Bio.Phylo.NewickIO module

I/O function wrappers for the Newick file format.

See: http://evolution.genetics.washington.edu/phylip/newick_doc.html

exception Bio.Phylo.NewickIO.NewickError

Bases: Exception

Exception raised when Newick object construction cannot continue.

Bio.Phylo.NewickIO.parse(handle, **kwargs)

Iterate over the trees in a Newick file handle.

Returns

generator of Bio.Phylo.Newick.Tree objects.

Bio.Phylo.NewickIO.write(trees, handle, plain=False, **kwargs)

Write a trees in Newick format to the given file handle.

Returns

number of trees written.

class Bio.Phylo.NewickIO.Parser(handle)

Bases: object

Parse a Newick tree given a file handle.

Based on the parser in Bio.Nexus.Trees.

__init__(self, handle)

Initialize file handle for the Newick Tree.

classmethod from_string(treetext)

Instantiate the Newick Tree class from the given string.

parse(self, values_are_confidence=False, comments_are_confidence=False, rooted=False)

Parse the text stream this object was initialized with.

new_clade(self, parent=None)

Return new Newick.Clade, optionally with temporary reference to parent.

process_clade(self, clade)

Remove node’s parent and return it. Final processing of parsed clade.

class Bio.Phylo.NewickIO.Writer(trees)

Bases: object

Based on the writer in Bio.Nexus.Trees (str, to_string).

__init__(self, trees)

Initialize parameter for Tree Writer object.

write(self, handle, **kwargs)

Write this instance’s trees to a file handle.

to_strings(self, confidence_as_branch_length=False, branch_length_only=False, plain=False, plain_newick=True, ladderize=None, max_confidence=1.0, format_confidence='%1.2f', format_branch_length='%1.5f')

Return an iterable of PAUP-compatible tree lines.