def test_name(self):
self.assertEqual(self.sgc.name, 'Standard')
self.assertEqual(GeneticCode('M' * 64, '-' * 64).name, '')
self.assertEqual(GeneticCode('M' * 64, '-' * 64, 'foo').name, 'foo')
with self.assertRaises(AttributeError):
self.sgc.name = 'foo'
def test_eq(self):
amino_acids = 'AMPM' * 16
starts = '--M-' * 16
equal_gcs = [
GeneticCode(amino_acids, starts),
# name should be ignored
GeneticCode(amino_acids, starts, 'foo'),
# metadata/positional metadata should be ignored if Sequence
# subclass is provided
GeneticCode(
Protein(amino_acids, metadata={'foo': 'bar'}),
Protein(starts, positional_metadata={'foo': range(64)}))
]
# every gc should be equal to itself
for gc in equal_gcs:
self.assertTrue(gc == gc)
self.assertFalse(gc != gc)
# every pair of gcs should be equal. use permutations instead of
# combinations to test that comparing gc1 to gc2 and gc2 to gc1 are
# both equal
for gc1, gc2 in itertools.permutations(equal_gcs, 2):
self.assertTrue(gc1 == gc2)
self.assertFalse(gc1 != gc2)
def test_translate_varied_genetic_codes(self):
# spot check using a few NCBI and custom genetic codes to translate
seq = RNA('AAUGAUGUGACUAUCAGAAGG')
# table_id=2
exp = Protein('NDVTI**')
obs = GeneticCode.from_ncbi(2).translate(seq)
self.assertEqual(obs, exp)
exp = Protein('MTI')
obs = GeneticCode.from_ncbi(2).translate(seq,
start='require',
stop='require')
self.assertEqual(obs, exp)
# table_id=22
exp = Protein('NDVTIRR')
obs = GeneticCode.from_ncbi(22).translate(seq)
self.assertEqual(obs, exp)
with six.assertRaisesRegex(self, ValueError,
'reading_frame=1.*start=\'require\''):
GeneticCode.from_ncbi(22).translate(seq,
start='require',
stop='require')
# custom, no start codons
gc = GeneticCode('MWN*' * 16, '-' * 64)
exp = Protein('MM*MWN*')
obs = gc.translate(seq)
self.assertEqual(obs, exp)
with six.assertRaisesRegex(self, ValueError,
'reading_frame=1.*start=\'require\''):
gc.translate(seq, start='require', stop='require')
def test_from_ncbi_valid_table_ids(self):
# spot check a few tables
self.assertEqual(GeneticCode.from_ncbi().name, 'Standard')
self.assertEqual(
GeneticCode.from_ncbi(2).name, 'Vertebrate Mitochondrial')
self.assertEqual(
GeneticCode.from_ncbi(12).name, 'Alternative Yeast Nuclear')
self.assertEqual(
GeneticCode.from_ncbi(25).name,
'Candidate Division SR1 and Gracilibacteria')
def test_from_ncbi_valid_table_ids(self):
# spot check a few tables
self.assertEqual(GeneticCode.from_ncbi().name,
'Standard')
self.assertEqual(GeneticCode.from_ncbi(2).name,
'Vertebrate Mitochondrial')
self.assertEqual(GeneticCode.from_ncbi(12).name,
'Alternative Yeast Nuclear')
self.assertEqual(GeneticCode.from_ncbi(25).name,
'Candidate Division SR1 and Gracilibacteria')
def test_translate_varied_genetic_codes(self):
# spot check using a few NCBI and custom genetic codes to translate
seq = RNA('AAUGAUGUGACUAUCAGAAGG')
# table_id=2
exp = Protein('NDVTI**')
obs = GeneticCode.from_ncbi(2).translate(seq)
self.assertEqual(obs, exp)
exp = Protein('MTI')
obs = GeneticCode.from_ncbi(2).translate(seq, start='require',
stop='require')
self.assertEqual(obs, exp)
# table_id=22
exp = Protein('NDVTIRR')
obs = GeneticCode.from_ncbi(22).translate(seq)
self.assertEqual(obs, exp)
with self.assertRaisesRegex(ValueError,
'reading_frame=1.*start=\'require\''):
GeneticCode.from_ncbi(22).translate(seq, start='require',
stop='require')
# custom, no start codons
gc = GeneticCode('MWN*' * 16, '-' * 64)
exp = Protein('MM*MWN*')
obs = gc.translate(seq)
self.assertEqual(obs, exp)
with self.assertRaisesRegex(ValueError,
'reading_frame=1.*start=\'require\''):
gc.translate(seq, start='require', stop='require')
def test_init_varied_equivalent_input(self):
for args in (('M' * 64, '-' * 64), (Protein('M' * 64),
Protein('-' * 64)),
(Sequence('M' * 64), Sequence('-' * 64))):
gc = GeneticCode(*args)
self.assertEqual(gc.name, '')
self.assertEqual(gc._amino_acids, Protein('M' * 64))
self.assertEqual(gc._starts, Protein('-' * 64))
npt.assert_array_equal(gc._m_character_codon,
np.asarray([0, 0, 0], dtype=np.uint8))
self.assertEqual(len(gc._start_codons), 0)
def test_translate_six_frames_genetic_code_object(self):
gc = GeneticCode('M' * 64, '-' * 64)
for seq in RNA('AAAUUG'), DNA('AAATTG'):
obs = list(seq.translate_six_frames(gc))
self.assertEqual(obs, [
Protein('MM'),
Protein('M'),
Protein('M'),
Protein('MM'),
Protein('M'),
Protein('M')
])
def test_init_invalid_input(self):
# `amino_acids` invalid protein
with six.assertRaisesRegex(self, ValueError, 'Invalid character.*J'):
GeneticCode('J' * 64, '-' * 64)
# wrong number of amino acids
with six.assertRaisesRegex(self, ValueError, 'amino_acids.*64.*42'):
GeneticCode('M' * 42, '-' * 64)
# `amino_acids` missing M
with six.assertRaisesRegex(self, ValueError,
'amino_acids.*M.*character'):
GeneticCode('A' * 64, '-' * 64)
# `starts` invalid protein
with six.assertRaisesRegex(self, ValueError, 'Invalid character.*J'):
GeneticCode('M' * 64, 'J' * 64)
# wrong number of starts
with six.assertRaisesRegex(self, ValueError, 'starts.*64.*42'):
GeneticCode('M' * 64, '-' * 42)
# invalid characters in `starts`
with six.assertRaisesRegex(self, ValueError,
'starts.*M and - characters'):
GeneticCode('M' * 64, '-M' * 30 + '*AQR')
def test_str(self):
# predefined
exp = (
' AAs = FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAA'
'DDEEGGGG\n'
'Starts = ---M---------------M---------------M--------------------'
'--------\n'
'Base1 = UUUUUUUUUUUUUUUUCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGG'
'GGGGGGGG\n'
'Base2 = UUUUCCCCAAAAGGGGUUUUCCCCAAAAGGGGUUUUCCCCAAAAGGGGUUUUCCCC'
'AAAAGGGG\n'
'Base3 = UCAGUCAGUCAGUCAGUCAGUCAGUCAGUCAGUCAGUCAGUCAGUCAGUCAGUCAG'
'UCAGUCAG')
self.assertEqual(str(self.sgc), exp)
# custom, no name
obs = str(GeneticCode('M' * 64, '-' * 64))
self.assertIn('M' * 64, obs)
self.assertIn('-' * 64, obs)
def test_ne(self):
class GeneticCodeSubclass(GeneticCode):
pass
amino_acids = 'AMPM' * 16
starts = '--M-' * 16
unequal_gcs = [
GeneticCode(amino_acids, starts),
# type must match
GeneticCodeSubclass(amino_acids, starts),
# completely different type
'foo'
]
# none of the NCBI genetic codes should be equal to each other
unequal_gcs.extend(_ncbi_genetic_codes.values())
for gc in unequal_gcs:
self.assertTrue(gc == gc)
self.assertFalse(gc != gc)
for gc1, gc2 in itertools.permutations(unequal_gcs, 2):
self.assertTrue(gc1 != gc2)
self.assertFalse(gc1 == gc2)
def test_from_ncbi_invalid_input(self):
with six.assertRaisesRegex(self, ValueError, 'table_id.*7'):
GeneticCode.from_ncbi(7)
with six.assertRaisesRegex(self, ValueError, 'table_id.*42'):
GeneticCode.from_ncbi(42)
def setUp(self):
self.sgc = GeneticCode.from_ncbi(1)
def test_translate_genetic_code_object(self):
gc = GeneticCode('M' * 64, '-' * 64)
for seq in RNA('AAAUUUAUGCAU'), DNA('AAATTTATGCAT'):
obs = seq.translate(gc)
self.assertEqual(obs, Protein('MMMM'))
def test_from_ncbi_invalid_input(self):
with self.assertRaisesRegex(ValueError, 'table_id.*7'):
GeneticCode.from_ncbi(7)
with self.assertRaisesRegex(ValueError, 'table_id.*42'):
GeneticCode.from_ncbi(42)
def setUp(self):
self.sgc = GeneticCode.from_ncbi(1)