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.
- 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.