Python _tabular_msa_to_phylip Examples

Example #1

File: test_phylip.py Project: zengqingsong/scikit-bio

    def test_write_invalid_alignment(self):
        for invalid_obj, error_msg_regexp in self.invalid_objs:
            fh = io.StringIO()
            with self.assertRaisesRegex(PhylipFormatError, error_msg_regexp):
                _tabular_msa_to_phylip(invalid_obj, fh)

            # ensure nothing was written to the file before the error was
            # thrown
            obs = fh.getvalue()
            fh.close()
            self.assertEqual(obs, '')

Example #2

File: test_phylip.py Project: ebolyen/scikit-bio

    def test_write(self):
        for fp, obj in zip(self.fps, self.objs):
            fh = io.StringIO()
            _tabular_msa_to_phylip(obj, fh)
            obs = fh.getvalue()
            fh.close()

            with io.open(fp) as fh:
                exp = fh.read()

            self.assertEqual(obs, exp)

Example #3

File: test_phylip.py Project: zengqingsong/scikit-bio

    def test_write(self):
        for fp, obj in zip(self.fps, self.objs):
            fh = io.StringIO()
            _tabular_msa_to_phylip(obj, fh)
            obs = fh.getvalue()
            fh.close()

            with io.open(fp) as fh:
                exp = fh.read()

            self.assertEqual(obs, exp)

Example #4

File: test_phylip.py Project: RNAer/scikit-bio

    def test_write_invalid_alignment(self):
        for invalid_obj, error_msg_regexp in self.invalid_objs:
            fh = io.StringIO()
            with self.assertRaisesRegex(PhylipFormatError, error_msg_regexp):
                _tabular_msa_to_phylip(invalid_obj, fh)

            # ensure nothing was written to the file before the error was
            # thrown
            obs = fh.getvalue()
            fh.close()
            self.assertEqual(obs, '')