# 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.

  __firstlineno__ = 21
  __static_attributes__ = ()

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.

  __annotate_func__ = None
  __annotations_cache__ = {}
  __firstlineno__ = 94
  __static_attributes__ = ('comments_are_confidence', 'handle', 'rooted', 'values_are_confidence')

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.

  __annotate_func__ = None
  __annotations_cache__ = {}
  __firstlineno__ = 257
  __static_attributes__ = ('trees',)

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