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python-biopython  1.60
Public Member Functions
test_EmbossPhylipNew.TreeComparisonTests Class Reference

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Public Member Functions

def tearDown
def test_fconsense
def test_ftreedist

Detailed Description

Tests for comparing phylogenetic trees with phylip tools

Definition at line 257 of file test_EmbossPhylipNew.py.


Member Function Documentation

Definition at line 260 of file test_EmbossPhylipNew.py.

00260 
00261     def tearDown(self):
00262         clean_up()

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Calculate a consensus tree with fconsense

Definition at line 263 of file test_EmbossPhylipNew.py.

00263 
00264     def test_fconsense(self):
00265         """Calculate a consensus tree with fconsense"""
00266         cline = FConsenseCommandline(exes["fconsense"],
00267                                      intreefile = "Phylip/horses.tree",
00268                                      outtreefile = "test_file",
00269                                      auto = True, filter = True)
00270         stdout, stderr = cline()
00271         #Split the next and get_taxa into two steps to help 2to3 work
00272         tree1 = parse_trees("test_file").next()
00273         taxa1 = tree1.get_taxa()
00274         for tree in parse_trees("Phylip/horses.tree"):
00275             taxa2 = tree.get_taxa()
00276             self.assertEqual(sorted(taxa1),sorted(taxa2))

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Calculate the distance between trees with ftreedist

Definition at line 277 of file test_EmbossPhylipNew.py.

00277 
00278     def test_ftreedist(self):
00279         """Calculate the distance between trees with ftreedist"""
00280         cline = FTreeDistCommandline(exes["ftreedist"],
00281                                      intreefile = "Phylip/horses.tree",
00282                                      outfile = "test_file",
00283                                      auto = True, filter = True)
00284         stdout, stderr = cline()
00285         self.assertTrue(os.path.isfile("test_file"))


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