def test_biom_data_from_vcfs_4(self):
"""Does the function return the correct output when given the correct input?"""
vcf = list(biom_data_from_vcfs(self.example_file4))
expected = [
array([[
0,
0,
], [
0,
0,
], [
0,
0,
], [0, 1]]), ['HG00096', 'HG00097'],
['10:89674917', '10:89674997', '10:89675036', '10:89675296'], None,
[{
'alleles': ('T', 'G'),
'rs': 'rs182708158'
}, {
'alleles': ('A', 'G'),
'rs': 'rs116819638'
}, {
'alleles': ('C', 'T'),
'rs': 'rs111627758'
}, {
'alleles': ('A', 'G'),
'rs': 'rs1234224'
}]
]
self.assertEqual(vcf, expected)
def test_biom_data_from_vcfs_8(self):
"""Does the function return the correct output when given the correct input?"""
vcf = list(biom_data_from_vcfs(self.example_file8))
expected = [
array([[1], [1], [2], [2], [2]]), ['ALO066'],
[
'chr1:43424812', 'chr1:158580428', 'chr1:158580759',
'chr1:158582646', 'chr1:158584091'
], None,
[{
'alleles': ('C', 'G'),
'rs': 'rs3754226'
}, {
'alleles': ('A', 'C'),
'rs': 'rs75855672'
}, {
'alleles': ('G', 'A'),
'rs': 'rs12601'
}, {
'alleles': ('T', 'C'),
'rs': 'rs2251969'
}, {
'alleles': ('A', 'G'),
'rs': 'rs952094'
}]
]
self.assertEqual(vcf, expected)
def test_biom_data_from_vcfs_5(self):
"""Does the function return the correct output when given the correct input?"""
vcf = list(biom_data_from_vcfs(self.example_file5))
expected = [
array([[2], [1], [1], [1], [1], [1]]), ['TNT028'],
[
'1:25611035', '1:25627613', '1:25627628', '1:25656531',
'1:25656673', '1:25688901'
], None,
[{
'alleles': ('G', 'C'),
'rs': 'rs2301153'
}, {
'alleles': ('C', 'A'),
'rs': '.'
}, {
'alleles': ('A', 'C'),
'rs': '.'
}, {
'alleles': ('T', 'C'),
'rs': '.'
}, {
'alleles': ('C', 'T'),
'rs': 'rs667179'
}, {
'alleles': ('T', 'G'),
'rs': '.'
}]
]
self.assertEqual(vcf, expected)
def test_biom_data_from_vcfs_9(self):
vcf = list(biom_data_from_vcfs([self.example_file9]))
expected = [
array([[1]]), ['ALO066'], ['chr4:144801728'], None,
[{
'alleles': ('C', 'T'),
'rs': '.'
}]
]
self.assertEqual(vcf, expected)
def test_biom_data_from_vcfs(self):
"""Does the function return the correct output when given the correct input?"""
vcf = list(biom_data_from_vcfs(self.example_file1))
expected = [
array([[0, 0, 0, 0, 0]]),
['HG00096', 'HG00097', 'HG00099', 'HG00100', 'HG00101'],
['10:89623323'], None, [{
'alleles': ('G', 'A'),
'rs': 'rs1044322'
}]
]
self.assertEqual(vcf, expected)
def test_biom_data_from_vcfs_7(self):
"""Does the function return the correct output when given the correct input?"""
vcf = list(biom_data_from_vcfs(self.example_file7))
expected = [
array([[0, 0], [0, 0], [0, 1]]), ['vac7wt', 'vac8wt'],
['NC_007779.1:10098', 'NC_007779.1:10099', 'NC_007779.1:10100'],
None,
[{
'alleles': ('C', 'T'),
'rs': '.'
}, {
'alleles': ('G', '.'),
'rs': '.'
}, {
'alleles': ('G', 'A'),
'rs': '.'
}]
]
self.assertEqual(vcf, expected)
def test_biom_data_from_vcfs_2(self):
"""Does the function return the correct output when given the correct input?"""
vcf = list(biom_data_from_vcfs(self.example_file2))
expected = [
array([[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]]),
[
'HG00096', 'HG00097', 'HG00099', 'HG00100', 'HG00101',
'HG00102', 'HG00103', 'HG00104', 'HG00106', 'HG00108',
'HG00109', 'HG00110'
], ['10:89674917', '10:89674997'], None,
[{
'alleles': ('T', 'G'),
'rs': 'rs182708158'
}, {
'alleles': ('A', 'G'),
'rs': 'rs116819638'
}]
]
self.assertEqual(vcf, expected)
def test_biom_data_from_vcfs(self):
"""Does the function return the correct output when given the correct input?"""
vcf = list(biom_data_from_vcfs(self.example_file1))
expected = [array([[0, 0, 0, 0, 0]]), ['HG00096', 'HG00097', 'HG00099', 'HG00100', 'HG00101'], ['10:89623323'], None, [{'alleles': ('G', 'A'), 'rs': 'rs1044322'}]]
self.assertEqual(vcf, expected)
def test_biom_data_from_vcfs_2(self):
"""Does the function return the correct output when given the correct input?"""
vcf = list(biom_data_from_vcfs(self.example_file2))
expected = [array([[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]]), ['HG00096', 'HG00097', 'HG00099', 'HG00100', 'HG00101', 'HG00102', 'HG00103', 'HG00104', 'HG00106', 'HG00108', 'HG00109', 'HG00110'], ['10:89674917', '10:89674997'], None, [{'alleles': ('T', 'G'), 'rs': 'rs182708158'}, {'alleles': ('A', 'G'), 'rs': 'rs116819638'}]]
self.assertEqual(vcf, expected)
def test_biom_data_from_vcfs_9(self):
vcf = list(biom_data_from_vcfs([self.example_file9]))
expected = [array([[1]]), ['ALO066'], ['chr4:144801728'], None, [{'alleles': ('C', 'T'), 'rs': '.'}]]
self.assertEqual(vcf, expected)
def test_biom_data_from_vcfs_8(self):
"""Does the function return the correct output when given the correct input?"""
vcf = list(biom_data_from_vcfs(self.example_file8))
expected = [array([[1], [1], [2], [2], [2]]), ['ALO066'], ['chr1:43424812', 'chr1:158580428', 'chr1:158580759', 'chr1:158582646', 'chr1:158584091'],
None, [{'alleles': ('C', 'G'), 'rs': 'rs3754226'}, {'alleles': ('A', 'C'), 'rs': 'rs75855672'}, {'alleles': ('G', 'A'), 'rs': 'rs12601'}, {'alleles': ('T', 'C'), 'rs': 'rs2251969'}, {'alleles': ('A', 'G'), 'rs': 'rs952094'}]]
self.assertEqual(vcf, expected)
def test_biom_data_from_vcfs_7(self):
"""Does the function return the correct output when given the correct input?"""
vcf = list(biom_data_from_vcfs(self.example_file7))
expected = [array([[0, 0], [0, 0], [0, 1]]), ['vac7wt', 'vac8wt'], ['NC_007779.1:10098', 'NC_007779.1:10099', 'NC_007779.1:10100'], None, [{'alleles': ('C', 'T'), 'rs': '.'}, {'alleles': ('G', '.'), 'rs': '.'}, {'alleles': ('G', 'A'), 'rs': '.'}]]
self.assertEqual(vcf, expected)
def test_biom_data_from_vcfs_5(self):
"""Does the function return the correct output when given the correct input?"""
vcf = list(biom_data_from_vcfs(self.example_file5))
expected = [array([[2],[1],[1],[1],[1],[1]]), ['TNT028'], ['1:25611035', '1:25627613', '1:25627628', '1:25656531', '1:25656673', '1:25688901'], None, [{'alleles': ('G', 'C'), 'rs': 'rs2301153'}, {'alleles': ('C', 'A'), 'rs': '.'}, {'alleles': ('A', 'C'), 'rs': '.'}, {'alleles': ('T', 'C'), 'rs': '.'}, {'alleles': ('C', 'T'), 'rs': 'rs667179'}, {'alleles': ('T', 'G'), 'rs': '.'}]]
self.assertEqual(vcf, expected)
def test_biom_data_from_vcfs_4(self):
"""Does the function return the correct output when given the correct input?"""
vcf = list(biom_data_from_vcfs(self.example_file4))
expected = [array([[0, 0,],[0, 0,],[0, 0,],[0, 1]]), ['HG00096', 'HG00097'], ['10:89674917', '10:89674997', '10:89675036', '10:89675296' ], None, [{'alleles': ('T', 'G'), 'rs': 'rs182708158'}, {'alleles': ('A', 'G'), 'rs': 'rs116819638'}, {'alleles': ('C', 'T'), 'rs': 'rs111627758'}, {'alleles': ('A', 'G'), 'rs': 'rs1234224'}]]
self.assertEqual(vcf, expected)