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__(handle)
Initialize file handle for the Newick Tree.
- classmethod from_string(treetext)
Instantiate the Newick Tree class from the given string.
- parse(values_are_confidence=False, comments_are_confidence=False, rooted=False)
Parse the text stream this object was initialized with.
- new_clade(parent=None)
Return new Newick.Clade, optionally with temporary reference to parent.
- process_clade(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__(trees)
Initialize parameter for Tree Writer object.
- write(handle, **kwargs)
Write this instance’s trees to a file handle.
- to_strings(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.