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python-biopython  1.60
Public Member Functions
test_phyml_tool.AppTests Class Reference

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def test_phyml

Detailed Description

Tests for application wrappers.

Definition at line 37 of file test_phyml_tool.py.


Member Function Documentation

Run PhyML using the wrapper.

Definition at line 40 of file test_phyml_tool.py.

00040 
00041     def test_phyml(self):
00042         """Run PhyML using the wrapper."""
00043         cmd = PhymlCommandline(phyml_exe, input=EX_PHYLIP, datatype='aa')
00044         # Smoke test
00045         try:
00046             out, err = cmd()
00047             self.assert_(len(out) > 0)
00048             self.assert_(len(err) == 0)
00049             # Check the output tree
00050             tree = Phylo.read(EX_PHYLIP + '_phyml_tree.txt', 'newick')
00051             self.assertEqual(tree.count_terminals(), 4)
00052         finally:
00053             # Clean up generated files
00054             for suffix in ['_phyml_tree.txt', '_phyml_stats.txt']:
00055                 fname = EX_PHYLIP + suffix
00056                 if os.path.isfile(fname):
00057                     os.remove(fname)
00058 
00059 
00060 # ---------------------------------------------------------


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