def test_normalize(self):
"""PositionalBaseUsage normalize should normalize each position"""
a, c, g = BaseUsage('AAGC'), BaseUsage('CCGA'), BaseUsage('GGCA')
p = PositionalBaseUsage(a, c, g)
self.assertEqual(p[0], {'A':2, 'C':1, 'G':1, 'U':0})
p.normalize()
self.assertEqual(p[0], {'A':0.5, 'C':0.25, 'G':0.25, 'U':0})
self.assertEqual(p[1], {'A':0.25, 'C':0.5, 'G':0.25, 'U':0})
self.assertEqual(p[2], {'A':0.25, 'C':0.25, 'G':0.5, 'U':0})
def test_info(self):
"""PositionalBaseUsage info should work as expected"""
#test a cycle of setting the Info and setting it back again
p = PositionalBaseUsage()
self.assertRaises(AttributeError, getattr, p, 'upper')
p.Info = 'xyz'
self.assertEqual(p.upper(), 'XYZ')
p.Info = None
self.assertRaises(AttributeError, getattr, p, 'upper')
def test_positionalBases(self):
"""PositionalBaseUsage positionalBases should return same object"""
p = PositionalBaseUsage()
x = p.positionalBases()
assert p is x
def test_bases(self):
"""PositionalBaseUsage bases should sum bases at each position"""
a, c, g = BaseUsage('AAGC'), BaseUsage('CCGA'), BaseUsage('GGCA')
p = PositionalBaseUsage(a, c, g)
b = p.bases()
self.assertEqual(b, BaseUsage('AAGCCCGAGGCA'))
