def test_aminoAcids(self):
"""CodonUsage aminoAcids should correctly count amino acids"""
freqs = {'UUC':5, 'AUA':10, 'AUG':10, 'CGC':3, 'AGG':2, 'XYZ':8,
'UAA':2, 'UGA':1}
u = CodonUsage(freqs, "test")
self.assertEqual(u.Info, 'test')
for key, val in u.items():
if key in freqs:
self.assertEqual(val, freqs[key])
else:
self.assertEqual(val, 0)
aa = u.aminoAcids()
self.assertEqual(aa,
AminoAcidUsage({'F':5,'I':10,'M':10,'R':5,'*':3,'X':8}))
#check that it works with a different genetic code
u.GeneticCode = GeneticCodes['2']
aa = u.aminoAcids()
self.assertEqual(aa,
AminoAcidUsage({'F':5,'I':0,'M':20,'R':3,'*':4,'W':1,'X':8}))
#check that it works if a genetic code is supplied explicitly
u.GeneticCode = GeneticCodes[1]
aa = u.aminoAcids()
self.assertEqual(aa,
AminoAcidUsage({'F':5,'I':10,'M':10,'R':5,'*':3,'X':8}))
aa_2 = u.aminoAcids(2)
self.assertEqual(aa_2,
AminoAcidUsage({'F':5,'I':0,'M':20,'R':3,'*':4,'W':1,'X':8}))
#check that we held onto the info object through the above
self.assertEqual(aa_2.Info, 'test')
def test_positionalBases(self):
"""CodonUsage bases should count bases at each position correctly"""
freqs = {'UUC':5, 'AUA':10, 'AUG':10, 'CGC':3, 'AGG':2, 'XYZ':8,
'UAA':2, 'UGA':1}
u = CodonUsage(freqs)
b = u.positionalBases()
assert isinstance(b, PositionalBaseUsage)
first, second, third = b
self.assertEqual(first, BaseUsage({'U':8,'C':3,'A':22,'X':8}))
self.assertEqual(second, BaseUsage({'U':25,'C':0,'A':2,'G':6,'Y':8}))
self.assertEqual(third, BaseUsage({'C':8,'A':13,'G':12,'Z':8}))
#check that it also works when we purge
p = u.positionalBases(purge_unwanted=True)
first, second, third = p
self.assertEqual(first, BaseUsage({'U':5,'C':3,'A':2}))
self.assertEqual(second, BaseUsage({'U':5,'G':5}))
self.assertEqual(third, BaseUsage({'C':8,'G':2}))
#check that it also works with a different genetic code, and,
#incidentally, that the purging didn't affect the original object
u.GeneticCode = GeneticCodes[2] #mt code: different stop codons
p = u.positionalBases(purge_unwanted=True)
first, second, third = p
self.assertEqual(first, BaseUsage({'U':6,'C':3,'A':20}))
self.assertEqual(second, BaseUsage({'U':25,'G':4}))
self.assertEqual(third, BaseUsage({'C':8,'A':11,'G':10}))
