Package Bio :: Package Phylo :: Module NewickIO

Module NewickIO

I/O function wrappers for the Newick file format.

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

Classes

NewickError
Exception raised when Newick object construction cannot continue.

Parser
Parse a Newick tree given a file handle.

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

Functions

parse(handle, **kwargs)
Iterate over the trees in a Newick file handle.

source code

write(trees, handle, plain=False, **kwargs)
Write a trees in Newick format to the given file handle.

source code

Variables

NODECOMMENT_START = '[&'

NODECOMMENT_END = ']'

Function Details

Iterate over the trees in a Newick file handle.

:returns: generator of Bio.Phylo.Newick.Tree objects.

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

:returns: number of trees written.