newick 1.3.2

A python module to read and write the Newick format

python-newick

python package to read and write the Newick format.

Reading Newick

Since Newick specifies a format for a set of trees, all functions to read Newick return a list of newick.Node objects.

• Reading from a string:

  >>> from newick import loads
  >>> trees = loads('(A,B,(C,D)E)F;')
  >>> trees[0].name
  'F'
  >>> [n.name for n in trees[0].descendants]
  ['A', 'B', 'E']
  

• Reading from a file-like object:

  >>> import io
  >>> from newick import load
  >>> with io.open('fname', encoding='utf8') as fp:
  ...     trees = load(fp)
  

• Reading from a path:

  >>> from newick import read
  >>> trees = read('fname')
  >>> import pathlib
  >>> trees = read(pathlib.Path('fname'))
  

Supported Newick dialects

The "Newick specification" states

Comments are enclosed in square brackets and may appear anywhere

This has spawned a host of ad-hoc mechanisms to insert additional data into Newick trees.

The newick package allows to deal with comments in two ways.

• Ignoring comments:

  >>> newick.loads('[a comment](a,b)c;', strip_comments=True)[0].newick
  '(a,b)c'
  

• Reading comments as node annotations: Several software packages use Newick comments to store node annotations, e.g. *BEAST, MrBayes or TreeAnnotator. Provided there are no comments in places where they cannot be interpreted as node annotations, newick supports reading and writing these annotations:

  >>> newick.loads('(a[annotation],b)c;')[0].descendants[0].name
  'a'
  >>> newick.loads('(a[annotation],b)c;')[0].descendants[0].comment
  'annotation'
  >>> newick.loads('(a[annotation],b)c;')[0].newick
  '(a[annotation],b)c'
  

  Annotations may come before or after the : which separates node label and length:

• >>> newick.loads('(a[annotation]:2,b)c;')[0].descendants[0].length
  2.0
  >>> newick.loads('(a:[annotation]2,b)c;')[0].descendants[0].length
  2.0
  

  but if they preceed the colon, they must not contain ::

• >>> newick.loads('(a[annotation:]:2,b)c;')[0].descendants[0].comment
  ...
  ValueError: Node names or branch lengths must not contain ":"
  

Note that square brackets inside quoted labels will not be interpreted as comments or annotations:

>>> newick.loads("('a[label]',b)c;")[0].descendants[0].name
"'a[label]'"
>>> newick.loads("('a[label]',b)c;")[0].newick
"('a[label]',b)c"

Writing Newick

In parallel to the read operations there are three functions to serialize a single Node object or a list of Node objects to Newick format:

• dumps(trees) -> str
• dump(trees, fp)
• write(trees, 'fname')

A tree may be assembled using the factory methods of the Node class:

• Node.__init__
• Node.create
• Node.add_descendant

Manipulating trees

• Displaying tree topology in the terminal:

  >>> import newick
  >>> tree = newick.loads('(b,(c,(d,(e,(f,g))h)i)a)')[0]
  >>> print(tree.ascii_art())
      ┌─b
  ────┤
      │   ┌─c
      └─a─┤
          │   ┌─d
          └─i─┤
              │   ┌─e
              └─h─┤
                  │   ┌─f
                  └───┤
                      └─g
  

• Pruning trees: The example below prunes the tree such that b, c and i are the only remaining leafs.

  >>> tree.prune_by_names(['b', 'c', 'i'], inverse=True)
  >>> print(tree.ascii_art())
      ┌─b
  ────┤
      │   ┌─c
      └─a─┤
          └─i
  

• Running a callable on a filtered set of nodes:

  >>> tree.visit(lambda n: setattr(n, 'name', n.name.upper()), lambda n: n.name in ['a', 'b'])
  >>> print(tree.ascii_art())
      ┌─B
  ────┤
      │   ┌─c
      └─A─┤
          └─i
  

• Removing (topologically) redundant internal nodes:

  >>> tree.prune_by_names(['B', 'c'], inverse=True)
  >>> print(tree.ascii_art())
      ┌─B
  ────┤
      └─A ──c
  >>> tree.remove_redundant_nodes(keep_leaf_name=True)
  >>> print(tree.ascii_art())
      ┌─B
  ────┤
      └─c