def __init__(self, **kwargs):
"""
__init__ recognizes the following keywords (in addition to those of `DataReader.__init__`):
- `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 unrooted
- `default_as_rooted=True` (or `default_as_unrooted=False`): interprets
all trees as rooted if rooting not given by `[&R]` or `[&U]` comments
- `default_as_unrooted=True` (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)
- `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
- `allow_duplicate_taxon_labels` : if True, allow duplicate labels
on trees
- `ignore_missing_node_info` : if True, then no errors will be thrown if
tree nodes do not have the the required information.
"""
if 'edge_len_type' not in kwargs:
kwargs['edge_len_type'] = float
NexusReader.__init__(self, **kwargs)
self.is_ignore_missing_node_info = kwargs.get('ignore_missing_node_info', False)
def read(self, stream):
"""
Instantiates and returns a DataSet object based on the
NEXUS-formatted contents given in the file-like object `stream`.
"""
if self.dataset is None:
new_tree_list_idx = 0
else:
new_tree_list_idx = len(self.dataset.tree_lists)
self.dataset = NexusReader.read(self, stream)
for tree_list in self.dataset.tree_lists[new_tree_list_idx:]:
for tree in tree_list:
BeastSummaryTreeReader.parse_beast_tree_node_info(tree,
set_node_attributes=True,
value_type=float,
create_field_if_missing=True,
ignore_missing=self.is_ignore_missing_node_info)
return self.dataset
def tree_source_iter(self, stream):
"""
Iterates over a NEXUS-formatted source of trees.
Only trees will be returned, and any and all character data will
be skipped. The iterator will span over multiple tree blocks,
but, because our NEXUS data model implementation currently does
not recognize multiple taxon collection definnitions, taxa in
those tree blocks will be aggregated into the same `TaxonSet` (a
new one created, or the one passed to this method via the
`taxon_set` argument). This behavior is similar to how multiple
tree blocks are handled by a full NEXUS data file read.
"""
for tree in NexusReader.tree_source_iter(self, stream):
BeastSummaryTreeReader.parse_beast_tree_node_info(tree,
set_node_attributes=True,
value_type=float,
create_field_if_missing=True,
ignore_missing=self.is_ignore_missing_node_info)
yield tree
