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_init_empty(self):
"""AminoAcidUsage should init with empty freqs"""
a = AminoAcidUsage()
for key, val in a.items():
self.assertEqual(val, 0)
self.assertEqual(len(a), 21)
assert 'A' in a
assert 'a' in a
def test_init_empty(self):
"""AminoAcidUsage should init with empty freqs"""
a = AminoAcidUsage()
for key, val in a.items():
self.assertEqual(val, 0)
self.assertEqual(len(a), 21)
assert 'A' in a
assert 'a' in a
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_init_data(self):
"""AminoAcidUsage should init with data"""
a = AminoAcidUsage('aadddx')
self.assertEqual(a['A'], 2)
self.assertEqual(a['d'], 3)
self.assertEqual(a['X'], 1)
a.normalize()
self.assertEqual(a['a'], 0.4)
self.assertEqual(a['d'], 0.6)
assert 'x' not in a
def test_init_data(self):
"""AminoAcidUsage should init with data"""
a = AminoAcidUsage('aadddx')
self.assertEqual(a['A'], 2)
self.assertEqual(a['d'], 3)
self.assertEqual(a['X'], 1)
a.normalize()
self.assertEqual(a['a'], 0.4)
self.assertEqual(a['d'], 0.6)
assert 'x' not in a
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_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):
"""AminoAcidUsage aminoAcids should return same object"""
a = AminoAcidUsage('REWQDFTDSF')
b = a.aminoAcids()
assert a is b
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_aminoAcids(self):
"""AminoAcidUsage aminoAcids should return same object"""
a = AminoAcidUsage('REWQDFTDSF')
b = a.aminoAcids()
assert a is b
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_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')