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')
