dendropy.dataobject.dataset – Primary Data Manager

class dendropy.dataobject.dataset.DataSet(*args, **kwargs)

The main data manager, consisting of a lists of taxa, trees, and character phylogenetic data objects, as well as methods to create, populate, access, and delete them.

__init__ takes a new DataSet object from another DataSet object or by parsing an input stream.

Can be invoked with:

• a single unnamed argument that is an instance of a DataSet (which will result in a deep copy of all taxa, trees and characters),
• 1 or more unnamed TaxonSet, TreeList or CharacterMatrix (which is like calling DataSet.add with each argument)
• keyword arguments that supply a file-like object (stream) to be parsed and a string (schema) specifying the schema of the data in the file-like object.

add(data_object, **kwargs)

Generic add for TaxonSet, TreeList or CharacterMatrix objects.

add_char_matrix(char_matrix)

Accession of existing CharacterMatrix into chars of self.

add_taxon_set(taxon_set)

Adds an existing TaxonSet object to this DataSet.

add_tree_list(tree_list)

Accession of existing TreeList object into tree_lists of self.

attach_taxon_set(taxon_set=None)

Forces all read() calls on this DataSet to use the same TaxonSet. If taxon_set If taxon_set is None, then a new TaxonSet will be created, added to self.taxa, and that is the TaxonSet that will be attached.

description(depth=1, indent=0, itemize='', output=None)

Returns description of object, up to level depth.

get_default_taxon_set(**kwargs)

Returns an existing TaxonSet object in this DataSet, selected by keywords oid or label.

get_tree_list(**kwargs)

Returns a TreeList object specified by one (and exactly one) of the following keyword arguments:

• label
• oid

Raises KeyError if no matching TreeList is found, unless ignore_error is set to True.

new_char_matrix(char_matrix_type, *args, **kwargs)

Creation and accession of new CharacterMatrix (of class char_matrix_type) into chars of self.”

new_taxon_set(*args, **kwargs)

Creates a new TaxonSet object, according to the arguments given (passed to TaxonSet()), and adds it to this DataSet.

new_tree_list(*args, **kwargs)

Creation and accession of new TreeList into trees of self.

read(stream, schema, **kwargs)

Populates this DataSet object from a file-like object data source stream, formatted in schema. schema must be a recognized and supported phylogenetic data file schema. If reading is not implemented for the schema specified, then a UnsupportedSchemaError is raised.

The following optional keyword arguments are also recognized:

• exclude_trees if True skips over tree data

• exclude_chars if True skips over character data

• encode_splits specifies whether or not split bitmasks will be

  calculated and attached to the edges.

• finish_node_func is a function that will be applied to each node

  after it has been constructed.

The following keyword arguments are recognized when parsing NEXUS or NEWICK sources:

• taxon_set TaxonSet object to use when reading data

• as_rooted=True (or as_unrooted=False) interprets trees as rooted

• as_unrooted=True (or as_rooted=False) interprets trees as rooted

• default_as_rooted (or default_as_unrooted=False) interprets

  all trees as rooted if rooting not given by [&R] or [&U] comments

• default_as_unrooted (or default_as_rooted=False) interprets

  all trees as rooted if rooting not given by [&R] or [&U] comments

• edge_len_type specifies the type of the edge lengths (int or float)

Additional keyword arguments may be handled by various readers specialized to handle specific data formats.

unify_taxa(taxon_set=None, bind=True)

Reindices taxa across all subcomponents, mapping to single taxon set.

write(stream, schema, **kwargs)

Writes this DataSet object to the file-like object stream in schema. schema must be a recognized and supported phylogenetic data file schema. If writing is not implemented for the schema specified, then a UnsupportedSchemaError is raised.

The following optional keyword arguments are also recognized:

• exclude_trees if True skips over tree data
• exclude_chars if True skips over character data

Additional keyword arguments may be handled by various writers specialized to handle specific data formats.