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_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_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_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_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_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)