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_aminoAcids(self):
"""BaseUsage aminoAcids should give the same results as the codons"""
known_data = {
'AAA' : .6 * .6 * .6,
'AAU' : .6 * .6 * .4,
'AUA' : .6 * .4 * .6,
'AUU' : .6 * .4 * .4,
'UAA' : .4 * .6 * .6,
'UAU' : .4 * .6 * .4,
'UUA' : .4 * .4 * .6,
'UUU' : .4 * .4 * .4,
}
known = CodonUsage(known_data)
b = BaseUsage({'a':3, 'T':2, 'X':1})
self.assertEqual(b.aminoAcids(), known.aminoAcids())
#check that the genetic code is passed through correctly
all_g = GeneticCode('G'*64)
self.assertEqual(b.aminoAcids(all_g), AminoAcidUsage({'G':1}))
def test_aminoAcids(self):
"""BaseUsage aminoAcids should give the same results as the codons"""
known_data = {
'AAA': .6 * .6 * .6,
'AAU': .6 * .6 * .4,
'AUA': .6 * .4 * .6,
'AUU': .6 * .4 * .4,
'UAA': .4 * .6 * .6,
'UAU': .4 * .6 * .4,
'UUA': .4 * .4 * .6,
'UUU': .4 * .4 * .4,
}
known = CodonUsage(known_data)
b = BaseUsage({'a': 3, 'T': 2, 'X': 1})
self.assertEqual(b.aminoAcids(), known.aminoAcids())
#check that the genetic code is passed through correctly
all_g = GeneticCode('G' * 64)
self.assertEqual(b.aminoAcids(all_g), AminoAcidUsage({'G': 1}))
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')
