def setUp(self): codonseq1 = CodonAlign.CodonSeq('AAATTT---TTTGGACCC', CodonAlign.default_codon_alphabet) codonseq2 = CodonAlign.CodonSeq('AAGTTT---TTTGGGCCC', CodonAlign.default_codon_alphabet) codonseq3 = CodonAlign.CodonSeq('AAGTAT---TTTGGACCC', CodonAlign.default_codon_alphabet) codonseq4 = CodonAlign.CodonSeq('AACTTT---TTTGGACGC', CodonAlign.default_codon_alphabet) self.seqrec = [SeqRecord(codonseq1, id="alpha"), SeqRecord(codonseq2, id="beta" ), SeqRecord(codonseq3, id="gamma"), SeqRecord(codonseq4, id="delta")]
def test_seq(self): codonseq1 = CodonAlign.CodonSeq('AAATTT---TTTGGACCC', rf_table=[0,3,6,9,12]) self.assertEqual(len(codonseq1), 18) self.assertEqual(codonseq1.get_codon_num(), 5) self.assertEqual(str(codonseq1.get_codon(0)), 'AAA') self.assertEqual(str(codonseq1.get_codon(-1)), 'CCC') self.assertEqual(str(codonseq1.get_codon(slice(1,3))), 'TTT---') self.assertEqual(str(codonseq1.get_codon(slice(None,None,-1))), 'CCCGGATTT---TTTAAA') self.assertRaises(ValueError, CodonAlign.CodonSeq, 'AAA-TT') self.assertRaises(AssertionError, CodonAlign.CodonSeq, 'AAA-T') self.assertRaises(ValueError, CodonAlign.CodonSeq, 'YVVRRDQQQ') self.assertTrue(isinstance(codonseq1.toSeq(), Seq))