# Bio.Phylo.CDAOIO module

I/O function wrappers for the RDF/CDAO file format.

This is an RDF format that conforms to the Comparative Data Analysis Ontology (CDAO). See: http://evolutionaryontology.org/cdao

This module requires the librdf Python bindings (http://www.librdf.org)

The CDAOIO.Parser, in addition to parsing text files, can also parse directly from a triple store that implements the Redland storage interface; similarly, the CDAOIO.Writer can store triples in a triple store instead of serializing them to a file.

Bio.Phylo.CDAOIO.qUri(x)

  Resolve URI for librdf.

Bio.Phylo.CDAOIO.format_label(x)

  Format label for librdf.

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

  Iterate over the trees in a CDAO file handle.

  Returns:

    generator of Bio.Phylo.CDAO.Tree objects.

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

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

  Returns:

    number of trees written.

class Bio.Phylo.CDAOIO.Parser(handle=None)

  Bases: `object`

  Parse a CDAO tree given a file handle.

  __init__(handle=None)

    Initialize CDAO tree parser.

  classmethod from_string(treetext)

    Instantiate the class from the given string.

  parse(**kwargs)

    Parse the text stream this object was initialized with.

  parse_handle_to_graph(rooted=False, parse_format='turtle', context=None, **kwargs)

    Parse self.handle into RDF model self.model.

  parse_graph(graph=None, context=None)

    Iterate over RDF model yielding CDAO.Tree instances.

  new_clade(node)

    Return a CDAO.Clade object for a given named node.

  get_node_info(graph, context=None)

    Create a dictionary containing information about all nodes in the tree.

  parse_children(node)

    Traverse the tree to create a nested clade structure.

    Return a CDAO.Clade, and calls itself recursively for each child, traversing the entire tree and creating a nested structure of CDAO.Clade objects.

  __annotate_func__ = None
  __annotations_cache__ = {}
  __firstlineno__ = 95
  __static_attributes__ = ('children', 'graph', 'handle', 'node_info', 'nodes', 'obj_info', 'rooted', 'tree_roots')

class Bio.Phylo.CDAOIO.Writer(trees)

  Bases: `object`

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

  prefixes = {'cdao': 'http://purl.obolibrary.org/obo/cdao.owl#', 'obo': 'http://purl.obolibrary.org/obo/', 'owl': 'http://www.w3.org/2002/07/owl#', 'rdf': 'http://www.w3.org/1999/02/22-rdf-syntax-ns#', 'rdfs': 'http://www.w3.org/2000/01/rdf-schema#'}
  __init__(trees)

    Initialize parameters for writing a CDAO tree.

  write(handle, tree_uri='', record_complete_ancestry=False, rooted=False, **kwargs)

    Write this instance’s trees to a file handle.

  add_stmt_to_handle(handle, stmt)

    Add URI prefix to handle.

  process_clade(clade, parent=None, root=False)

    Recursively generate triples describing a tree of clades.

  __annotate_func__ = None
  __annotations_cache__ = {}
  __firstlineno__ = 260
  __static_attributes__ = ('edge_counter', 'node_counter', 'record_complete_ancestry', 'rooted', 'tree_counter', 'tree_uri', 'trees', 'tu_counter')

Biopython v: 1.86

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