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)
