예제 #1
0
파일: FtreeIO.py 프로젝트: BIGtigr/xgcode
def newick_to_RBN(s):
    """
    @param s: newick string
    @return: directed topology, branch lengths, vertex name map
    """
    tree = NewickIO.parse_simple(s, _IO_Tree())
    Ftree.RB_assert_branch_lengths(tree.R, tree.B)
    return tree.R, tree.B, tree.v_to_name
예제 #2
0
파일: FtreeIO.py 프로젝트: BIGtigr/xgcode
def newick_to_TN(s):
    """
    Everything to do with branch lengths is ignored.
    @param s: newick string
    @return: undirected topology, vertex name map
    """
    tree = NewickIO.parse_simple(s, _IO_Tree())
    return Ftree.R_to_T(tree.R), tree.v_to_name
예제 #3
0
파일: FtreeIO.py 프로젝트: BIGtigr/xgcode
def newick_to_TBN(s):
    """
    @param s: newick string
    @return: undirected topology, branch lengths, vertex name map
    """
    tree = NewickIO.parse_simple(s, _IO_Tree())
    T = Ftree.R_to_T(tree.R)
    Ftree.TB_assert_branch_lengths(T, tree.B)
    return T, tree.B, tree.v_to_name
예제 #4
0
파일: FtreeIO.py 프로젝트: BIGtigr/xgcode
def newick_to_R(s, name_type=None):
    tree = NewickIO.parse_simple(s, _IO_Tree())
    N = get_validated_name_map(tree.v_to_name, name_type)
    return set((N[a], N[b]) for a, b in tree.R)