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_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_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_getitem(self):
"""PositionalBaseUsage getitem should return 1st, 2nd, 3rd in order"""
a, c, g = BaseUsage('A'), BaseUsage('C'), BaseUsage('G')
p = PositionalBaseUsage(a, c, g)
assert p.First is a
assert p.Second is c
assert p.Third is g
#make sure they're not all the same object
assert p.First is not g
#test positive indices
assert p[0] is p.First
assert p[1] is p.Second
assert p[2] is p.Third
#test negative indices
assert p[-1] is p.Third
assert p[-2] is p.Second
assert p[-3] is p.First
try:
x = p[3]
except IndexError:
pass
else:
self.fail("Failed to raise IndexError on bad index")
#test iteration
for o, e in zip(p, [a, c, g]):
assert o is e
def test_init_empty(self):
"""PositionalBaseUsage init when empty should set all freqs to 0"""
p = PositionalBaseUsage()
assert p[0] is not p[1]
assert p[1] is not p[2]
assert p[0] is not p[2]
for i in p:
self.assertEqual(i, BaseUsage())
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'))
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'))