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_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_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_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_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)
