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), Protein('GGGGG'))
self.assertEqual(allg.translate(seq, 1), Protein('GGGG'))
self.assertEqual(allg.translate(seq, 2), Protein('GGGG'))
self.assertEqual(allg.translate(seq, 3), Protein('GGGG'))
self.assertEqual(allg.translate(seq, 4), Protein('GGG'))
self.assertEqual(allg.translate(seq, 12), Protein('G'))
self.assertEqual(allg.translate(seq, 14), Protein(''))
self.assertRaises(ValueError, allg.translate, seq, 15)
self.assertRaises(ValueError, allg.translate, seq, 20)
self.assertEqual(sgc.translate(seq), Protein('MHDF*'))
self.assertEqual(sgc.translate(seq, 3), Protein('HDF*'))
self.assertEqual(sgc.translate(seq, 6), Protein('DF*'))
self.assertEqual(sgc.translate(seq, 9), Protein('F*'))
self.assertEqual(sgc.translate(seq, 12), Protein('*'))
self.assertEqual(sgc.translate(seq, 14), Protein(''))
# check shortest translatable sequences
self.assertEqual(sgc.translate('AAA'), Protein('K'))
self.assertEqual(sgc.translate(''), Protein(''))
# check that different code gives different results
self.assertEqual(mt.translate(seq), Protein('MHDFW'))
# check translation with invalid codon(s)
self.assertEqual(sgc.translate('AAANNNCNC123UUU'), Protein('KXXXF'))
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), Protein('GGGGG'))
self.assertEqual(allg.translate(seq, 1), Protein('GGGG'))
self.assertEqual(allg.translate(seq, 2), Protein('GGGG'))
self.assertEqual(allg.translate(seq, 3), Protein('GGGG'))
self.assertEqual(allg.translate(seq, 4), Protein('GGG'))
self.assertEqual(allg.translate(seq, 12), Protein('G'))
self.assertEqual(allg.translate(seq, 14), Protein(''))
self.assertRaises(ValueError, allg.translate, seq, 15)
self.assertRaises(ValueError, allg.translate, seq, 20)
self.assertEqual(sgc.translate(seq), Protein('MHDF*'))
self.assertEqual(sgc.translate(seq, 3), Protein('HDF*'))
self.assertEqual(sgc.translate(seq, 6), Protein('DF*'))
self.assertEqual(sgc.translate(seq, 9), Protein('F*'))
self.assertEqual(sgc.translate(seq, 12), Protein('*'))
self.assertEqual(sgc.translate(seq, 14), Protein(''))
# check shortest translatable sequences
self.assertEqual(sgc.translate('AAA'), Protein('K'))
self.assertEqual(sgc.translate(''), Protein(''))
# check that different code gives different results
self.assertEqual(mt.translate(seq), Protein('MHDFW'))
# check translation with invalid codon(s)
self.assertEqual(sgc.translate('AAANNNCNC123UUU'), Protein('KXXXF'))
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), Protein("GGGGG"))
self.assertEqual(allg.translate(seq, 1), Protein("GGGG"))
self.assertEqual(allg.translate(seq, 2), Protein("GGGG"))
self.assertEqual(allg.translate(seq, 3), Protein("GGGG"))
self.assertEqual(allg.translate(seq, 4), Protein("GGG"))
self.assertEqual(allg.translate(seq, 12), Protein("G"))
self.assertEqual(allg.translate(seq, 14), Protein(""))
self.assertRaises(ValueError, allg.translate, seq, 15)
self.assertRaises(ValueError, allg.translate, seq, 20)
self.assertEqual(sgc.translate(seq), Protein("MHDF*"))
self.assertEqual(sgc.translate(seq, 3), Protein("HDF*"))
self.assertEqual(sgc.translate(seq, 6), Protein("DF*"))
self.assertEqual(sgc.translate(seq, 9), Protein("F*"))
self.assertEqual(sgc.translate(seq, 12), Protein("*"))
self.assertEqual(sgc.translate(seq, 14), Protein(""))
# check shortest translatable sequences
self.assertEqual(sgc.translate("AAA"), Protein("K"))
self.assertEqual(sgc.translate(""), Protein(""))
# check that different code gives different results
self.assertEqual(mt.translate(seq), Protein("MHDFW"))
# check translation with invalid codon(s)
self.assertEqual(sgc.translate("AAANNNCNC123UUU"), Protein("KXXXF"))
