg18", 200000)
experiment.annotate_genes(genes)
experiment.remove_duplicates(args)
self.assertEqual(len(experiment), 1)
for fusion in experiment:
self.assertEqual(len(fusion.annotated_genes_left), 1) # subset = (1A)
self.assertEqual(len(fusion.annotated_genes_right), 1) # subset = (2A)
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_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_10(self):
"""
May not have overlap:
{1} = a,b,c
{2} = a,d
Break {1}:
|
Break {2}: :
| :
a: [ : : ]
b: : [ : ]
c: : [ : ]
d: [ : ] :
"""
args = CLI(['-m','subset','--no-strand-specific-matching','-s',''])
fusion_1 = Fusion("chr1","chr2",15000,30000,"+","+","Experiment","",True)
fusion_2 = Fusion("chr1","chr2",15000,25000,"+","+","Experiment","",True)
experiment = FusionDetectionExperiment("Experiment_1")
experiment.add_fusion(fusion_1)
experiment.add_fusion(fusion_2)
self.assertEqual(len(experiment), 2)
self.assertEqual(str(experiment), "---------------------\nShowing experiment: Experiment_1\n\nFusion '' (from dataset 'Experiment'): chr1:15000(+)->chr2:30000(+)\nFusion '' (from dataset 'Experiment'): chr1:15000(+)->chr2:25000(+)\n---------------------\n")
genes = ParseBED("tests/data/test_FusionDetectionExperiment.TestFusionDetectionExperiment.test_10.bed","hg18", 200000)
experiment.annotate_genes(genes)
for fusion in experiment:
if(fusion.get_right_break_position() == 30000):
self.assertEqual(len(fusion.annotated_genes_right), 3)
self.assertTrue("NM_00002A" in [str(gene_name) for gene_name in fusion.annotated_genes_right])
self.assertTrue("NM_00002B" in [str(gene_name) for gene_name in fusion.annotated_genes_right])
self.assertTrue("NM_00002C" in [str(gene_name) for gene_name in fusion.annotated_genes_right])
if(fusion.get_right_break_position() == 25000):
self.assertEqual(len(fusion.annotated_genes_right), 2)
self.assertTrue("NM_00002A" in [str(gene_name) for gene_name in fusion.annotated_genes_right])
self.assertTrue("NM_00002D" in [str(gene_name) for gene_name in fusion.annotated_genes_right])
experiment.remove_duplicates(args)
self.assertEqual(len(experiment), 2)
def test_12(self):
"""
{a} = 1 , 4 , 5
{b} = 2 , 6
{c} = 7 , 8
{d} = 3
| f1 | f2 | f3 | f4 | f5 | f6 | f7 | f8 |
---+----+----+----+----+----+----+----+----+
f1 | * | | | a | a | | | |
---+----+----+----+----+----+----+----+----+
f2 | | * | | | | b | | |
---+----+----+----+----+----+----+----+----+
f3 | | | d | | | | | |
---+----+----+----+----+----+----+----+----+
f4 | a | | | * | a | | | |
---+----+----+----+----+----+----+----+----+
f5 | a | | | a | * | | | |
---+----+----+----+----+----+----+----+----+
f6 | | b | | | | * | | |
---+----+----+----+----+----+----+----+----+
f7 | | | | | | | * | d |
---+----+----+----+----+----+----+----+----+
f8 | | | | | | | c | * |
---+----+----+----+----+----+----+----+----+
"""
args = CLI(['-m','subset','--no-strand-specific-matching','-s',''])
fusion_1 = Fusion("chr1","chr1",15010,80040,"+","+","Experiment","",True)
fusion_2 = Fusion("chr2","chr2",15030,80030,"+","+","Experiment","",True)
fusion_3 = Fusion("chr4","chr4",15050,80070,"+","+","Experiment","",True)
fusion_4 = Fusion("chr1","chr1",15060,80010,"+","+","Experiment","",True)
fusion_5 = Fusion("chr1","chr1",15020,80050,"+","+","Experiment","",True)
fusion_6 = Fusion("chr2","chr2",15080,80080,"+","+","Experiment","",True)
fusion_7 = Fusion("chr3","chr3",15040,80020,"+","+","Experiment","",True)
fusion_8 = Fusion("chr3","chr3",15070,80060,"+","+","Experiment","",True)
experiment = FusionDetectionExperiment("Experiment_1")
experiment.add_fusion(fusion_2)
experiment.add_fusion(fusion_8)
experiment.add_fusion(fusion_6)
experiment.add_fusion(fusion_4)
experiment.add_fusion(fusion_5)
experiment.add_fusion(fusion_3)
experiment.add_fusion(fusion_1)
experiment.add_fusion(fusion_7)
self.assertEqual(len(experiment), 8)
genes = ParseBED("tests/data/test_FusionDetectionExperiment.TestFusionDetectionExperiment.test_12.bed","hg18", 200000)
experiment.annotate_genes(genes)
experiment.remove_duplicates(args)
self.assertEqual(len(experiment), 4)
def test_12(self):
"""
{a} = 1 , 4 , 5
{b} = 2 , 6
{c} = 7 , 8
{d} = 3
| f1 | f2 | f3 | f4 | f5 | f6 | f7 | f8 |
---+----+----+----+----+----+----+----+----+
f1 | * | | | a | a | | | |
---+----+----+----+----+----+----+----+----+
f2 | | * | | | | b | | |
---+----+----+----+----+----+----+----+----+
f3 | | | d | | | | | |
---+----+----+----+----+----+----+----+----+
f4 | a | | | * | a | | | |
---+----+----+----+----+----+----+----+----+
f5 | a | | | a | * | | | |
---+----+----+----+----+----+----+----+----+
f6 | | b | | | | * | | |
---+----+----+----+----+----+----+----+----+
f7 | | | | | | | * | d |
---+----+----+----+----+----+----+----+----+
f8 | | | | | | | c | * |
---+----+----+----+----+----+----+----+----+
"""
args = CLI(['-m','subset','--no-strand-specific-matching','-s',''])
fusion_1 = Fusion("chr1","chr1",15010,80040,"+","+","Experiment","",True)
fusion_2 = Fusion("chr2","chr2",15030,80030,"+","+","Experiment","",True)
fusion_3 = Fusion("chr4","chr4",15050,80070,"+","+","Experiment","",True)
fusion_4 = Fusion("chr1","chr1",15060,80010,"+","+","Experiment","",True)
fusion_5 = Fusion("chr1","chr1",15020,80050,"+","+","Experiment","",True)
fusion_6 = Fusion("chr2","chr2",15080,80080,"+","+","Experiment","",True)
fusion_7 = Fusion("chr3","chr3",15040,80020,"+","+","Experiment","",True)
fusion_8 = Fusion("chr3","chr3",15070,80060,"+","+","Experiment","",True)
experiment = FusionDetectionExperiment("Experiment_1")
experiment.add_fusion(fusion_2)
experiment.add_fusion(fusion_8)
experiment.add_fusion(fusion_6)
experiment.add_fusion(fusion_4)
experiment.add_fusion(fusion_5)
experiment.add_fusion(fusion_3)
experiment.add_fusion(fusion_1)
experiment.add_fusion(fusion_7)
self.assertEqual(len(experiment), 8)
genes = ParseBED("tests/data/test_FusionDetectionExperiment.TestFusionDetectionExperiment.test_12.bed","hg18", 200000)
experiment.annotate_genes(genes)
experiment.remove_duplicates(args)
self.assertEqual(len(experiment), 4)
def test_11(self):
"""
May not have overlap:
{1} = a,b,c
{2} = a,b,d
Break {1}:
|
Break {2}: :
| :
a: [ : : ]
b: [ | : ]
c: : [ : ]
d: [ : ]
"""
args = CLI(['-m','subset','--no-strand-specific-matching','-s',''])
fusion_1 = Fusion("chr1","chr2",15000,27500,"+","+","Experiment","",True)
fusion_2 = Fusion("chr1","chr2",15000,25500,"+","+","Experiment","",True)
experiment = FusionDetectionExperiment("Experiment_1")
experiment.add_fusion(fusion_1)
experiment.add_fusion(fusion_2)
self.assertEqual(len(experiment), 2)
genes = ParseBED("tests/data/test_FusionDetectionExperiment.TestFusionDetectionExperiment.test_11.bed","hg18", 200000)
experiment.annotate_genes(genes)
for fusion in experiment:
if(fusion.get_right_break_position() == 30000):
self.assertEqual(len(fusion.annotated_genes_right), 3)
self.assertTrue("NM_00002A" in [str(gene_name) for gene_name in fusion.annotated_genes_right])
self.assertTrue("NM_00002B" in [str(gene_name) for gene_name in fusion.annotated_genes_right])
self.assertTrue("NM_00002C" in [str(gene_name) for gene_name in fusion.annotated_genes_right])
if(fusion.get_right_break_position() == 25000):
self.assertEqual(len(fusion.annotated_genes_right), 3)
self.assertTrue("NM_00002A" in [str(gene_name) for gene_name in fusion.annotated_genes_right])
self.assertTrue("NM_00002B" in [str(gene_name) for gene_name in fusion.annotated_genes_right])
self.assertTrue("NM_00002D" in [str(gene_name) for gene_name in fusion.annotated_genes_right])
experiment.remove_duplicates(args)
self.assertEqual(len(experiment), 2)
def test_11(self):
"""
May not have overlap:
{1} = a,b,c
{2} = a,b,d
Break {1}:
|
Break {2}: :
| :
a: [ : : ]
b: [ | : ]
c: : [ : ]
d: [ : ]
"""
args = CLI(['-m','subset','--no-strand-specific-matching','-s',''])
fusion_1 = Fusion("chr1","chr2",15000,27500,None,None,"+","+","Experiment")
fusion_2 = Fusion("chr1","chr2",15000,25500,None,None,"+","+","Experiment")
experiment = FusionDetectionExperiment("Experiment_1")
experiment.add_fusion(fusion_1)
experiment.add_fusion(fusion_2)
self.assertEqual(len(experiment), 2)
genes = ParseBED("tests/data/test_FusionDetectionExperiment.TestFusionDetectionExperiment.test_11.bed","hg18", 200000)
experiment.annotate_genes(genes)
for fusion in experiment:
if(fusion.get_right_break_position() == 30000):
self.assertEqual(len(fusion.annotated_genes_right), 3)
self.assertTrue("NM_00002A" in [str(gene_name) for gene_name in fusion.annotated_genes_right])
self.assertTrue("NM_00002B" in [str(gene_name) for gene_name in fusion.annotated_genes_right])
self.assertTrue("NM_00002C" in [str(gene_name) for gene_name in fusion.annotated_genes_right])
if(fusion.get_right_break_position() == 25000):
self.assertEqual(len(fusion.annotated_genes_right), 3)
self.assertTrue("NM_00002A" in [str(gene_name) for gene_name in fusion.annotated_genes_right])
self.assertTrue("NM_00002B" in [str(gene_name) for gene_name in fusion.annotated_genes_right])
self.assertTrue("NM_00002D" in [str(gene_name) for gene_name in fusion.annotated_genes_right])
experiment.remove_duplicates(args)
self.assertEqual(len(experiment), 2)
def test_09(self):
"""
Check the duplication removal - 2 fusions where both are missing
annotations -> bothshould be lost because it isn't gene
spanning
"""
args = CLI(['-m','subset','--no-strand-specific-matching','-s',''])
fusion_1 = Fusion("chr1","chr2",15000,20000,None,None,"+","+","Experiment")
fusion_2 = Fusion("chr1","chr2",15000,20000,None,None,"+","+","Experiment")
experiment = FusionDetectionExperiment("Experiment_1")
experiment.add_fusion(fusion_1)
experiment.add_fusion(fusion_2)
self.assertEqual(len(experiment), 2)
genes = ParseBED("tests/data/test_FusionDetectionExperiment.TestFusionDetectionExperiment.test_09.bed","hg18", 200000)
experiment.annotate_genes(genes)
experiment.remove_duplicates(args)
self.assertEqual(len(experiment), 0)
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)
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_02(self):
"""
#1:
break1 break2
| |
[ --- Gene A --- ] [ --- Gene B --- ]
#2:
break1 break2
| |
[ --- Gene B --- ] [ --- Gene A --- ]
"""
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 )
# -> & <- = unknown
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)
self.assertEqual(overlap[0][0].acceptor_donor_direction, None)
# <- & -> = unknown
overlapping_complex = OverlapComplex()
overlapping_complex.add_experiment(experiment_2)
overlapping_complex.add_experiment(experiment_1)
overlap = overlapping_complex.overlay_fusions(True,False,args_off)
self.assertEqual(len(overlap[0]), 1)
self.assertEqual(overlap[0][0].acceptor_donor_direction, None)
# -> & -> = ->
overlapping_complex = OverlapComplex()
overlapping_complex.add_experiment(experiment_1)
overlapping_complex.add_experiment(experiment_1)
overlap = overlapping_complex.overlay_fusions(True,False,args_off)
self.assertEqual(len(overlap[0]), 1)
self.assertEqual(overlap[0][0].acceptor_donor_direction, AD_DIRECTION_FORWARD )
# <- & <- = <-
overlapping_complex = OverlapComplex()
overlapping_complex.add_experiment(experiment_2)
overlapping_complex.add_experiment(experiment_2)
overlap = overlapping_complex.overlay_fusions(True,False,args_off)
self.assertEqual(len(overlap[0]), 1)
self.assertEqual(overlap[0][0].acceptor_donor_direction, AD_DIRECTION_REVERSE )
def test_13(self):
"""
Crazy stuff:
{a} = 1 , 2
{b} = 1 , 3
| f1 | f2 | f3 |
---+----+----+----+
f1 | * | 1 | 2 |
---+----+----+----+
f2 | 1 | * | |
---+----+----+----+
f3 | 2 | | * |
---+----+----+----+
1 = [a,b,c]
2 = [a,c]
3 = [a,b]
>> Try in all possible orders
Break {1}:
|
Break {2}: :
| :
Break {3}: : :
: : |
a: [ : : : ]
b: : [ : : ]
c: [ : : ] :
"""
args = CLI(['-m','subset','--no-strand-specific-matching','-s',''])
fusion_1_exp_1 = Fusion("chr1","chr2",15000,70000,"+","+","Experiment_1","",True)
fusion_2_exp_1 = Fusion("chr1","chr2",15000,80000,"+","+","Experiment_1","",True)
fusion_3_exp_1 = Fusion("chr1","chr2",15000,60000,"+","+","Experiment_1","",True)
fusion_1_exp_2 = Fusion("chr1","chr2",15000,70000,"+","+","Experiment_2","",True)
fusion_2_exp_2 = Fusion("chr1","chr2",15000,80000,"+","+","Experiment_2","",True)
fusion_3_exp_2 = Fusion("chr1","chr2",15000,60000,"+","+","Experiment_2","",True)
fusion_1_exp_3 = Fusion("chr1","chr2",15000,70000,"+","+","Experiment_3","",True)
fusion_2_exp_3 = Fusion("chr1","chr2",15000,80000,"+","+","Experiment_3","",True)
fusion_3_exp_3 = Fusion("chr1","chr2",15000,60000,"+","+","Experiment_3","",True)
fusion_1_exp_4 = Fusion("chr1","chr2",15000,70000,"+","+","Experiment_4","",True)
fusion_2_exp_4 = Fusion("chr1","chr2",15000,80000,"+","+","Experiment_4","",True)
fusion_3_exp_4 = Fusion("chr1","chr2",15000,60000,"+","+","Experiment_4","",True)
fusion_1_exp_5 = Fusion("chr1","chr2",15000,70000,"+","+","Experiment_5","",True)
fusion_2_exp_5 = Fusion("chr1","chr2",15000,80000,"+","+","Experiment_5","",True)
fusion_3_exp_5 = Fusion("chr1","chr2",15000,60000,"+","+","Experiment_5","",True)
fusion_1_exp_6 = Fusion("chr1","chr2",15000,70000,"+","+","Experiment_6","",True)
fusion_2_exp_6 = Fusion("chr1","chr2",15000,80000,"+","+","Experiment_6","",True)
fusion_3_exp_6 = Fusion("chr1","chr2",15000,60000,"+","+","Experiment_6","",True)
experiment_1 = FusionDetectionExperiment("Experiment_1")
experiment_2 = FusionDetectionExperiment("Experiment_2")
experiment_3 = FusionDetectionExperiment("Experiment_3")
experiment_4 = FusionDetectionExperiment("Experiment_4")
experiment_5 = FusionDetectionExperiment("Experiment_5")
experiment_6 = FusionDetectionExperiment("Experiment_6")
experiment_1.add_fusion(fusion_1_exp_1)
experiment_1.add_fusion(fusion_2_exp_1)
experiment_1.add_fusion(fusion_3_exp_1)
experiment_2.add_fusion(fusion_1_exp_2)
experiment_2.add_fusion(fusion_3_exp_2)
experiment_2.add_fusion(fusion_2_exp_2)
experiment_3.add_fusion(fusion_2_exp_3)
experiment_3.add_fusion(fusion_1_exp_3)
experiment_3.add_fusion(fusion_3_exp_3)
experiment_4.add_fusion(fusion_2_exp_4)
experiment_4.add_fusion(fusion_3_exp_4)
experiment_4.add_fusion(fusion_1_exp_4)
experiment_5.add_fusion(fusion_3_exp_5)
experiment_5.add_fusion(fusion_1_exp_5)
experiment_5.add_fusion(fusion_2_exp_5)
experiment_6.add_fusion(fusion_3_exp_6)
experiment_6.add_fusion(fusion_2_exp_6)
experiment_6.add_fusion(fusion_1_exp_6)
self.assertEqual(len(experiment_1), 3)
self.assertEqual(len(experiment_2), 3)
self.assertEqual(len(experiment_3), 3)
self.assertEqual(len(experiment_4), 3)
self.assertEqual(len(experiment_5), 3)
self.assertEqual(len(experiment_6), 3)
genes = ParseBED("tests/data/test_FusionDetectionExperiment.TestFusionDetectionExperiment.test_13.bed","hg18", 200000)
experiment_1.annotate_genes(genes)
experiment_2.annotate_genes(genes)
experiment_3.annotate_genes(genes)
experiment_4.annotate_genes(genes)
experiment_5.annotate_genes(genes)
experiment_6.annotate_genes(genes)
experiment_1.remove_duplicates(args)
experiment_2.remove_duplicates(args)
experiment_3.remove_duplicates(args)
experiment_4.remove_duplicates(args)
experiment_5.remove_duplicates(args)
experiment_6.remove_duplicates(args)
# Removing duplicates:
#
# order 1:
# -> [A,B] <-> [A,C] = [A,B] & [A,C] & [A,B,C]
# -> [A,B] <-> [A,B,C] = [A,B*] & [A,C]
# -> [A,B*] <-> [A,C] = [A,B*] & [A,C]
# order 2:
# -> [A,B] <-> [A,B,C] = [A,B*] & [A,C]
# -> [A,B*] <-> [A,C] = [A,B*] & [A,C]
# order 3:
# -> [A,C] <-> [A,B] = [A,C] & [A,B] & [A,B,C]
# -> [A,C] <-> [A,B,C] = [A,C*] & [A,B]
# -> [A,C*] <-> [A,B] = [A,C*] & [A,B]
# order 4:
# -> [A,C] <-> [A,B,C] = [A,C*] & [A,B]
# -> [A,C*] <-> [A,B] = [A,C*] & [A,B]
# order 5:
# -> [A,B,C] <-> [A,B] = [A,B*] & [A,C]
# -> [A,B*] <-> [A,C] = [A,B*] & [A,C]
# order 6:
# -> [A,B,C] <-> [A,C] = [A,C*] & [A,B]
# -> [A,C*] <-> [A,B] = [A,C*] & [A,B]
self.assertEqual(len(experiment_1), 2)
self.assertEqual(len(experiment_2), 2)
self.assertEqual(len(experiment_3), 2)
self.assertEqual(len(experiment_4), 2)
self.assertEqual(len(experiment_5), 2)
self.assertEqual(len(experiment_6), 2)
def test_13(self):
"""
Crazy stuff:
{a} = 1 , 2
{b} = 1 , 3
| f1 | f2 | f3 |
---+----+----+----+
f1 | * | 1 | 2 |
---+----+----+----+
f2 | 1 | * | |
---+----+----+----+
f3 | 2 | | * |
---+----+----+----+
1 = [a,b,c]
2 = [a,c]
3 = [a,b]
>> Try in all possible orders
Break {1}:
|
Break {2}: :
| :
Break {3}: : :
: : |
a: [ : : : ]
b: : [ : : ]
c: [ : : ] :
"""
args = CLI(['-m','subset','--no-strand-specific-matching','-s',''])
fusion_1_exp_1 = Fusion("chr1","chr2",15000,70000,"+","+","Experiment_1","",True)
fusion_2_exp_1 = Fusion("chr1","chr2",15000,80000,"+","+","Experiment_1","",True)
fusion_3_exp_1 = Fusion("chr1","chr2",15000,60000,"+","+","Experiment_1","",True)
fusion_1_exp_2 = Fusion("chr1","chr2",15000,70000,"+","+","Experiment_2","",True)
fusion_2_exp_2 = Fusion("chr1","chr2",15000,80000,"+","+","Experiment_2","",True)
fusion_3_exp_2 = Fusion("chr1","chr2",15000,60000,"+","+","Experiment_2","",True)
fusion_1_exp_3 = Fusion("chr1","chr2",15000,70000,"+","+","Experiment_3","",True)
fusion_2_exp_3 = Fusion("chr1","chr2",15000,80000,"+","+","Experiment_3","",True)
fusion_3_exp_3 = Fusion("chr1","chr2",15000,60000,"+","+","Experiment_3","",True)
fusion_1_exp_4 = Fusion("chr1","chr2",15000,70000,"+","+","Experiment_4","",True)
fusion_2_exp_4 = Fusion("chr1","chr2",15000,80000,"+","+","Experiment_4","",True)
fusion_3_exp_4 = Fusion("chr1","chr2",15000,60000,"+","+","Experiment_4","",True)
fusion_1_exp_5 = Fusion("chr1","chr2",15000,70000,"+","+","Experiment_5","",True)
fusion_2_exp_5 = Fusion("chr1","chr2",15000,80000,"+","+","Experiment_5","",True)
fusion_3_exp_5 = Fusion("chr1","chr2",15000,60000,"+","+","Experiment_5","",True)
fusion_1_exp_6 = Fusion("chr1","chr2",15000,70000,"+","+","Experiment_6","",True)
fusion_2_exp_6 = Fusion("chr1","chr2",15000,80000,"+","+","Experiment_6","",True)
fusion_3_exp_6 = Fusion("chr1","chr2",15000,60000,"+","+","Experiment_6","",True)
experiment_1 = FusionDetectionExperiment("Experiment_1")
experiment_2 = FusionDetectionExperiment("Experiment_2")
experiment_3 = FusionDetectionExperiment("Experiment_3")
experiment_4 = FusionDetectionExperiment("Experiment_4")
experiment_5 = FusionDetectionExperiment("Experiment_5")
experiment_6 = FusionDetectionExperiment("Experiment_6")
experiment_1.add_fusion(fusion_1_exp_1)
experiment_1.add_fusion(fusion_2_exp_1)
experiment_1.add_fusion(fusion_3_exp_1)
experiment_2.add_fusion(fusion_1_exp_2)
experiment_2.add_fusion(fusion_3_exp_2)
experiment_2.add_fusion(fusion_2_exp_2)
experiment_3.add_fusion(fusion_2_exp_3)
experiment_3.add_fusion(fusion_1_exp_3)
experiment_3.add_fusion(fusion_3_exp_3)
experiment_4.add_fusion(fusion_2_exp_4)
experiment_4.add_fusion(fusion_3_exp_4)
experiment_4.add_fusion(fusion_1_exp_4)
experiment_5.add_fusion(fusion_3_exp_5)
experiment_5.add_fusion(fusion_1_exp_5)
experiment_5.add_fusion(fusion_2_exp_5)
experiment_6.add_fusion(fusion_3_exp_6)
experiment_6.add_fusion(fusion_2_exp_6)
experiment_6.add_fusion(fusion_1_exp_6)
self.assertEqual(len(experiment_1), 3)
self.assertEqual(len(experiment_2), 3)
self.assertEqual(len(experiment_3), 3)
self.assertEqual(len(experiment_4), 3)
self.assertEqual(len(experiment_5), 3)
self.assertEqual(len(experiment_6), 3)
genes = ParseBED("tests/data/test_FusionDetectionExperiment.TestFusionDetectionExperiment.test_13.bed","hg18", 200000)
experiment_1.annotate_genes(genes)
experiment_2.annotate_genes(genes)
experiment_3.annotate_genes(genes)
experiment_4.annotate_genes(genes)
experiment_5.annotate_genes(genes)
experiment_6.annotate_genes(genes)
experiment_1.remove_duplicates(args)
experiment_2.remove_duplicates(args)
experiment_3.remove_duplicates(args)
experiment_4.remove_duplicates(args)
experiment_5.remove_duplicates(args)
experiment_6.remove_duplicates(args)
# Removing duplicates:
#
# order 1:
# -> [A,B] <-> [A,C] = [A,B] & [A,C] & [A,B,C]
# -> [A,B] <-> [A,B,C] = [A,B*] & [A,C]
# -> [A,B*] <-> [A,C] = [A,B*] & [A,C]
# order 2:
# -> [A,B] <-> [A,B,C] = [A,B*] & [A,C]
# -> [A,B*] <-> [A,C] = [A,B*] & [A,C]
# order 3:
# -> [A,C] <-> [A,B] = [A,C] & [A,B] & [A,B,C]
# -> [A,C] <-> [A,B,C] = [A,C*] & [A,B]
# -> [A,C*] <-> [A,B] = [A,C*] & [A,B]
# order 4:
# -> [A,C] <-> [A,B,C] = [A,C*] & [A,B]
# -> [A,C*] <-> [A,B] = [A,C*] & [A,B]
# order 5:
# -> [A,B,C] <-> [A,B] = [A,B*] & [A,C]
# -> [A,B*] <-> [A,C] = [A,B*] & [A,C]
# order 6:
# -> [A,B,C] <-> [A,C] = [A,C*] & [A,B]
# -> [A,C*] <-> [A,B] = [A,C*] & [A,B]
self.assertEqual(len(experiment_1), 2)
self.assertEqual(len(experiment_2), 2)
self.assertEqual(len(experiment_3), 2)
self.assertEqual(len(experiment_4), 2)
self.assertEqual(len(experiment_5), 2)
self.assertEqual(len(experiment_6), 2)