class ConnectWriterTest(unittest.TestCase):
    def setUp(self):
        dot_parser = DB.Parser('((..))')
        dot_parser.sequence = 'ccaagg'
        self.writer = Writer()
        self.connect = self.writer.format(dot_parser)

    def test_formats_correctly(self):
        ans = ['6 Energy = ', 
               '1\tc\t0\t2\t6\t1',
               '2\tc\t1\t3\t5\t2',
               '3\ta\t2\t4\t0\t3',
               '4\ta\t3\t5\t0\t4',
               '5\tg\t4\t6\t2\t5',
               '6\tg\t5\t0\t1\t6',
               '']
        val = self.connect.split('\n')
        self.assertEqual(val, ans)

    def test_roundtrip(self):
        lines = StringIO(self.connect)
        parser = Parser(lines)
        val = parser.indices()['hairpin']
        ans = [([2, 3],)]
        self.assertEqual(val, ans)
class ConnectWriterTest(unittest.TestCase):
    def setUp(self):
        dot_parser = DB.Parser('((..))')
        self.writer = Writer()
        self.connect = self.writer.format(dot_parser)

    def test_formats_correctly(self):
        ans = [
            '6 Energy = ', '1\t?\t0\t2\t6\t1', '2\t?\t1\t3\t5\t2',
            '3\t?\t2\t4\t0\t3', '4\t?\t3\t5\t0\t4', '5\t?\t4\t6\t2\t5',
            '6\t?\t5\t0\t1\t6', ''
        ]
        val = self.connect.split('\n')
        self.assertEqual(val, ans)

    def test_roundtrip(self):
        lines = StringIO(self.connect)
        parser = Parser(lines)
        val = parser.indices()['hairpin']
        ans = [([2, 3], )]
        self.assertEqual(val, ans)
 def setUp(self):
     dot_parser = DB.Parser('((..))')
     self.writer = Writer()
     self.connect = self.writer.format(dot_parser)
 def setUp(self):
     dot_parser = DB.Parser('((..))')
     dot_parser.sequence = 'ccaagg'
     self.writer = Writer()
     self.connect = self.writer.format(dot_parser)
 def setUp(self):
     dot_parser = DB.Parser('((..))')
     self.writer = Writer()
     self.connect = self.writer.format(dot_parser)
 def setUp(self):
     dot_parser = DB.Parser('((..))')
     dot_parser.sequence = 'ccaagg'
     self.writer = Writer()
     self.connect = self.writer.format(dot_parser)
Exemple #7
0
 def input_file(self, input_file, raw):
     """Takes the parsed secondary structure and generates the Connect file
     needed for RemovePseudoknots
     """
     formatter = CtWriter()
     formatter.write(input_file, raw)