def test_pr2bias(self):
"""CodonUsage pr2bias should give correct ratios."""
c = EqualBases.codons()
b = c.pr2bias('UU')
self.assertEqual(len(b), 6)
self.assertEqual(b, tuple([.5]*6))
c = CodonUsage()
c['ACU'] = 10
c['ACC'] = 5
c['ACA'] = 15
c['ACG'] = 20
self.assertEqual(c.pr2bias('AC'), (20/25,15/25,20/35,5/15,20/30,5/20))
def test_pr2bias(self):
"""CodonUsage pr2bias should give correct ratios."""
c = EqualBases.codons()
b = c.pr2bias('UU')
self.assertEqual(len(b), 6)
self.assertEqual(b, tuple([.5] * 6))
c = CodonUsage()
c['ACU'] = 10
c['ACC'] = 5
c['ACA'] = 15
c['ACG'] = 20
self.assertEqual(c.pr2bias('AC'),
(20 / 25, 15 / 25, 20 / 35, 5 / 15, 20 / 30, 5 / 20))
def test_fingerprint(self):
"""CodonUsage fingerprint should give correct ratios."""
c = EqualBases.codons()
f = c.fingerprint()
self.assertEqual(len(f), 9)
self.assertEqual(f, \
[[.5,.5,.125] for i in range(8)] + [[.5,.5,1]])
#should be able to omit mean...
f = c.fingerprint(include_mean=False)
self.assertEqual(f, [[.5,.5,.125] for i in range(8)])
#...or use all doublets
f = c.fingerprint(include_mean=False, which_blocks='all')
self.assertEqual(len(f), 16)
#...or do just the non-quartet ones
f = c.fingerprint(include_mean=False, which_blocks='split')
self.assertEqual(len(f), 6)
#check that it doesn't fail on an empty codon usage
c = CodonUsage('')
f = c.fingerprint()
self.assertEqual(f[0], [0.5, 0.5, 0])
def test_fingerprint(self):
"""CodonUsage fingerprint should give correct ratios."""
c = EqualBases.codons()
f = c.fingerprint()
self.assertEqual(len(f), 9)
self.assertEqual(f, \
[[.5,.5,.125] for i in range(8)] + [[.5,.5,1]])
#should be able to omit mean...
f = c.fingerprint(include_mean=False)
self.assertEqual(f, [[.5, .5, .125] for i in range(8)])
#...or use all doublets
f = c.fingerprint(include_mean=False, which_blocks='all')
self.assertEqual(len(f), 16)
#...or do just the non-quartet ones
f = c.fingerprint(include_mean=False, which_blocks='split')
self.assertEqual(len(f), 6)
#check that it doesn't fail on an empty codon usage
c = CodonUsage('')
f = c.fingerprint()
self.assertEqual(f[0], [0.5, 0.5, 0])
def test_positionalGC(self):
"""CodonUsage positionalGC should give correct GC contents."""
c = EqualBases.codons()
self.assertEqual(c.positionalGC(False), [0.5,0.5,0.5,0.5])
c = EqualBases.codons()
self.assertNotEqual(c.positionalGC(True), [0.5,0.5,0.5,0.5])
def test_positionalGC(self):
"""CodonUsage positionalGC should give correct GC contents."""
c = EqualBases.codons()
self.assertEqual(c.positionalGC(False), [0.5, 0.5, 0.5, 0.5])
c = EqualBases.codons()
self.assertNotEqual(c.positionalGC(True), [0.5, 0.5, 0.5, 0.5])