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 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::')
class WussStructureTests(StructureStringTests):
"""Test that WussStructure methods and properties work"""
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_wuss_toPairs(self):
"""WussStructure toPairs() should return a valid Pairs object"""
self.assertEqual(self.WussNoPairs.toPairs(), [])
self.assertEqualItems(self.WussOneHelix.toPairs(),\
[(0,12),(2,11),(3,10),(4,7)])
self.assertEqualItems(self.WussTwoHelix.toPairs(),\
[(0,4),(1,3),(5,8),(6,7)])
self.assertEqualItems(self.WussThreeHelix.toPairs(),\
[(2,25),(3,24),(4,23),(5,10),(6,9),(13,20),(14,19),(15,18)])
self.assertEqualItems(self.WussPseudo.toPairs(),\
[(0,7),(1,6)])
def test_wuss_toPartners(self):
"""WussStructure toPartners() should return valid Partners object"""
self.assertEqual(self.WussNoPairs.toPartners(), [None] * 6)
self.assertEqualItems(self.WussThreeHelix.toPartners(),\
[None,None,25,24,23,10,9,None,None,6,5,None,None,20,19,\
18,None,None,15,14,13,None,None,4,3,2])
self.assertEqualItems(self.WussPseudo.toPartners(),\
[7,6,None,None,None,None,1,0,None,None,None,None,None])
class WussStructureTests(StructureStringTests):
"""Test that WussStructure methods and properties work"""
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_wuss_toPairs(self):
"""WussStructure toPairs() should return a valid Pairs object"""
self.assertEqual(self.WussNoPairs.toPairs(),[])
self.assertEqualItems(self.WussOneHelix.toPairs(),\
[(0,12),(2,11),(3,10),(4,7)])
self.assertEqualItems(self.WussTwoHelix.toPairs(),\
[(0,4),(1,3),(5,8),(6,7)])
self.assertEqualItems(self.WussThreeHelix.toPairs(),\
[(2,25),(3,24),(4,23),(5,10),(6,9),(13,20),(14,19),(15,18)])
self.assertEqualItems(self.WussPseudo.toPairs(),\
[(0,7),(1,6)])
def test_wuss_toPartners(self):
"""WussStructure toPartners() should return valid Partners object"""
self.assertEqual(self.WussNoPairs.toPartners(),[None]*6)
self.assertEqualItems(self.WussThreeHelix.toPartners(),\
[None,None,25,24,23,10,9,None,None,6,5,None,None,20,19,\
18,None,None,15,14,13,None,None,4,3,2])
self.assertEqualItems(self.WussPseudo.toPartners(),\
[7,6,None,None,None,None,1,0,None,None,None,None,None])
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)