Ejemplos de L_newick.safe_newick_string en Python

Ejemplo n.º 1

Archivo: L_parsimony.py Proyecto: digling/tukano-paper

def swap_tree(tree):
    
    # make safe tree
    if not '"' in tree:
        tree = nwk.safe_newick_string(tree)

    # swap two nodes of the tree
    nodes = list(nwk.nodes_in_tree(tree))[1:]
    random.shuffle(nodes)
    
    # choose two nodes to be swapped
    nodeA = nodes.pop(0)

    # get another node that can be interchanged
    while nodes:
        nodeB = nodes.pop(0)
        if nodeB in nodeA or nodeA in nodeB:
            pass
        else:
            break

    tree = tree.replace(nodeA+',', '#dummyA#,')
    tree = tree.replace(nodeA+')', '#dummyA#)')
    tree = tree.replace(nodeB+',', '#dummyB#,')
    tree = tree.replace(nodeB+')', '#dummyB#)')

    tree = tree.replace('#dummyA#', nodeB)
    tree = tree.replace('#dummyB#', nodeA)

    return nwk.sort_tree(tree).replace('"','')

Ejemplo n.º 2

def swap_tree(tree):

    # make safe tree
    if not '"' in tree:
        tree = nwk.safe_newick_string(tree)

    # swap two nodes of the tree
    nodes = list(nwk.nodes_in_tree(tree))[1:]
    random.shuffle(nodes)

    # choose two nodes to be swapped
    nodeA = nodes.pop(0)

    # get another node that can be interchanged
    while nodes:
        nodeB = nodes.pop(0)
        if nodeB in nodeA or nodeA in nodeB:
            pass
        else:
            break

    tree = tree.replace(nodeA + ',', '#dummyA#,')
    tree = tree.replace(nodeA + ')', '#dummyA#)')
    tree = tree.replace(nodeB + ',', '#dummyB#,')
    tree = tree.replace(nodeB + ')', '#dummyB#)')

    tree = tree.replace('#dummyA#', nodeB)
    tree = tree.replace('#dummyB#', nodeA)

    return nwk.sort_tree(tree).replace('"', '')