biopython v1.71.0 Bio.Phylo.CDAOIO.Parser

Parse a CDAO tree given a file handle.

Link to this section Summary

Initialize CDAO tree parser

Instantiate the class from the given string

Create a dictionary containing information about all nodes in the tree

Return a CDAO.Clade object for a given named node

parse()

Parse the text stream this object was initialized with

Traverse the tree to create a nested clade structure

Iterate over RDF model yielding CDAO.Tree instances

Parse self.handle into RDF model self.model

__init__()

Initialize CDAO tree parser.

from_string()

Instantiate the class from the given string.

get_node_info()

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

new_clade()

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

parse()

Parse the text stream this object was initialized with.

parse_children()

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.

parse_graph()

Iterate over RDF model yielding CDAO.Tree instances.

parse_handle_to_graph()

Parse self.handle into RDF model self.model.