def test_analyze_with_NA_with_nontranslate(self):
"""pm.analyze should give the expection value"""
seq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGCT'
stdseq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGCC'
status = analyze(seq, stdseq, translate=False)
self.assertEqual(status, NA(nt_pm=1, aa_pm=None, gaps=0, stdseq=stdseq))
self.assertEqual(status.seq, seq.replace('-', ''))
self.assertEqual(status.stdseq, stdseq)
self.assertEqual(status.gaps, 0)
self.assertEqual(status.length, len(seq))
self.assertEqual(status.nt_pm, 1)
self.assertEqual(status.aa_pm, None)
self.assertIsInstance(status.pattern, PlainPattern)
def test_analyze_with_NA(self):
"""pm.analyze should give the expection value"""
seq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGC-TT'
stdseq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGTT'
status = analyze(seq, stdseq)
self.assertEqual(status, NA(gaps=1, stdseq=stdseq, aa_pm=0))
self.assertEqual(status.seq, seq)
self.assertEqual(status.stdseq, stdseq)
self.assertEqual(status.gaps, 1)
self.assertEqual(status.length, len(seq))
self.assertEqual(status.nt_pm, 0)
self.assertEqual(status.aa_pm, 0)
self.assertIsInstance(status.pattern, TranslatedPattern)