def test_standard_code_lookup(self):
"""GeneticCodes should hold codes keyed by id as string and number"""
sgc_new = GeneticCode(*self.NcbiStandard)
sgc_number = GeneticCodes[1]
sgc_string = GeneticCodes['1']
for sgc in sgc_new, sgc_number, sgc_string:
self.assertEqual(sgc.CodeSequence,
'FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG')
self.assertEqual(sgc.StartCodonSequence,
'---M---------------M---------------M----------------------------')
self.assertEqual(sgc.StartCodons, {'TTG':'M', 'CTG':'M', 'ATG':'M'})
self.assertEqual(sgc.ID, 1)
self.assertEqual(sgc.Name, 'Standard Nuclear')
self.assertEqual(sgc['TTT'], 'F')
self.assertEqual(sgc.isStart('ATG'), True)
self.assertEqual(sgc.isStart('AAA'), False)
self.assertEqual(sgc.isStop('TAA'), True)
self.assertEqual(sgc.isStop('AAA'), False)
mtgc = GeneticCodes[2]
self.assertEqual(mtgc.Name, 'Vertebrate Mitochondrial')
self.assertEqual(mtgc.isStart('AUU'), True)
self.assertEqual(mtgc.isStop('UGA'), False)
self.assertEqual(sgc_new.changes(mtgc), {'AGA':'R*', 'AGG':'R*',
'ATA':'IM', 'TGA':'*W'})
self.assertEqual(mtgc.changes(sgc_new), {'AGA':'*R', 'AGG':'*R',
'ATA':'MI', 'TGA':'W*'})
self.assertEqual(mtgc.changes(mtgc), {})
self.assertEqual(mtgc.changes(
'FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG'),
{'AGA':'*R', 'AGG':'*R', 'ATA':'MI', 'TGA':'W*'})
def test_getitem_aa(self):
"""GeneticCode getitem should return codon set for aa"""
#for all G, should return all the codons (in some order)
allg = GeneticCode(self.AllG)
codons = [a+b+c for a in 'TCAG' for b in 'TCAG' for c in 'TCAG']
g_codons = allg['G']
codons_copy = codons[:]
self.assertEqual(g_codons, codons_copy)
#check some known cases in the standard genetic code
sgc = GeneticCode(self.SGC)
exp_ile = ['ATT', 'ATC', 'ATA']
obs_ile = sgc['I']
self.assertEqual(obs_ile, exp_ile)
exp_arg = ['AGA', 'AGG', 'CGT', 'CGC', 'CGA', 'CGG']
obs_arg = sgc['R']
self.assertEqual(obs_ile, exp_ile)
exp_leu = ['TTA','TTG','CTT','CTC','CTA','CTG']
obs_leu = sgc['L']
self.assertEqual(obs_leu, exp_leu)
exp_met = ['ATG']
obs_met = sgc['M']
self.assertEqual(obs_met, exp_met)
#unknown aa should return []
self.assertEqual(sgc['U'], [])
def test_standard_code_lookup(self):
"""GeneticCodes should hold codes keyed by id as string and number"""
sgc_new = GeneticCode(*self.NcbiStandard)
sgc_number = GeneticCodes[1]
sgc_string = GeneticCodes["1"]
for sgc in sgc_new, sgc_number, sgc_string:
self.assertEqual(sgc.CodeSequence, "FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG")
self.assertEqual(sgc.StartCodonSequence, "---M---------------M---------------M----------------------------")
self.assertEqual(sgc.StartCodons, {"TTG": "M", "CTG": "M", "ATG": "M"})
self.assertEqual(sgc.ID, 1)
self.assertEqual(sgc.Name, "Standard Nuclear")
self.assertEqual(sgc["TTT"], "F")
self.assertEqual(sgc.isStart("ATG"), True)
self.assertEqual(sgc.isStart("AAA"), False)
self.assertEqual(sgc.isStop("TAA"), True)
self.assertEqual(sgc.isStop("AAA"), False)
mtgc = GeneticCodes[2]
self.assertEqual(mtgc.Name, "Vertebrate Mitochondrial")
self.assertEqual(mtgc.isStart("AUU"), True)
self.assertEqual(mtgc.isStop("UGA"), False)
self.assertEqual(sgc_new.changes(mtgc), {"AGA": "R*", "AGG": "R*", "ATA": "IM", "TGA": "*W"})
self.assertEqual(mtgc.changes(sgc_new), {"AGA": "*R", "AGG": "*R", "ATA": "MI", "TGA": "W*"})
self.assertEqual(mtgc.changes(mtgc), {})
self.assertEqual(
mtgc.changes("FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG"),
{"AGA": "*R", "AGG": "*R", "ATA": "MI", "TGA": "W*"},
)
def test_stop_indexes(self):
"""should return stop codon indexes for a specified frame"""
sgc = GeneticCode(self.SGC)
seq = DNA.makeSequence("ATGCTAACATAAA")
expected = [[9], [4], []]
for frame, expect in enumerate(expected):
got = sgc.getStopIndices(seq, start=frame)
self.assertEqual(got, expect)
def test_stop_indexes(self):
"""should return stop codon indexes for a specified frame"""
sgc = GeneticCode(self.SGC)
seq = DNA.makeSequence('ATGCTAACATAAA')
expected = [[9], [4], []]
for frame, expect in enumerate(expected):
got = sgc.getStopIndices(seq, start=frame)
self.assertEqual(got, expect)
def test_cmp(self):
"""GeneticCode cmp() should act on code strings"""
sgc_1 = GeneticCode(self.SGC)
sgc_2 = GeneticCode(self.SGC)
self.assertEqual(sgc_1 is sgc_2, False) #ensure different objects
#self.assertNotEqual(sgc_1, sgc_2) # GREG
self.assertEqual(sgc_1, sgc_2)
mtgc = GeneticCode(self.mt)
self.assertNotEqual(sgc_1, mtgc)
def test_init(self):
"""GeneticCode init should work with correct-length sequences"""
sgc = GeneticCode(self.SGC)
self.assertEqual(sgc['UUU'], 'F')
mt = GeneticCode(self.mt)
self.assertEqual(mt['UUU'], 'F')
allg = GeneticCode(self.AllG)
self.assertEqual(allg['UUU'], 'G')
for i in self.WrongLength:
self.assertRaises(GeneticCodeInitError, GeneticCode, i)
def test_Anticodons(self):
"""GeneticCode Anticodons should return correct list"""
sgc = GeneticCode(self.SGC)
exp_anticodons = {
'F': ['AAA', 'GAA',],
'L': ['TAA', 'CAA', 'AAG','GAG','TAG','CAG'],
'Y': ['ATA','GTA'],
'*': ['TTA','CTA', 'TCA'],
'C': ['ACA','GCA'],
'W': ['CCA'],
'S': ['AGA','GGA','TGA','CGA','ACT','GCT'],
'P': ['AGG','GGG','TGG','CGG'],
'H': ['ATG','GTG'],
'Q': ['TTG','CTG'],
'R': ['ACG','GCG','TCG','CCG','TCT','CCT'],
'I': ['AAT','GAT','TAT'],
'M': ['CAT',],
'T': ['AGT','GGT','TGT','CGT'],
'N': ['ATT','GTT'],
'K': ['TTT','CTT'],
'V': ['AAC','GAC','TAC','CAC'],
'A': ['AGC','GGC','TGC','CGC'],
'D': ['ATC','GTC'],
'E': ['TTC','CTC'],
'G': ['ACC','GCC','TCC','CCC'],
}
self.assertEqual(sgc.Anticodons, exp_anticodons)
def test_Blocks(self):
"""GeneticCode Blocks should return correct list"""
sgc = GeneticCode(self.SGC)
exp_blocks = [
['TTT', 'TTC',],
['TTA', 'TTG',],
['TCT','TCC','TCA','TCG'],
['TAT','TAC'],
['TAA','TAG'],
['TGT','TGC'],
['TGA'],
['TGG'],
['CTT','CTC','CTA','CTG'],
['CCT','CCC','CCA','CCG'],
['CAT','CAC'],
['CAA','CAG'],
['CGT','CGC','CGA','CGG'],
['ATT','ATC'],
['ATA',],
['ATG',],
['ACT','ACC','ACA','ACG'],
['AAT','AAC'],
['AAA','AAG'],
['AGT','AGC'],
['AGA','AGG'],
['GTT','GTC','GTA','GTG'],
['GCT','GCC','GCA','GCG'],
['GAT','GAC'],
['GAA','GAG'],
['GGT','GGC','GGA','GGG'],
]
self.assertEqual(sgc.Blocks, exp_blocks)
def test_Synonyms(self):
"""GeneticCode Synonyms should return aa -> codon set mapping."""
expected_synonyms = {
'A':['GCT','GCC','GCA','GCG'],
'C':['TGT', 'TGC'],
'D':['GAT', 'GAC'],
'E':['GAA','GAG'],
'F':['TTT','TTC'],
'G':['GGT','GGC','GGA','GGG'],
'H':['CAT','CAC'],
'I':['ATT','ATC','ATA'],
'K':['AAA','AAG'],
'L':['TTA','TTG','CTT','CTC','CTA','CTG'],
'M':['ATG'],
'N':['AAT','AAC'],
'P':['CCT','CCC','CCA','CCG'],
'Q':['CAA','CAG'],
'R':['AGA','AGG','CGT','CGC','CGA','CGG'],
'S':['TCT','TCC','TCA','TCG','AGT','AGC'],
'T':['ACT','ACC','ACA','ACG'],
'V':['GTT','GTC','GTA','GTG'],
'W':['TGG'],
'Y':['TAT','TAC'],
'*':['TAA','TAG', 'TGA'],
}
obs_synonyms = GeneticCode(self.SGC).Synonyms
#note that the lists will be arbitrary-order
for i in expected_synonyms:
self.assertEqualItems(obs_synonyms[i], expected_synonyms[i])
def test_standard_code(self):
"""Standard genetic code from NCBI should have correct properties"""
sgc = GeneticCode(*self.NcbiStandard)
self.assertEqual(sgc.CodeSequence, "FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG")
self.assertEqual(sgc.StartCodonSequence, "---M---------------M---------------M----------------------------")
self.assertEqual(sgc.StartCodons, {"TTG": "M", "CTG": "M", "ATG": "M"})
self.assertEqual(sgc.ID, 1)
self.assertEqual(sgc.Name, "Standard Nuclear")
self.assertEqual(sgc["UUU"], "F")
self.assertEqual(sgc.isStart("ATG"), True)
self.assertEqual(sgc.isStart("AAA"), False)
self.assertEqual(sgc.isStop("UAA"), True)
self.assertEqual(sgc.isStop("AAA"), False)
self.assertEqual(len(sgc.SenseCodons), 61)
self.assertContains(sgc.SenseCodons, "AAA")
self.assertNotContains(sgc.SenseCodons, "TGA")
def test_getitem_codon(self):
"""GeneticCode getitem should return amino acid for codon"""
#specific checks of a particular codon in the standard code
variant_codons = ['AUU', 'AUU', 'AUU', 'ATT', 'ATU', 'ATU']
sgc = GeneticCode(self.SGC)
for i in variant_codons:
self.assertEqual(sgc[i], 'I')
#full check for the standard code
codons = [a+b+c for a in 'UCAG' for b in 'TCAG' for c in 'UCAG']
for codon, aa in zip(codons, self.SGC):
self.assertEqual(sgc[codon], aa)
#full check for another code
allg = GeneticCode(self.AllG)
for codon, aa in zip(codons, self.AllG):
self.assertEqual(allg[codon], aa)
#check that degenerate codon returns X
self.assertEqual(sgc['NNN'], 'X')
def test_standard_code(self):
"""Standard genetic code from NCBI should have correct properties"""
sgc = GeneticCode(*self.NcbiStandard)
self.assertEqual(sgc.CodeSequence,
'FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG')
self.assertEqual(sgc.StartCodonSequence,
'---M---------------M---------------M----------------------------')
self.assertEqual(sgc.StartCodons, {'TTG':'M', 'CTG':'M', 'ATG':'M'})
self.assertEqual(sgc.ID, 1)
self.assertEqual(sgc.Name, 'Standard Nuclear')
self.assertEqual(sgc['UUU'], 'F')
self.assertEqual(sgc.isStart('ATG'), True)
self.assertEqual(sgc.isStart('AAA'), False)
self.assertEqual(sgc.isStop('UAA'), True)
self.assertEqual(sgc.isStop('AAA'), False)
self.assertEqual(len(sgc.SenseCodons), 61)
self.assertContains(sgc.SenseCodons, 'AAA')
self.assertNotContains(sgc.SenseCodons, 'TGA')
def test_sixframes(self):
"""GeneticCode sixframes should provide six-frame translation"""
class fake_rna(str):
"""Fake RNA class with reverse-complement"""
def __new__(cls, seq, rev):
return str.__new__(cls, seq)
def __init__(self, seq, rev):
self.seq = seq
self.rev = rev
def rc(self):
return self.rev
test_rna = fake_rna('AUGCUAACAUAAA', 'UUUAUGUUAGCAU')
# . . . . . . . . . .
sgc = GeneticCode(self.SGC)
self.assertEqual(sgc.sixframes(test_rna), [
'MLT*', 'C*HK', 'ANI', 'FMLA', 'LC*H', 'YVS'])
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_sixframes(self):
"""GeneticCode sixframes should provide six-frame translation"""
class fake_rna(str):
"""Fake RNA class with reverse-complement"""
def __new__(cls, seq, rev):
return str.__new__(cls, seq)
def __init__(self, seq, rev):
self.seq = seq
self.rev = rev
def rc(self):
return self.rev
test_rna = fake_rna("AUGCUAACAUAAA", "UUUAUGUUAGCAU")
# . . . . . . . . . .
sgc = GeneticCode(self.SGC)
self.assertEqual(sgc.sixframes(test_rna), ["MLT*", "C*HK", "ANI", "FMLA", "LC*H", "YVS"])
# should also actually work with an RNA or DNA sequence!!!
test_rna = RNA.makeSequence("AUGCUAACAUAAA")
self.assertEqual(sgc.sixframes(test_rna), ["MLT*", "C*HK", "ANI", "FMLA", "LC*H", "YVS"])
def get_genetic_code(code_name):
if code_name is None:
code = DEFAULT
else:
code = None
for gc in GeneticCodes.itervalues():
if gc.Name == code_name:
code = gc
if code is None:
try:
code = GeneticCode(code_name, Name=code_name)
except:
raise RuntimeError('Error selecting genetic code ' + code_name)
return code
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_translate(self):
"""GeneticCode translate should return correct amino acid string"""
allg = GeneticCode(self.AllG)
sgc = GeneticCode(self.SGC)
mt = GeneticCode(self.mt)
seq = "AUGCAUGACUUUUGA"
# . . . . . markers for codon start
self.assertEqual(allg.translate(seq), "GGGGG")
self.assertEqual(allg.translate(seq, 1), "GGGG")
self.assertEqual(allg.translate(seq, 2), "GGGG")
self.assertEqual(allg.translate(seq, 3), "GGGG")
self.assertEqual(allg.translate(seq, 4), "GGG")
self.assertEqual(allg.translate(seq, 12), "G")
self.assertEqual(allg.translate(seq, 14), "")
self.assertRaises(ValueError, allg.translate, seq, 15)
self.assertRaises(ValueError, allg.translate, seq, 20)
self.assertEqual(sgc.translate(seq), "MHDF*")
self.assertEqual(sgc.translate(seq, 3), "HDF*")
self.assertEqual(sgc.translate(seq, 6), "DF*")
self.assertEqual(sgc.translate(seq, 9), "F*")
self.assertEqual(sgc.translate(seq, 12), "*")
self.assertEqual(sgc.translate(seq, 14), "")
# check shortest translatable sequences
self.assertEqual(sgc.translate("AAA"), "K")
self.assertEqual(sgc.translate(""), "")
# check that different code gives different results
self.assertEqual(mt.translate(seq), "MHDFW")
# check translation with invalid codon(s)
self.assertEqual(sgc.translate("AAANNNCNC123UUU"), "KXXXF")
def test_getitem_invalid_length(self):
"""GeneticCode getitem should raise InvalidCodonError on wrong length"""
sgc = GeneticCode(self.SGC)
self.assertRaises(InvalidCodonError, sgc.__getitem__, 'AAAA')
self.assertRaises(InvalidCodonError, sgc.__getitem__, 'AA')
def test_translate(self):
"""GeneticCode translate should return correct amino acid string"""
allg = GeneticCode(self.AllG)
sgc = GeneticCode(self.SGC)
mt = GeneticCode(self.mt)
seq = 'AUGCAUGACUUUUGA'
# . . . . . markers for codon start
self.assertEqual(allg.translate(seq), 'GGGGG')
self.assertEqual(allg.translate(seq, 1), 'GGGG')
self.assertEqual(allg.translate(seq, 2), 'GGGG')
self.assertEqual(allg.translate(seq, 3), 'GGGG')
self.assertEqual(allg.translate(seq, 4), 'GGG')
self.assertEqual(allg.translate(seq, 12), 'G')
self.assertEqual(allg.translate(seq, 14), '')
self.assertRaises(ValueError, allg.translate, seq, 15)
self.assertRaises(ValueError, allg.translate, seq, 20)
self.assertEqual(sgc.translate(seq), 'MHDF*')
self.assertEqual(sgc.translate(seq, 3), 'HDF*')
self.assertEqual(sgc.translate(seq, 6), 'DF*')
self.assertEqual(sgc.translate(seq, 9), 'F*')
self.assertEqual(sgc.translate(seq, 12), '*')
self.assertEqual(sgc.translate(seq, 14), '')
#check shortest translatable sequences
self.assertEqual(sgc.translate('AAA'), 'K')
self.assertEqual(sgc.translate(''), '')
#check that different code gives different results
self.assertEqual(mt.translate(seq), 'MHDFW')
#check translation with invalid codon(s)
self.assertEqual(sgc.translate('AAANNNCNC123UUU'), 'KXXXF')
