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python-biopython  1.60
Public Member Functions | Public Attributes
test_Restriction.SimpleEnzyme Class Reference

List of all members.

Public Member Functions

def setUp
def test_eco_cutting
def test_circular_sequences

Public Attributes

 ecosite_seq

Detailed Description

Tests for dealing with basic enzymes using the Restriction package.

Definition at line 11 of file test_Restriction.py.


Member Function Documentation

Definition at line 14 of file test_Restriction.py.

00014 
00015     def setUp(self):
00016         base_seq = Seq("AAAA", IUPACAmbiguousDNA())
00017         self.ecosite_seq = base_seq + Seq(EcoRI.site,
00018                 IUPACAmbiguousDNA()) + base_seq

Deal with cutting circular sequences.

Definition at line 35 of file test_Restriction.py.

00035 
00036     def test_circular_sequences(self):
00037         """Deal with cutting circular sequences.
00038         """
00039         parts = EcoRI.catalyse(self.ecosite_seq, linear = False)
00040         self.assertEqual(len(parts), 1)
00041         locations = EcoRI.search(parts[0], linear = False)
00042         self.assertEqual(locations, [1])
00043 

Test basic cutting with EcoRI.

Definition at line 19 of file test_Restriction.py.

00019 
00020     def test_eco_cutting(self):
00021         """Test basic cutting with EcoRI.
00022         """
00023         self.assertEqual(EcoRI.site, 'GAATTC')
00024         self.assertFalse(EcoRI.is_blunt())
00025         self.assertTrue(EcoRI.is_5overhang())
00026         self.assertFalse(EcoRI.is_3overhang())
00027         self.assertEqual(EcoRI.elucidate(), "G^AATT_C")
00028         self.assertEqual(EcoRI.search(self.ecosite_seq), [6])
00029 
00030         parts = EcoRI.catalyse(self.ecosite_seq)
00031         self.assertEqual(len(parts), 2)
00032         self.assertEqual(parts[1].tostring(), "AATTCAAAA")
00033         parts = EcoRI.catalyze(self.ecosite_seq)
00034         self.assertEqual(len(parts), 2)

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Member Data Documentation

Definition at line 16 of file test_Restriction.py.


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