def test_distance(self):
"""BaseUsage distance() should return dist between two BUs"""
#absolute numbers, will normalize to calculate distance
self.assertFloatEqual(BaseUsage('GC').distance(BaseUsage('AU')),1)
self.assertFloatEqual(BaseUsage('AU').distance(BaseUsage('GC')),1)
self.assertFloatEqual(BaseUsage('GCAU').distance(BaseUsage('AUAU')),.5)
#should work even against dict with 'T's
self.assertFloatEqual(BaseUsage('GCAU').distance(\
BaseUsage({'A':2,'T':2,'C':0,'G':0,})),.5)
#rounding error
self.assertEqual(BaseUsage('ACG').distance(BaseUsage('CCGGAA')),0)
#normalized - as in unit simplex
ag = BaseUsage('AG')
ag.normalize()
uc = BaseUsage('UC')
uc.normalize()
self.assertFloatEqual(ag.distance(uc),1)
self.assertFloatEqual(BaseUsage({'A':0.4,'G':0.1,'C':0.4,'U':0.1})\
.distance(BaseUsage({'A':0.1,'G':0.4,'U':0.4,'C':0.1})),0.6)
self.assertFloatEqual(BaseUsage({'A':0.25,'G':0.25,'C':0.25,'U':0.25})\
.distance(BaseUsage({'A':0.25,'G':0.25,'U':0.25,'C':0.25})),0.0)
self.assertFloatEqual(BaseUsage({'A':0.245,'G':0.255,'C':0.245,\
'U':0.255}).distance(BaseUsage({'A':0.255,'G':0.245,'U':0.245,\
'C':0.255})),0.02)
self.assertFloatEqual(BaseUsage({'A':0.245,'G':0.255,'C':0.245,\
'U':0.255}).distance(BaseUsage({'A':0.25,'G':0.25,'U':0.25,\
'C':0.25})),0.01)
self.assertFloatEqual(BaseUsage({'A':0.248,'G':0.252,'C':0.248,\
'U':0.252}).distance(BaseUsage({'A':0.25,'G':0.25,'U':0.25,\
'C':0.25})),0.004)
def test_distance(self):
"""BaseUsage distance() should return dist between two BUs"""
#absolute numbers, will normalize to calculate distance
self.assertFloatEqual(BaseUsage('GC').distance(BaseUsage('AU')), 1)
self.assertFloatEqual(BaseUsage('AU').distance(BaseUsage('GC')), 1)
self.assertFloatEqual(
BaseUsage('GCAU').distance(BaseUsage('AUAU')), .5)
#should work even against dict with 'T's
self.assertFloatEqual(BaseUsage('GCAU').distance(\
BaseUsage({'A':2,'T':2,'C':0,'G':0,})),.5)
#rounding error
self.assertEqual(BaseUsage('ACG').distance(BaseUsage('CCGGAA')), 0)
#normalized - as in unit simplex
ag = BaseUsage('AG')
ag.normalize()
uc = BaseUsage('UC')
uc.normalize()
self.assertFloatEqual(ag.distance(uc), 1)
self.assertFloatEqual(BaseUsage({'A':0.4,'G':0.1,'C':0.4,'U':0.1})\
.distance(BaseUsage({'A':0.1,'G':0.4,'U':0.4,'C':0.1})),0.6)
self.assertFloatEqual(BaseUsage({'A':0.25,'G':0.25,'C':0.25,'U':0.25})\
.distance(BaseUsage({'A':0.25,'G':0.25,'U':0.25,'C':0.25})),0.0)
self.assertFloatEqual(BaseUsage({'A':0.245,'G':0.255,'C':0.245,\
'U':0.255}).distance(BaseUsage({'A':0.255,'G':0.245,'U':0.245,\
'C':0.255})),0.02)
self.assertFloatEqual(BaseUsage({'A':0.245,'G':0.255,'C':0.245,\
'U':0.255}).distance(BaseUsage({'A':0.25,'G':0.25,'U':0.25,\
'C':0.25})),0.01)
self.assertFloatEqual(BaseUsage({'A':0.248,'G':0.252,'C':0.248,\
'U':0.252}).distance(BaseUsage({'A':0.25,'G':0.25,'U':0.25,\
'C':0.25})),0.004)
def test_normalize(self):
"""BaseUsage normalize should work when empty"""
b = BaseUsage()
b.normalize()
self.assertEqual(b, {'U':0,'C':0,'A':0,'G':0})
b = BaseUsage('AACG')
b.normalize()
self.assertEqual(b, {'U':0, 'C':0.25, 'A':0.5, 'G':0.25})
def test_normalize(self):
"""BaseUsage normalize should work when empty"""
b = BaseUsage()
b.normalize()
self.assertEqual(b, {'U': 0, 'C': 0, 'A': 0, 'G': 0})
b = BaseUsage('AACG')
b.normalize()
self.assertEqual(b, {'U': 0, 'C': 0.25, 'A': 0.5, 'G': 0.25})
def test_setitem(self):
"""BaseUsage should map keys on setitem"""
b = BaseUsage()
b['t'] = 3
b['G'] = 3
b.normalize()
i = b.items()
i.sort()
self.assertEqual(i, [('A',0.0),('C',0.0),('G',0.5),('U',0.5)])
def test_setitem(self):
"""BaseUsage should map keys on setitem"""
b = BaseUsage()
b['t'] = 3
b['G'] = 3
b.normalize()
i = b.items()
i.sort()
self.assertEqual(i, [('A', 0.0), ('C', 0.0), ('G', 0.5), ('U', 0.5)])
def test_getitem(self):
"""BaseUsage should map key on getitem"""
b = BaseUsage({'a':3, 'T':2, 'X':1})
self.assertEqual(b['X'], 1)
self.assertEqual(b['A'], 3)
self.assertEqual(b['U'], 2)
self.assertEqual(b['a'], 3)
self.assertEqual(b['t'], 2)
b.normalize()
assert 'X' not in b
self.assertFloatEqual(b['A'], 0.6)
self.assertFloatEqual(b['u'], 0.4)
def test_getitem(self):
"""BaseUsage should map key on getitem"""
b = BaseUsage({'a': 3, 'T': 2, 'X': 1})
self.assertEqual(b['X'], 1)
self.assertEqual(b['A'], 3)
self.assertEqual(b['U'], 2)
self.assertEqual(b['a'], 3)
self.assertEqual(b['t'], 2)
b.normalize()
assert 'X' not in b
self.assertFloatEqual(b['A'], 0.6)
self.assertFloatEqual(b['u'], 0.4)
def test_init_data(self):
"""BaseUsage should init with arbitrary data"""
b = BaseUsage('UUUUUGGGCA')
self.assertEqual(b, {'U':5, 'G':3, 'C':1, 'A':1})
b.normalize()
self.assertEqual(b, {'U':0.5, 'G':0.3, 'C':0.1, 'A':0.1})
def test_init_data(self):
"""BaseUsage should init with arbitrary data"""
b = BaseUsage('UUUUUGGGCA')
self.assertEqual(b, {'U': 5, 'G': 3, 'C': 1, 'A': 1})
b.normalize()
self.assertEqual(b, {'U': 0.5, 'G': 0.3, 'C': 0.1, 'A': 0.1})
