def test_wuss_to_vienna(self):
"""wuss_to_vienna() should transform Wuss into Vienna"""
empty = WussStructure('.....')
normal = WussStructure('[.{[<...}}}}')
pseudo = WussStructure('[..AA..]..aa')
self.assertEqual(wuss_to_vienna(normal), '(.(((...))))')
self.assertEqual(wuss_to_vienna(empty), '.....')
self.assertEqual(wuss_to_vienna(pseudo), '(......)....')
def setUp(self):
"""Define three standard structures: note differences in whitespace
and number formatting"""
self.Struct = WussStructure
super(WussStructureTests, self).setUp()
self.WussNoPairs = WussStructure('.-_,~:')
self.WussOneHelix = WussStructure('[-{<(__)-->}]', -0.01)
self.WussTwoHelix = WussStructure('{[.]}(<>).', 1.11)
self.WussThreeHelix = WussStructure('::(<<({__}),,([(__)])-->>)')
self.WussPseudo = WussStructure('<<__AA>>_aa::')
def test_MinimalStockholmParser_w_valid_data(self):
"""MinimalStockholmParser: integrity of output """
# Some ugly constructions here, but this is what the output of
# parsing fake_two_records should be
headers = ['#=GF AC RF00014', '#=GF AU Mifsud W']
sequences =\
{'U17136.1/898-984':\
''.join(['AACACAUCAGAUUUCCUGGUGUAACGAAUUUUUUAAGUGCUUCUUGCUUA',\
'AGCAAGUUUCAUCCCGACCCCCUCAGGGUCGGGAUUU']),\
'M15749.1/155-239':\
''.join(['AACGCAUCGGAUUUCCCGGUGUAACGAA-UUUUCAAGUGCUUCUUGCAUU',\
'AGCAAGUUUGAUCCCGACUCCUG-CGAGUCGGGAUUU']),\
'AF090431.1/222-139':\
''.join(['CUCACAUCAGAUUUCCUGGUGUAACGAA-UUUUCAAGUGCUUCUUGCAUA',\
'AGCAAGUUUGAUCCCGACCCGU--AGGGCCGGGAUUU'])}
structure = WussStructure(''.join(\
['...<<<<<<<.....>>>>>>>....................<<<<<...',\
'.>>>>>....<<<<<<<<<<.....>>>>>>>>>>..']))
data = []
for r in MinimalStockholmParser(self._fake_two_records, strict=False):
data.append(r)
self.assertEqual(\
(data[0][0]['GF'],data[0][1].todict(),\
str(data[0][2])),(headers,sequences,structure))
assert isinstance(data[0][1], Alignment)
# This line tests that invalid entries are ignored when strict=False
# Note, there are two records in self._fake_two_records, but 2nd is
# invalid
self.assertEqual(len(data), 1)
