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python-biopython  1.60
Public Member Functions
test_pairwise2.TestPairwiseSeparateGapPenaltiesWithExtension Class Reference

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def test_separate_gap_penalties_with_extension

Detailed Description

Definition at line 248 of file test_pairwise2.py.


Member Function Documentation

Definition at line 250 of file test_pairwise2.py.

00250 
00251     def test_separate_gap_penalties_with_extension(self):
00252         aligns = pairwise2.align.localxd(list("GAAT"), list("GTCCT"), -0.1, 0, -0.1, -0.1, gap_char=["-"])
00253         self.assertEqual(len(aligns), 3)
00254         aligns.sort()
00255         seq1, seq2, score, begin, end = aligns[0]
00256         alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)
00257         self.assertEqual(alignment, """\
00258 ['G', '-', 'A', 'A', 'T']
00259 |||||
00260 ['G', 'T', 'C', 'C', 'T']
00261   Score=1.9
00262 """)
00263         seq1, seq2, score, begin, end = aligns[1]
00264         alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)
00265         self.assertEqual(alignment, """\
00266 ['G', 'A', '-', 'A', 'T']
00267 |||||
00268 ['G', 'T', 'C', 'C', 'T']
00269   Score=1.9
00270 """)
00271         seq1, seq2, score, begin, end = aligns[2]
00272         alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)
00273         self.assertEqual(alignment, """\
00274 ['G', 'A', 'A', '-', 'T']
00275 |||||
00276 ['G', 'T', 'C', 'C', 'T']
00277   Score=1.9
00278 """)
00279 


The documentation for this class was generated from the following file: