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 setUp(self): codonseq1 = codonalign.CodonSeq("AAATTT---TTTGGACCC") codonseq2 = codonalign.CodonSeq("AAGTTT---TTTGGGCCC") codonseq3 = codonalign.CodonSeq("AAGTAT---TTTGGACCC") codonseq4 = codonalign.CodonSeq("AACTTT---TTTGGACGC") 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))
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-T") self.assertIsInstance(codonseq1.toSeq(), Seq)