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src/b/i/biopython-HEAD/Tests/test_Phylo.py   biopython(Download)
    def test_newick_read_multiple(self):
        """Parse a Nexus file with multiple trees."""
        trees = list(Phylo.parse(EX_NEXUS, 'nexus'))
        self.assertEqual(len(trees), 3)
        for tree in trees:
    def setUp(self):
        self.phylogenies = list(Phylo.parse(EX_PHYLO, 'phyloxml'))
 
    # Traversal methods
 

src/b/i/biopython-1.63/Tests/test_Phylo.py   biopython(Download)
    def test_newick_read_multiple(self):
        """Parse a Nexus file with multiple trees."""
        trees = list(Phylo.parse(EX_NEXUS, 'nexus'))
        self.assertEqual(len(trees), 3)
        for tree in trees:
    def setUp(self):
        self.phylogenies = list(Phylo.parse(EX_PHYLO, 'phyloxml'))
 
    # Traversal methods
 

src/b/i/biopython-HEAD/Tests/test_Consensus.py   biopython(Download)
    def setUp(self):
        self.trees = list(Phylo.parse('./TreeConstruction/trees.tre', 'newick'))
 
    def test_count_clades(self):
        bitstr_counts = Consensus._count_clades(self.trees)
    def test_strict_consensus(self):
        ref_trees = list(Phylo.parse('./TreeConstruction/strict_refs.tre', 'newick'))
        # three trees
        consensus_tree = Consensus.strict_consensus(self.trees)
        #tree_file = StringIO()
    def test_majority_consensus(self):
        ref_trees = Phylo.parse('./TreeConstruction/majority_ref.tre', 'newick')
        ref_tree = next(ref_trees)
        consensus_tree = Consensus.majority_consensus(self.trees)
        self.assertTrue(Consensus._equal_topology(consensus_tree, ref_tree))
    def test_adam_consensus(self):
        ref_trees = list(Phylo.parse('./TreeConstruction/adam_refs.tre', 'newick'))
        # three trees
        consensus_tree = Consensus.adam_consensus(self.trees)
        #tree_file = '/home/yeyanbo/adam.tres'