Beispiel #1
0
    def test_write(self):
        for fp, obj in zip(self.fps, self.objs):
            fh = StringIO()
            _alignment_to_phylip(obj, fh)
            obs = fh.getvalue()
            fh.close()

            with open(fp, 'U') as fh:
                exp = fh.read()

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

            with open(fp, 'U') as fh:
                exp = fh.read()

            self.assertEqual(obs, exp)
    def test_write_invalid_alignment(self):
        for invalid_obj, error_msg_regexp in self.invalid_objs:
            fh = StringIO()
            with self.assertRaisesRegexp(PhylipFormatError, error_msg_regexp):
                _alignment_to_phylip(invalid_obj, fh)

            # ensure nothing was written to the file before the error was
            # thrown. TODO remove this check when #674 is resolved
            obs = fh.getvalue()
            fh.close()
            self.assertEqual(obs, '')
Beispiel #4
0
    def test_write_invalid_alignment(self):
        for invalid_obj, error_msg_regexp in self.invalid_objs:
            fh = StringIO()
            with self.assertRaisesRegexp(PhylipFormatError, error_msg_regexp):
                _alignment_to_phylip(invalid_obj, fh)

            # ensure nothing was written to the file before the error was
            # thrown. TODO remove this check when #674 is resolved
            obs = fh.getvalue()
            fh.close()
            self.assertEqual(obs, '')