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)
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)