def test_positive_three_path_merged_exon(self):
'''
[]-----[]---->[*********]
[]---->[]--->[]
[]-----[======]------>[]
'''
self.ex7 = Exon('chrX', 1000, 4000, 'ex1.1', '+')
self.exonsDB[str(self.ex7)] = self.ex7
self.ex8 = Exon('chrX', 2000, 5000, 'ex1.1', '+')
self.exonsDB[str(self.ex8)] = self.ex8
path1 = ['start', str(self.ex4), str(self.ex1),
str(self.ex2), 'end']
path2 = ['start', str(self.ex4), str(self.ex1),
str(self.ex8), 'end']
path3 = ['start', str(self.ex4), str(self.ex7),
str(self.ex3), 'end']
self.transcripts = [path1, path2, path3]
self.graph.add_path(path1)
self.graph.add_path(path2)
self.graph.add_path(path3)
paths = list(find_ALE(self.graph, self.exonsDB, self.transcripts))
self.assertEqual(len(paths[0]), 2)
self.assertItemsEqual(get_num_exons(paths), [2, 2])
def test_positive_one_path_one_exon(self):
'''
[]-------->[]
'''
self.graph.add_path(['start', str(self.ex1),
str(self.ex2), 'end'])
self.transcripts = [[str(self.ex1), str(self.ex2)]]
paths = list(find_ALE(self.graph, self.exonsDB, self.transcripts))
self.assertEqual(len(paths[0]), 0)
def test_negative_one_path_one_exon(self):
'''
[]<------[]
'''
path = ['end', str(self.ex1), str(self.ex2), 'start']
path.reverse()
self.graph.add_path(path)
self.transcripts = [path]
paths = list(find_ALE(self.graph, self.exonsDB, self.transcripts))
self.assertEqual(len(paths[0]), 0)
def test_positive_two_path_one_exon(self):
'''
[]---------->[*]
[]------>[]
'''
path1 = ['start', str(self.ex1), str(self.ex2), 'end']
path2 = ['start', str(self.ex1), str(self.ex5), 'end']
self.graph.add_path(path1)
self.graph.add_path(path2)
self.transcripts = [path1, path2]
paths = list(find_ALE(self.graph, self.exonsDB, self.transcripts))
self.assertEqual(len(paths[0]), 2)
self.assertItemsEqual(get_num_exons(paths), [2, 2])
def test_positive_no_ALE_with_AFE(self):
'''
[]--------->[]--------->[]
[]------->[]--------->[]
'''
path1 = ['start', str(self.ex1), str(self.ex2),
str(self.ex3), 'end']
path2 = ['start', str(self.ex4), str(self.ex2),
str(self.ex3), 'end']
self.graph.add_path(path1)
self.graph.add_path(path2)
self.transcripts = [path1, path2]
paths = list(find_ALE(self.graph, self.exonsDB, self.transcripts))
self.assertEqual(len(paths[0]), 0)
def test_negative_two_path_one_exon(self):
'''
[]<-----------[]
[*]<------[]
'''
path1 = ['end', str(self.ex1), str(self.ex2), 'start']
path2 = ['end', str(self.ex4), str(self.ex2), 'start']
path1.reverse()
path2.reverse()
self.graph.add_path(path1)
self.graph.add_path(path2)
self.transcripts = [path1, path2]
paths = list(find_ALE(self.graph, self.exonsDB, self.transcripts))
self.assertEqual(len(paths[0]), 2)
self.assertItemsEqual(get_num_exons(paths), [2, 2])
def test_positive_two_path_two_exon(self):
'''
[]-------->[]------->[]
[]-------->[]----->[*]---->[*]
'''
self.ex6 = Exon('chrX', 7000, 8000, 'ex1.1', '+')
self.exonsDB[str(self.ex6)] = self.ex6
path1 = ['start', str(self.ex4),
str(self.ex1), str(self.ex2), 'end']
path2 = ['start', str(self.ex4), str(self.ex1),
str(self.ex5), str(self.ex6), 'end']
self.graph.add_path(path1)
self.graph.add_path(path2)
self.transcripts = [path1, path2]
paths = list(find_ALE(self.graph, self.exonsDB, self.transcripts))
self.assertEqual(len(paths[0]), 2)
self.assertItemsEqual(get_num_exons(paths), [2, 3])
def test_negative_no_ALE_with_AFE(self):
'''
[]<------[]<-----[]<-------[]
[]<------[]<--[*]
'''
path1 = (['end', str(self.ex4), str(self.ex1),
str(self.ex2), str(self.ex3), 'start'])
path2 = (['end', str(self.ex4),
str(self.ex1), str(self.ex5), 'start'])
path1.reverse()
path2.reverse()
self.graph.add_path(path1)
self.graph.add_path(path2)
self.transcripts = [path1, path2]
paths = list(find_ALE(self.graph, self.exonsDB, self.transcripts))
self.assertEqual(len(paths[0]), 0)
def test_negative_single_ALE_with_AFE(self):
'''
[]<-------[]<-------[]
[*]<---[]<----------[]
'''
self.ex6 = Exon('chrX', 7000, 8000, 'ex1.1', '+')
self.exonsDB[str(self.ex6)] = self.ex6
path1 = (['end', str(self.ex4), str(self.ex2),
str(self.ex3), 'start'])
path2 = (['end', str(self.ex1),
str(self.ex2), str(self.ex6), 'start'])
path1.reverse()
path2.reverse()
self.graph.add_path(path1)
self.graph.add_path(path2)
self.transcripts = [path1, path2]
paths = list(find_ALE(self.graph, self.exonsDB, self.transcripts))
self.assertEqual(len(paths[0]), 2)
self.assertItemsEqual(get_num_exons(paths), [2, 2])