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python-biopython  1.60
Public Member Functions | Public Attributes | Static Public Attributes
test_PAML_tools.CodemlTest Class Reference
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List of all members.

Public Member Functions

def setUp
def testCodemlBinary

Public Attributes

 cml

Static Public Attributes

list del_files = []

Detailed Description

Definition at line 66 of file test_PAML_tools.py.


Member Function Documentation

Definition at line 69 of file test_PAML_tools.py.

00069 
00070     def setUp(self):
00071         self.cml = codeml.Codeml()

Test that the codeml binary runs and generates correct output
and is the correct version.

Definition at line 72 of file test_PAML_tools.py.

00072 
00073     def testCodemlBinary(self):
00074         """Test that the codeml binary runs and generates correct output
00075         and is the correct version.
00076         """
00077         ctl_file = os.path.join("PAML", "Control_files", "codeml", "codeml.ctl")
00078         self.cml.read_ctl_file(ctl_file)
00079         self.cml.alignment = os.path.join("PAML", "Alignments", "alignment.phylip")
00080         self.cml.tree = os.path.join("PAML", "Trees", "species.tree")
00081         self.cml.out_file = os.path.join("PAML", "temp.out")
00082         self.cml.working_dir = os.path.join("PAML", "codeml_test")
00083         results = self.cml.run()
00084         self.assertTrue(results["version"] > "4.0")
00085         self.assertTrue("NSsites" in results)
00086         self.assertEqual(len(results["NSsites"]), 1)
00087         self.assertEqual(len(results["NSsites"][0]), 5)
00088 


Member Data Documentation

Definition at line 70 of file test_PAML_tools.py.

list test_PAML_tools.Common.del_files = [] [static, inherited]

Definition at line 56 of file test_PAML_tools.py.


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