Python parse_model_file Examples

Example #1

    def test_parse_model_table_file(self):
        path = self.write_model_file(
            'model_1.tsv', '\n'.join([
                '# comment', 'rxn_1', 'rxn_2', 'rxn_3', 'rxn_4  # line comment'
            ]))

        reactions = list(native.parse_model_file(path))
        self.assertEqual(reactions, ['rxn_1', 'rxn_2', 'rxn_3', 'rxn_4'])

Example #2

File: test_yaml.py Project: amenge/psamm

    def test_parse_model_table_file(self):
        path = self.write_model_file('model_1.tsv', '\n'.join([
            '# comment',
            'rxn_1',
            'rxn_2',
            'rxn_3',
            'rxn_4  # line comment']))

        reactions = list(native.parse_model_file(path))
        self.assertEqual(reactions, ['rxn_1', 'rxn_2', 'rxn_3', 'rxn_4'])

Example #3

File: test_yaml.py Project: amenge/psamm

    def test_parse_model_yaml_file(self):
        path = self.write_model_file('model_1.yaml', '''---
            - include: model_2.yaml
            - reactions:
              - rxn_3
              - rxn_4''')

        self.write_model_file('model_2.yaml', '''---
            - groups:
              - name: First group
                reactions: [rxn_1]
              - name: Second group
                reactions: [rxn_2]''')

        reactions = list(native.parse_model_file(path))
        self.assertEqual(reactions, ['rxn_1', 'rxn_2', 'rxn_3', 'rxn_4'])

Example #4

    def test_parse_model_yaml_file(self):
        path = self.write_model_file('model_1.yaml', '''---
            - include: model_2.yaml
            - reactions:
              - rxn_3
              - rxn_4''')

        self.write_model_file('model_2.yaml', '''---
            - groups:
              - name: First group
                reactions: [rxn_1]
              - name: Second group
                reactions: [rxn_2]''')

        reactions = list(native.parse_model_file(path))
        self.assertEqual(reactions, ['rxn_1', 'rxn_2', 'rxn_3', 'rxn_4'])