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

Public Member Functions

def setUp
def testBasemlBinary

Public Attributes

 bml

Static Public Attributes

list del_files = []

Detailed Description

Tests for PAML tool baseml.

Definition at line 89 of file test_PAML_tools.py.


Member Function Documentation

Definition at line 92 of file test_PAML_tools.py.

00092 
00093     def setUp(self):
00094         self.bml = baseml.Baseml()

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

Definition at line 95 of file test_PAML_tools.py.

00095 
00096     def testBasemlBinary(self):
00097         """Test that the baseml binary runs and generates correct output
00098         and is the correct version.
00099         """
00100         ctl_file = os.path.join("PAML", "Control_files", "baseml", "baseml.ctl")
00101         self.bml.read_ctl_file(ctl_file)
00102         self.bml.alignment = os.path.join("PAML", "Alignments", "alignment.phylip")
00103         self.bml.tree = os.path.join("PAML", "Trees", "species.tree")
00104         self.bml.out_file = os.path.join("PAML", "temp.out")
00105         self.bml.working_dir = os.path.join("PAML", "baseml_test")
00106         results = self.bml.run()
00107         self.assertTrue(results["version"] > "4.0")
00108         self.assertTrue("parameters" in results)
00109         self.assertEqual(len(results["parameters"]), 5)
00110 


Member Data Documentation

Definition at line 93 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: