skbio.tree.TreeNode.shuffle

TreeNode.shuffle(k=None, names=None, shuffle_f=<built-in method shuffle of mtrand.RandomState object at 0x2ab64d54a8e8>, n=1)[source]

Yield trees with shuffled tip names

Parameters:

k : int, optional

The number of tips to shuffle. If k is not None, k tips are randomly selected, and only those names will be shuffled.

names : list, optional

The specific tip names to shuffle. k and names cannot be specified at the same time.

shuffle_f : func

Shuffle method, this function must accept a list and modify inplace.

n : int, optional

The number of iterations to perform. Value must be > 0 and np.inf can be specified for an infinite number of iterations.

Returns:

GeneratorType

Yielding TreeNode

Raises:

ValueError

If k is < 2 If n is < 1

ValueError

If both k and names are specified

MissingNodeError

If names is specified but one of the names cannot be found

Notes

Tip names are shuffled inplace. If neither k nor names are provided, all tips are shuffled.

Examples

Alternate the names on two of the tips, ‘a’, and ‘b’, and do this 5 times.

>>> from six import StringIO
>>> from skbio import TreeNode
>>> tree = TreeNode.read(StringIO("((a,b),(c,d));"))
>>> rev = lambda items: items.reverse()
>>> shuffler = tree.shuffle(names=['a', 'b'], shuffle_f=rev, n=5)
>>> for shuffled_tree in shuffler:
...     print(shuffled_tree)
((b,a),(c,d));

((a,b),(c,d));

((b,a),(c,d));

((a,b),(c,d));

((b,a),(c,d));