def test_process_data_entry_line(self):
"""Does this work when given correct input?"""
ids = ['HG00096', 'HG00097', 'HG00099', 'HG00100', 'HG00101']
line = '10 89623323 rs1044322 G A 100 PASS . GT:AP 0|0:0.015,0.000 0|0:0.000,0.000 0|0:0.002,0.000 0|0:0.000,0.052 0|0:0.000,0.000'
expected = ('10', '89623323', 'rs1044322', 'G', 'A',
[('HG00096', [0, 0]), ('HG00097', [0, 0]),
('HG00099', [0, 0]), ('HG00100', [0, 0]),
('HG00101', [0, 0])])
self.assertEqual(process_data_entry_line(line, ids), expected)
def test_process_data_entry_line_3(self):
"""Does this work when given correct input?"""
ids = [
'HG00096', 'HG00097', 'HG00099', 'HG00100', 'HG00101', 'HG00102',
'HG00103', 'HG00104', 'HG00106', 'HG00108', 'HG00109', 'HG00110'
]
line = '10 89674997 rs116819638 A TGC,GA 100 PASS ERATE=0.0004;AN=2184;AC=13;VT=SNP;RSQ=0.9179;AA=A;AVGPOST=0.9989;LDAF=0.0063;SNPSOURCE=LOWCOV;THETA=0.0013;AF=0.01;AFR_AF=0.03 GT:DS:GL 0|0:0.000:-0.03,-1.23,-5.00 0|0:0.000:-0.02,-1.33,-5.00 0|0:0.000:-0.02,-1.33,-5.00 0|0:0.000:-0.03,-1.21,-5.00 0|0:0.000:-0.06,-0.87,-5.00 0|0:0.000:-0.48,-0.48,-0.48 0|0:0.000:-0.10,-0.69,-4.70 0|0:0.000:-0.03,-1.22,-5.00 0|0:0.000:-0.01,-1.49,-5.00 0|0:0.000:-0.00,-2.05,-5.00 0|0:0.000:-0.06,-0.87,-5.00 0|0:0.000:-0.06,-0.90,-5.00'
expected = ('10', '89674997', 'rs116819638', 'A', 'TGC,GA',
[('HG00096', [0, 0]), ('HG00097', [0, 0]),
('HG00099', [0, 0]), ('HG00100', [0, 0]),
('HG00101', [0, 0]), ('HG00102', [0, 0]),
('HG00103', [0, 0]), ('HG00104', [0, 0]),
('HG00106', [0, 0]), ('HG00108', [0, 0]),
('HG00109', [0, 0]), ('HG00110', [0, 0])])
self.assertEqual(process_data_entry_line(line, ids), expected)
def test_process_data_entry_line_3(self):
"""Does this work when given correct input?"""
line = '10 89674997 rs116819638 A TGC,GA 100 PASS ERATE=0.0004;AN=2184;AC=13;VT=SNP;RSQ=0.9179;AA=A;AVGPOST=0.9989;LDAF=0.0063;SNPSOURCE=LOWCOV;THETA=0.0013;AF=0.01;AFR_AF=0.03 GT:DS:GL 0|0:0.000:-0.03,-1.23,-5.00 0|0:0.000:-0.02,-1.33,-5.00 0|0:0.000:-0.02,-1.33,-5.00 0|0:0.000:-0.03,-1.21,-5.00 0|0:0.000:-0.06,-0.87,-5.00 0|0:0.000:-0.48,-0.48,-0.48 0|0:0.000:-0.10,-0.69,-4.70 0|0:0.000:-0.03,-1.22,-5.00 0|0:0.000:-0.01,-1.49,-5.00 0|0:0.000:-0.00,-2.05,-5.00 0|0:0.000:-0.06,-0.87,-5.00 0|0:0.000:-0.06,-0.90,-5.00'
expected = ('10', '89674997', 'rs116819638', 'A', 'TGC,GA', ['0|0:0.000:-0.03,-1.23,-5.00', '0|0:0.000:-0.02,-1.33,-5.00', '0|0:0.000:-0.02,-1.33,-5.00', '0|0:0.000:-0.03,-1.21,-5.00', '0|0:0.000:-0.06,-0.87,-5.00', '0|0:0.000:-0.48,-0.48,-0.48', '0|0:0.000:-0.10,-0.69,-4.70', '0|0:0.000:-0.03,-1.22,-5.00', '0|0:0.000:-0.01,-1.49,-5.00', '0|0:0.000:-0.00,-2.05,-5.00', '0|0:0.000:-0.06,-0.87,-5.00', '0|0:0.000:-0.06,-0.90,-5.00'])
self.assertEqual(process_data_entry_line(line), expected)
def test_process_data_entry_line(self):
"""Does this work when given correct input?"""
line = '10 89623323 rs1044322 G A 100 PASS . GT:AP 0|0:0.015,0.000 0|0:0.000,0.000 0|0:0.002,0.000 0|0:0.000,0.052 0|0:0.000,0.000'
expected = ('10', '89623323', 'rs1044322', 'G', 'A', ['0|0:0.015,0.000', '0|0:0.000,0.000', '0|0:0.002,0.000', '0|0:0.000,0.052', '0|0:0.000,0.000'])
self.assertEqual(process_data_entry_line(line), expected)
def test_process_data_entry_line_2(self):
"""Does this work when given correct input?"""
ids = ['HG00096', 'HG00097', 'HG00099', 'HG00100', 'HG00101', 'HG00102', 'HG00103', 'HG00104', 'HG00106', 'HG00108', 'HG00109', 'HG00110']
line = '10 89674997 rs116819638 A G 100 PASS ERATE=0.0004;AN=2184;AC=13;VT=SNP;RSQ=0.9179;AA=A;AVGPOST=0.9989;LDAF=0.0063;SNPSOURCE=LOWCOV;THETA=0.0013;AF=0.01;AFR_AF=0.03 GT:DS:GL 0|0:0.000:-0.03,-1.23,-5.00 0|0:0.000:-0.02,-1.33,-5.00 0|0:0.000:-0.02,-1.33,-5.00 0|0:0.000:-0.03,-1.21,-5.00 0|0:0.000:-0.06,-0.87,-5.00 0|0:0.000:-0.48,-0.48,-0.48 0|0:0.000:-0.10,-0.69,-4.70 0|0:0.000:-0.03,-1.22,-5.00 0|0:0.000:-0.01,-1.49,-5.00 0|0:0.000:-0.00,-2.05,-5.00 0|0:0.000:-0.06,-0.87,-5.00 0|0:0.000:-0.06,-0.90,-5.00'
expected = ('10', '89674997', 'rs116819638', 'A', 'G', [('HG00096', [0, 0]), ('HG00097', [0, 0]), ('HG00099', [0, 0]), ('HG00100', [0, 0]), ('HG00101', [0, 0]), ('HG00102', [0, 0]), ('HG00103', [0, 0]), ('HG00104', [0, 0]), ('HG00106', [0, 0]), ('HG00108', [0, 0]), ('HG00109', [0, 0]), ('HG00110', [0, 0])])
self.assertEqual(process_data_entry_line(line, ids), expected)
def test_process_data_entry_line(self):
"""Does this work when given correct input?"""
ids = ['HG00096', 'HG00097', 'HG00099', 'HG00100', 'HG00101']
line = '10 89623323 rs1044322 G A 100 PASS . GT:AP 0|0:0.015,0.000 0|0:0.000,0.000 0|0:0.002,0.000 0|0:0.000,0.052 0|0:0.000,0.000'
expected = ('10', '89623323', 'rs1044322', 'G', 'A', [('HG00096',[0,0]), ('HG00097', [0,0]), ('HG00099', [0,0]), ('HG00100', [0,0]), ('HG00101', [0,0])])
self.assertEqual(process_data_entry_line(line, ids), expected)
