def test_positionalBases(self):
"""AminoAcidUsage positionalBases should return best positional bases"""
a = AminoAcidUsage('WQRSFADDQW')
exp = a.codons().positionalBases()
obs = a.positionalBases()
for o, e in zip(obs, exp):
self.assertFloatEqual(o, e)
def test_positionalBases(self):
"""AminoAcidUsage positionalBases should return best positional bases"""
a = AminoAcidUsage('WQRSFADDQW')
exp = a.codons().positionalBases()
obs = a.positionalBases()
for o, e in zip(obs, exp):
self.assertFloatEqual(o, e)
def test_bases(self):
"""AminoAcidUsage bases should return most likely base freqs"""
a = AminoAcidUsage('GGG')
self.assertEqual(a.bases(),
{'G':9.0/12,'U':1.0/12,'C':1.0/12,'A':1.0/12})
a = AminoAcidUsage('CAGTWERQWE')
exp = a.codons().bases()
exp.normalize()
self.assertFloatEqual(a.bases(), exp)
def test_bases(self):
"""AminoAcidUsage bases should return most likely base freqs"""
a = AminoAcidUsage('GGG')
self.assertEqual(a.bases(), {
'G': 9.0 / 12,
'U': 1.0 / 12,
'C': 1.0 / 12,
'A': 1.0 / 12
})
a = AminoAcidUsage('CAGTWERQWE')
exp = a.codons().bases()
exp.normalize()
self.assertFloatEqual(a.bases(), exp)
def test_codons(self):
"""AminoAcidUsage codons should return most likely codon freqs"""
a = AminoAcidUsage('GGG')
c = CodonUsage('GGUGGCGGAGGG')
c.normalize()
self.assertEqual(a.codons(), c)
a = AminoAcidUsage('D')
c = CodonUsage('GAUGAC')
c.normalize()
self.assertEqual(a.codons(), c)
a = AminoAcidUsage('GDDFMM')
c = CodonUsage('GGUGGCGGAGGG' + 'GAUGAC' * 4 + 'UUUUUC' * 2 +
'AUG' * 8)
c.normalize()
self.assertEqual(a.codons(), c)
a = AminoAcidUsage('II*')
c = CodonUsage('AUUAUCAUA' * 2 + 'UAAUAGUGA')
c.normalize()
self.assertEqual(a.codons(), c)
#check that it works with a nonstandard code
code = GeneticCode('A' * 4 + 'C' * 28 + 'G' * 32)
a = AminoAcidUsage('AAA')
c = CodonUsage('UUUUUCUUAUUG')
c.normalize()
self.assertEqual(a.codons(code), c)
#check that it works with unequal codon frequencies
unequal = CodonUsage({
'GGU': 5,
'GGC': 2,
'GGA': 2,
'GGG': 1,
'UUU': 3,
'UUC': 1
})
a = AminoAcidUsage('GFFF')
exp = {
'GGU': 0.5 * 0.25,
'GGC': 0.2 * 0.25,
'GGA': 0.2 * 0.25,
'GGG': 0.1 * 0.25,
'UUU': 0.75 * 0.75,
'UUC': 0.25 * 0.75
}
obs = a.codons(codon_usage=unequal)
for codon, freq in obs.items():
self.assertFloatEqual(freq, exp.get(codon, 0))
def test_codons(self):
"""AminoAcidUsage codons should return most likely codon freqs"""
a = AminoAcidUsage('GGG')
c = CodonUsage('GGUGGCGGAGGG')
c.normalize()
self.assertEqual(a.codons(), c)
a = AminoAcidUsage('D')
c = CodonUsage('GAUGAC')
c.normalize()
self.assertEqual(a.codons(), c)
a = AminoAcidUsage('GDDFMM')
c = CodonUsage('GGUGGCGGAGGG'+'GAUGAC'*4+'UUUUUC'*2+'AUG'*8)
c.normalize()
self.assertEqual(a.codons(), c)
a = AminoAcidUsage('II*')
c = CodonUsage('AUUAUCAUA'*2+'UAAUAGUGA')
c.normalize()
self.assertEqual(a.codons(), c)
#check that it works with a nonstandard code
code = GeneticCode('A'*4+'C'*28+'G'*32)
a = AminoAcidUsage('AAA')
c = CodonUsage('UUUUUCUUAUUG')
c.normalize()
self.assertEqual(a.codons(code), c)
#check that it works with unequal codon frequencies
unequal = CodonUsage({'GGU':5,'GGC':2,'GGA':2,'GGG':1,'UUU':3,'UUC':1})
a = AminoAcidUsage('GFFF')
exp = {
'GGU':0.5*0.25,
'GGC':0.2*0.25,
'GGA':0.2*0.25,
'GGG':0.1*0.25,
'UUU':0.75*0.75,
'UUC':0.25*0.75
}
obs = a.codons(codon_usage=unequal)
for codon, freq in obs.items():
self.assertFloatEqual(freq, exp.get(codon, 0))
