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src/c/g/CGAT-0.2.0/CGAT/TreeTools.py   CGAT(Download)
import Bio
from Bio.Nexus.Nexus import Nexus
from Bio.Nexus.Trees import Tree
 
import Tree

src/c/g/CGAT-0.2.0/CGAT/Tree.py   CGAT(Download)
class Tree( Bio.Nexus.Trees.Tree ):
 
    def __init__(self, *args, **kwargs ):
        Bio.Nexus.Trees.Tree.__init__( self, *args, **kwargs )
 

src/c/g/cgat-HEAD/CGAT/TreeTools.py   cgat(Download)
import Bio
from Bio.Nexus.Nexus import Nexus
from Bio.Nexus.Trees import Tree
 
from CGAT import Tree as Tree

src/c/g/cgat-HEAD/CGAT/Tree.py   cgat(Download)
class Tree(Bio.Nexus.Trees.Tree):
 
    def __init__(self, *args, **kwargs):
        Bio.Nexus.Trees.Tree.__init__(self, *args, **kwargs)
 

src/b/i/biopython-HEAD/Tests/test_Nexus.py   biopython(Download)
        ts1b = "(Cephalotaxus:125.000000,(Taxus:100.000000,Torreya:100.000000)"\
               "TT1:25.000000)Taxaceae:90.000000;"
        tree = Trees.Tree(ts1b)
        self.assertEqual(self._get_flat_nodes(tree), [('Taxaceae', 90.0, None, None),
                                                      ('Cephalotaxus', 125.0, None, None),
        ts1c = "(Cephalotaxus:125.000000,(Taxus:100.000000,Torreya:100.000000)"\
                "25.000000)90.000000;"
        tree = Trees.Tree(ts1c)
        self.assertEqual(self._get_flat_nodes(tree), [(None, 90.0, None, None),
                                                      ('Cephalotaxus', 125.0, None, None),
          "t7:0.482152)E:0.0268148, ((t5:0.0984167,t3:0.488578)G:0.0349662,"\
          "t1:0.130208)F:0.0318288)D:0.0273876);"
        tree = Trees.Tree(ts2)
 
        large_ex_handle = open(os.path.join(self.testfile_dir,
            "int_node_labels.nwk"))
        tree = Trees.Tree(large_ex_handle.read())

src/b/i/biopython-HEAD/Tests/test_EmbossPhylipNew.py   biopython(Download)
    for tree_str in data.split(";\n"):
        if tree_str:
            yield Trees.Tree(tree_str+";")
 
 

src/b/i/biopython-1.63/Tests/test_Nexus.py   biopython(Download)
        ts1b = "(Cephalotaxus:125.000000,(Taxus:100.000000,Torreya:100.000000)"\
               "TT1:25.000000)Taxaceae:90.000000;"
        tree = Trees.Tree(ts1b)
        self.assertEqual(self._get_flat_nodes(tree), [('Taxaceae', 90.0, None, None),
                                                      ('Cephalotaxus', 125.0, None, None),
        ts1c = "(Cephalotaxus:125.000000,(Taxus:100.000000,Torreya:100.000000)"\
                "25.000000)90.000000;"
        tree = Trees.Tree(ts1c)
        self.assertEqual(self._get_flat_nodes(tree), [(None, 90.0, None, None),
                                                      ('Cephalotaxus', 125.0, None, None),
          "t7:0.482152)E:0.0268148, ((t5:0.0984167,t3:0.488578)G:0.0349662,"\
          "t1:0.130208)F:0.0318288)D:0.0273876);"
        tree = Trees.Tree(ts2)
 
        large_ex_handle = open(os.path.join(self.testfile_dir,
            "int_node_labels.nwk"))
        tree = Trees.Tree(large_ex_handle.read())

src/b/i/biopython-1.63/Tests/test_EmbossPhylipNew.py   biopython(Download)
    for tree_str in data.split(";\n"):
        if tree_str:
            yield Trees.Tree(tree_str+";")