def test_parse_medium_yaml_file(self):
path = self.write_model_file(
'medium.yaml', '\n'.join([
'compartment: e',
'compounds:',
' - id: cpd_A',
' reaction: EX_A',
' lower: -40',
' - id: cpd_B',
' upper: 100',
' - id: cpd_C',
' lower: -100.0',
' upper: 500.0',
' - id: cpd_D',
' compartment: c',
' - id: cpd_E',
' fixed: 100.0',
]))
medium = list(native.parse_medium_file(path, 'e'))
self.assertEqual(medium, [(Compound('cpd_A', 'e'), 'EX_A', -40, None),
(Compound('cpd_B', 'e'), None, None, 100),
(Compound('cpd_C', 'e'), None, -100, 500),
(Compound('cpd_D', 'c'), None, None, None),
(Compound('cpd_E', 'e'), None, 100, 100)])
def test_parse_medium_table_file(self):
path = self.write_model_file(
'medium.tsv', '\n'.join([
'', '# comment', 'cpd_A\tc', 'cpd_B\te\t-1000',
'cpd_C\te\t-\t20 # line comment', 'cpd_D\te\t-100\t-10'
]))
medium = list(native.parse_medium_file(path, 'e'))
self.assertEqual(medium, [(Compound('cpd_A', 'c'), None, None, None),
(Compound('cpd_B', 'e'), None, -1000, None),
(Compound('cpd_C', 'e'), None, None, 20),
(Compound('cpd_D', 'e'), None, -100, -10)])
def test_parse_medium_table_file(self):
path = self.write_model_file('medium.tsv', '\n'.join([
'',
'# comment',
'cpd_A\tc',
'cpd_B\te\t-1000',
'cpd_C\te\t-\t20 # line comment',
'cpd_D\te\t-100\t-10'
]))
medium = list(native.parse_medium_file(path))
self.assertEqual(medium, [
(Compound('cpd_A', 'c'), None, None, None),
(Compound('cpd_B', 'e'), None, -1000, None),
(Compound('cpd_C', 'e'), None, None, 20),
(Compound('cpd_D', 'e'), None, -100, -10)
])
def test_parse_medium_yaml_file(self):
path = self.write_model_file('medium.yaml', '\n'.join([
'compartment: e',
'compounds:',
' - id: cpd_A',
' reaction: EX_A',
' lower: -40',
' - id: cpd_B',
' upper: 100',
' - id: cpd_C',
' lower: -100.0',
' upper: 500.0',
' - id: cpd_D',
' compartment: c'
]))
medium = list(native.parse_medium_file(path))
self.assertEqual(medium, [
(Compound('cpd_A', 'e'), 'EX_A', -40, None),
(Compound('cpd_B', 'e'), None, None, 100),
(Compound('cpd_C', 'e'), None, -100, 500),
(Compound('cpd_D', 'c'), None, None, None)
])
