def test_group_nucs_blank(self):
output_file = StringIO("""\
sample,seed,region,query.nuc.pos,coverage
s1,R1-seed,R1,100,10
s1,R1-seed,R1,110,10
s1,R1-seed,R1,,0
""")
expected_groups = dict(
s1={
('R1-seed', 'R1'): [('x', {
'coverage': '10',
'query.nuc.pos': '100',
'region': 'R1',
'sample': 's1',
'seed': 'R1-seed'
}),
('x', {
'coverage': '10',
'query.nuc.pos': '110',
'region': 'R1',
'sample': 's1',
'seed': 'R1-seed'
}),
('x', {
'coverage': '0',
'query.nuc.pos': '',
'region': 'R1',
'sample': 's1',
'seed': 'R1-seed'
})]
})
groups = group_nucs_file(output_file)
self.assertEqual(expected_groups, groups)
def test_group_nucs_single(self):
output_file = StringIO("""\
sample,seed,region,query.nuc.pos
s1,R1-seed,R1,100
s1,R1-seed,R1,110
""")
expected_groups = dict(s1={'R1-seed': [('R1', 100, 110)]})
groups = group_nucs_file(output_file)
self.assertEqual(expected_groups, groups)
def test_group_nucs_single(self):
output_file = StringIO("""\
sample,seed,region,query.nuc.pos
s1,R1-seed,R1,100
s1,R1-seed,R1,110
""")
expected_groups = dict(s1={'R1-seed': [('R1', 100, 110)]})
groups = group_nucs_file(output_file)
self.assertEqual(expected_groups, groups)
def test_group_nucs_two_regions(self):
output_file = StringIO("""\
sample,seed,region,query.nuc.pos
s1,R1-seed,R1a,100
s1,R1-seed,R1a,110
s1,R1-seed,R1b,201
s1,R1-seed,R1b,211
""")
expected_groups = dict(
s1={'R1-seed': [('R1a', 100, 110), ('R1b', 201, 211)]})
groups = group_nucs_file(output_file)
self.assertEqual(expected_groups, groups)
def test_group_nucs_two_regions(self):
output_file = StringIO("""\
sample,seed,region,query.nuc.pos
s1,R1-seed,R1a,100
s1,R1-seed,R1a,110
s1,R1-seed,R1b,201
s1,R1-seed,R1b,211
""")
expected_groups = dict(s1={'R1-seed': [('R1a', 100, 110),
('R1b', 201, 211)]})
groups = group_nucs_file(output_file)
self.assertEqual(expected_groups, groups)
def test_group_nucs_with_coverage(self):
output_file = StringIO("""\
sample,seed,region,query.nuc.pos,A,C,G,T,del,ins,coverage
s1,R1-seed,R1,100,100,0,0,0,0,0,100
s1,R1-seed,R1,101,99,1,0,0,0,0,100
s1,R1-seed,R1,102,1,99,0,0,0,0,100
s1,R1-seed,R1,103,0,99,0,0,0,0,99
""")
expected_groups = dict(
s1={
('R1-seed', 'R1'): [('A', {
'A': '100',
'C': '0',
'G': '0',
'T': '0',
'coverage': '100',
'del': '0',
'ins': '0',
'query.nuc.pos': '100',
'region': 'R1',
'sample': 's1',
'seed': 'R1-seed'
}),
('A', {
'A': '99',
'C': '1',
'G': '0',
'T': '0',
'coverage': '100',
'del': '0',
'ins': '0',
'query.nuc.pos': '101',
'region': 'R1',
'sample': 's1',
'seed': 'R1-seed'
}),
('C', {
'A': '1',
'C': '99',
'G': '0',
'T': '0',
'coverage': '100',
'del': '0',
'ins': '0',
'query.nuc.pos': '102',
'region': 'R1',
'sample': 's1',
'seed': 'R1-seed'
}),
('x', {
'A': '0',
'C': '99',
'G': '0',
'T': '0',
'coverage': '99',
'del': '0',
'ins': '0',
'query.nuc.pos': '103',
'region': 'R1',
'sample': 's1',
'seed': 'R1-seed'
})]
})
groups = group_nucs_file(output_file)
self.assertEqual(expected_groups, groups)