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python-biopython  1.60
Public Member Functions | Static Public Attributes
test_pairwise2.TestPairwiseMatchDictionary Class Reference

List of all members.

Public Member Functions

def test_match_dictionary1
def test_match_dictionary2
def test_match_dictionary3

Static Public Attributes

dictionary match_dict

Detailed Description

Definition at line 280 of file test_pairwise2.py.


Member Function Documentation

Definition at line 288 of file test_pairwise2.py.

00288 
00289     def test_match_dictionary1(self):
00290         aligns = pairwise2.align.localds("ATAT", "ATT", self.match_dict, -.5, 0)
00291         self.assertEqual(len(aligns), 2)
00292         aligns.sort()
00293         seq1, seq2, score, begin, end = aligns[0]
00294         alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)
00295         self.assertEqual(alignment, """\
00296 ATAT
00297 ||||
00298 AT-T
00299   Score=3
00300 """)
00301         seq1, seq2, score, begin, end = aligns[1]
00302         alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)
00303         self.assertEqual(alignment, """\
00304 ATAT
00305 |||
00306 ATT-
00307   Score=3
00308 """)

Definition at line 309 of file test_pairwise2.py.

00309 
00310     def test_match_dictionary2(self):
00311         aligns = pairwise2.align.localds("ATAT", "ATT", self.match_dict, -1, 0)
00312         self.assertEqual(len(aligns), 1)
00313         seq1, seq2, score, begin, end = aligns[0]
00314         alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)
00315         self.assertEqual(alignment, """\
00316 ATAT
00317 |||
00318 ATT-
00319   Score=3
00320 """)

Definition at line 321 of file test_pairwise2.py.

00321 
00322     def test_match_dictionary3(self):
00323         aligns = pairwise2.align.localds("ATT", "ATAT", self.match_dict, -1, 0)
00324         self.assertEqual(len(aligns), 1)
00325         seq1, seq2, score, begin, end = aligns[0]
00326         alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)
00327         self.assertEqual(alignment, """\
00328 ATT-
00329 |||
00330 ATAT
00331   Score=3
00332 """)
00333 


Member Data Documentation

Initial value:
{
        ("A", "A") : 1.5,
        ("A", "T") : 0.5,
        ("T", "T") : 1.0
        }

Definition at line 282 of file test_pairwise2.py.


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