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')