Bio.Phylo.NeXMLIO module
I/O function wrappers for the NeXML file format.
See: http://www.nexml.org
- Bio.Phylo.NeXMLIO.qUri(s)
Given a prefixed URI, return the full URI.
- Bio.Phylo.NeXMLIO.cdao_to_obo(s)
Optionally converts a CDAO-prefixed URI into an OBO-prefixed URI.
- Bio.Phylo.NeXMLIO.matches(s)
Check for matches in both CDAO and OBO namespaces.
- exception Bio.Phylo.NeXMLIO.NeXMLError
Bases:
Exception
Exception raised when NeXML object construction cannot continue.
- Bio.Phylo.NeXMLIO.parse(handle, **kwargs)
Iterate over the trees in a NeXML file handle.
- Returns:
generator of Bio.Phylo.NeXML.Tree objects.
- Bio.Phylo.NeXMLIO.write(trees, handle, plain=False, **kwargs)
Write a trees in NeXML format to the given file handle.
- Returns:
number of trees written.
- class Bio.Phylo.NeXMLIO.Parser(handle)
Bases:
object
Parse a NeXML tree given a file handle.
Based on the parser in
Bio.Nexus.Trees
.- __init__(handle)
Initialize parameters for NeXML file parser.
- classmethod from_string(treetext)
Convert file handle to StringIO object.
- add_annotation(node_dict, meta_node)
Add annotations for the NeXML parser.
- parse(values_are_confidence=False, rooted=False)
Parse the text stream this object was initialized with.
- class Bio.Phylo.NeXMLIO.Writer(trees)
Bases:
object
Based on the writer in Bio.Nexus.Trees (str, to_string).
- __init__(trees)
Initialize parameters for NeXML writer.
- new_label(obj_type)
Create new labels for the NeXML writer.
- write(handle, cdao_to_obo=True, **kwargs)
Write this instance’s trees to a file handle.