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))
