pycldf.trees

Support for the CLDF TreeTable component.

The peculiarity of a tree object in CLDF lies in the fact that the actual tree data is pulled in from a media file in newick or Nexus format. This “pulling in” is implemented in the method Tree.newick().

Accessing Tree instances associated with a dataset is done using a Trees instance.

>>> from pycldf import Dataset
>>> from pycldf.trees import TreeTable
>>> ds = Dataset.from_metadata('tests/data/dataset_with_trees/metadata.json')
>>> trees = list(TreeTable(ds))
>>> print(trees[0].newick().ascii_art())
          ┌─l1
     ┌────┤
     │    └─l2
─────┤
     ├─l3
     └─l4

class pycldf.trees.Tree(trees, row, file)

Represents a tree object as specified in a row of TreeTable.

Parameters:

• trees (pycldf.trees.TreeTable) –

• row (dict) –

• file (pycldf.media.File) –

newick(d=None, strip_comments=False)

Retrieve a newick.Node instance for the tree from the associated tree file.

Parameters:

• d (typing.Optional[pathlib.Path]) – Directory where the tree file was saved earlier, using pycldf.media.File.save().

• strip_comments (bool) – Flag signaling whether to strip comments enclosed in square brackets.

Return type:

newick.Node

Returns:

newick.Node representing the root of the associated tree.

newick_string(d=None)

Retrieve the Newick representation of the tree from the associated tree file.

Parameters:

d (typing.Optional[pathlib.Path]) – Directory where the tree file was saved earlier, using pycldf.media.File.save().

Return type:

str

Returns:

Newick representation of the associated tree.

class pycldf.trees.TreeTable(ds)

Container class for a Dataset’s TreeTable.

Parameters:

ds (pycldf.dataset.Dataset) –