def compose_node(self, node):
"""
Given a DendroPy Node, this returns the Node as a NEWICK
statement according to the class-defined formatting rules.
"""
child_nodes = node.child_nodes()
if child_nodes:
subnodes = [self.compose_node(child) for child in child_nodes]
statement = '(' + ','.join(subnodes) + ')'
if not (self.suppress_internal_taxon_labels and self.suppress_internal_node_labels):
statement = statement + self.choose_display_tag(node)
if node.edge and node.edge.length != None and not self.suppress_edge_lengths:
statement = "%s:%s" % (statement, self.edge_label_compose_func(node.edge))
else:
statement = self.choose_display_tag(node)
if node.edge and node.edge.length != None and not self.suppress_edge_lengths:
statement = "%s:%s" % (statement, self.edge_label_compose_func(node.edge))
if not self.suppress_annotations or self.annotations_as_nhx:
node_annotation_comments = nexustokenizer.format_annotation_as_comments(node, nhx=self.annotations_as_nhx)
edge_annotation_comments = nexustokenizer.format_annotation_as_comments(node.edge, nhx=self.annotations_as_nhx)
statement = statement + node_annotation_comments + edge_annotation_comments
#if self.nhx_key_to_func:
# nhx_to_print = []
# for k, v in self.nhx_key_to_func.items():
# r = v(node.edge)
# if r is not None:
# nhx_to_print.append("%s=%s" % (k, str(r)))
# if nhx_to_print:
# statement = statement + ('[&&NHX:%s]' % ':'.join(nhx_to_print))
node_comment_str = self.compose_comment_string(node)
statement += node_comment_str
return statement
def write_taxa_block(self, taxon_set, stream):
block = []
block.append("BEGIN TAXA;")
if not self.suppress_annotations:
block.append(nexustokenizer.format_annotation_as_comments(taxon_set, nhx=self.annotations_as_nhx))
if self._link_blocks():
title = self.compose_block_title(taxon_set)
if title:
block.append(" %s;" % title)
block.append(" DIMENSIONS NTAX=%d;" % len(taxon_set))
block.append(" TAXLABELS")
for taxon in taxon_set:
if self.suppress_annotations:
annotation_str = ""
else:
annotation_str = " " + nexustokenizer.format_annotation_as_comments(taxon, nhx=self.annotations_as_nhx)
block.append(
" %s%s"
% (
textutils.escape_nexus_token(
taxon.label,
preserve_spaces=self.preserve_spaces,
quote_underscores=not self.unquoted_underscores,
),
annotation_str,
)
)
block.append(" ;")
block.append("END;\n\n")
stream.write("\n".join(block))
def write_taxa_block(self, taxon_set, stream):
block = []
block.append('BEGIN TAXA;')
if not self.suppress_annotations:
block.append(
nexustokenizer.format_annotation_as_comments(
taxon_set, nhx=self.annotations_as_nhx))
if self._link_blocks():
title = self.compose_block_title(taxon_set)
if title:
block.append(' %s;' % title)
block.append(' DIMENSIONS NTAX=%d;' % len(taxon_set))
block.append(' TAXLABELS')
for taxon in taxon_set:
if self.suppress_annotations:
annotation_str = ""
else:
annotation_str = " " + nexustokenizer.format_annotation_as_comments(
taxon, nhx=self.annotations_as_nhx)
block.append(' %s%s' % (textutils.escape_nexus_token(
taxon.label,
preserve_spaces=self.preserve_spaces,
quote_underscores=not self.unquoted_underscores),
annotation_str))
block.append(' ;')
block.append('END;\n\n')
stream.write('\n'.join(block))
def write_tree(self, tree, stream):
"""
Composes and writes `tree` to `stream`.
"""
if tree.rooting_state_is_undefined or self.suppress_rooting:
rooting = ""
elif tree.is_rooted:
rooting = "[&R] "
elif not tree.is_rooted:
rooting = "[&U] "
else:
rooting = ""
if self.store_tree_weights and tree.weight is not None:
weight = "[&W %s] " % tree.weight
else:
weight = ""
if not self.suppress_annotations or self.annotations_as_nhx:
annotation_comments = nexustokenizer.format_annotation_as_comments(tree, nhx=self.annotations_as_nhx)
else:
annotation_comments = ""
tree_comments = self.compose_comment_string(tree)
stream.write("%s%s%s%s%s;\n" % (rooting,
weight,
annotation_comments,
tree_comments,
self.compose_node(tree.seed_node)))
def write_tree(self, tree, stream):
"""
Composes and writes `tree` to `stream`.
"""
if tree.rooting_state_is_undefined or self.suppress_rooting:
rooting = ""
elif tree.is_rooted:
rooting = "[&R] "
elif not tree.is_rooted:
rooting = "[&U] "
else:
rooting = ""
if self.store_tree_weights and tree.weight is not None:
weight = "[&W %s] " % tree.weight
else:
weight = ""
if not self.suppress_annotations or self.annotations_as_nhx:
annotation_comments = nexustokenizer.format_annotation_as_comments(
tree, nhx=self.annotations_as_nhx)
else:
annotation_comments = ""
tree_comments = self.compose_comment_string(tree)
stream.write("%s%s%s%s%s;\n" %
(rooting, weight, annotation_comments, tree_comments,
self.compose_node(tree.seed_node)))
def write(self, stream):
"""
Writes attached `DataSource` or `TaxonDomain` to the file-like object
`stream`.
"""
assert self.dataset is not None, "NexusWriter instance is not attached to a DataSet: no source of data"
if (
self.is_write_block_titles == False
and self.attached_taxon_set is None
and (len(self.dataset.taxon_sets) > 1)
):
_LOG.warn(
"Multiple taxon sets in data, but directed not to write block titles: data file may not be interpretable"
)
stream.write("#NEXUS\n\n")
if self.file_comments is not None:
if isinstance(self.file_comments, list):
for line in self.file_comments:
if line.strip().replace("\n", "").replace("\r", ""):
stream.write("[ %s ]\n" % line)
else:
stream.write("\n")
stream.write("\n")
else:
stream.write("[ %s ]\n\n" % self.file_comments)
if not self.suppress_annotations:
stream.write(nexustokenizer.format_annotation_as_comments(self.dataset, nhx=self.annotations_as_nhx))
stream.write("\n")
if self.preamble_blocks:
for block in self.preamble_blocks:
stream.write(block)
stream.write("\n")
stream.write("\n")
if (
(
((not self.exclude_chars) and self.dataset.char_matrices)
or ((not self.exclude_trees) and self.dataset.tree_lists)
)
and (not self.simple)
and (not self.suppress_taxa_block)
):
for taxon_set in self.dataset.taxon_sets:
if self.attached_taxon_set is None or taxon_set is self.attached_taxon_set:
self.write_taxa_block(taxon_set, stream=stream)
if not self.exclude_chars:
for char_matrix in self.dataset.char_matrices:
if self.attached_taxon_set is None or char_matrix.taxon_set is self.attached_taxon_set:
self.write_char_block(char_matrix=char_matrix, stream=stream)
if not self.exclude_trees:
for tree_list in self.dataset.tree_lists:
if self.attached_taxon_set is None or tree_list.taxon_set is self.attached_taxon_set:
self.write_trees_block(tree_list=tree_list, stream=stream)
if self.supplemental_blocks:
for block in self.supplemental_blocks:
stream.write(block)
stream.write("\n")
def write(self, stream):
"""
Writes attached `DataSource` or `TaxonDomain` to the file-like object
`stream`.
"""
assert self.dataset is not None, \
"NexusWriter instance is not attached to a DataSet: no source of data"
if self.is_write_block_titles == False \
and self.attached_taxon_set is None \
and (len(self.dataset.taxon_sets) > 1):
_LOG.warn(
"Multiple taxon sets in data, but directed not to write block titles: data file may not be interpretable"
)
stream.write('#NEXUS\n\n')
if self.file_comments is not None:
if isinstance(self.file_comments, list):
for line in self.file_comments:
if line.strip().replace("\n", "").replace("\r", ""):
stream.write("[ %s ]\n" % line)
else:
stream.write("\n")
stream.write("\n")
else:
stream.write("[ %s ]\n\n" % self.file_comments)
if not self.suppress_annotations:
stream.write(
nexustokenizer.format_annotation_as_comments(
self.dataset, nhx=self.annotations_as_nhx))
stream.write("\n")
if self.preamble_blocks:
for block in self.preamble_blocks:
stream.write(block)
stream.write("\n")
stream.write("\n")
if (( (not self.exclude_chars) and self.dataset.char_matrices) \
or ( (not self.exclude_trees) and self.dataset.tree_lists)) \
and (not self.simple) \
and (not self.suppress_taxa_block):
for taxon_set in self.dataset.taxon_sets:
if self.attached_taxon_set is None or taxon_set is self.attached_taxon_set:
self.write_taxa_block(taxon_set, stream=stream)
if not self.exclude_chars:
for char_matrix in self.dataset.char_matrices:
if self.attached_taxon_set is None or char_matrix.taxon_set is self.attached_taxon_set:
self.write_char_block(char_matrix=char_matrix,
stream=stream)
if not self.exclude_trees:
for tree_list in self.dataset.tree_lists:
if self.attached_taxon_set is None or tree_list.taxon_set is self.attached_taxon_set:
self.write_trees_block(tree_list=tree_list, stream=stream)
if self.supplemental_blocks:
for block in self.supplemental_blocks:
stream.write(block)
stream.write("\n")
def write_trees_block(self, tree_list, stream):
block = []
newick_writer = newick.NewickWriter(
suppress_rooting=self.suppress_rooting,
suppress_edge_lengths=self.suppress_edge_lengths,
unquoted_underscores=self.unquoted_underscores,
preserve_spaces=self.preserve_spaces,
store_tree_weights=self.store_tree_weights,
suppress_annotations=self.suppress_annotations,
annotations_as_nhx=self.annotations_as_nhx,
suppress_item_comments=self.suppress_item_comments,
suppress_leaf_taxon_labels=self.suppress_leaf_taxon_labels,
suppress_leaf_node_labels=self.suppress_leaf_node_labels,
suppress_internal_taxon_labels=self.suppress_internal_taxon_labels,
suppress_internal_node_labels=self.suppress_internal_node_labels,
node_label_element_separator=self.node_label_element_separator,
node_label_compose_func=self.node_label_compose_func,
edge_label_compose_func=self.edge_label_compose_func,
)
block.append("BEGIN TREES;")
if not self.suppress_annotations:
block.append(nexustokenizer.format_annotation_as_comments(tree_list, nhx=self.annotations_as_nhx))
if self._link_blocks():
title = self.compose_block_title(tree_list)
if title:
block.append(" %s;" % title)
if tree_list.taxon_set.labels:
block.append(
" LINK TAXA = %s;"
% textutils.escape_nexus_token(
tree_list.taxon_set.label,
preserve_spaces=self.preserve_spaces,
quote_underscores=not self.unquoted_underscores,
)
)
for treeidx, tree in enumerate(tree_list):
if tree.label:
tree_name = tree.label
else:
tree_name = str(treeidx)
newick_str = newick_writer.compose_tree(tree)
block.append(
" TREE %s = %s"
% (
textutils.escape_nexus_token(
tree_name, preserve_spaces=self.preserve_spaces, quote_underscores=not self.unquoted_underscores
),
newick_str,
)
)
block.append("END;\n\n")
stream.write("\n".join(block))
def compose_node(self, node):
"""
Given a DendroPy Node, this returns the Node as a NEWICK
statement according to the class-defined formatting rules.
"""
child_nodes = node.child_nodes()
if child_nodes:
subnodes = [self.compose_node(child) for child in child_nodes]
statement = '(' + ','.join(subnodes) + ')'
if not (self.suppress_internal_taxon_labels
and self.suppress_internal_node_labels):
statement = statement + self.choose_display_tag(node)
if node.edge and node.edge.length != None and not self.suppress_edge_lengths:
statement = "%s:%s" % (statement,
self.edge_label_compose_func(node.edge))
else:
statement = self.choose_display_tag(node)
if node.edge and node.edge.length != None and not self.suppress_edge_lengths:
statement = "%s:%s" % (statement,
self.edge_label_compose_func(node.edge))
if not self.suppress_annotations or self.annotations_as_nhx:
node_annotation_comments = nexustokenizer.format_annotation_as_comments(
node, nhx=self.annotations_as_nhx)
edge_annotation_comments = nexustokenizer.format_annotation_as_comments(
node.edge, nhx=self.annotations_as_nhx)
statement = statement + node_annotation_comments + edge_annotation_comments
#if self.nhx_key_to_func:
# nhx_to_print = []
# for k, v in self.nhx_key_to_func.items():
# r = v(node.edge)
# if r is not None:
# nhx_to_print.append("%s=%s" % (k, str(r)))
# if nhx_to_print:
# statement = statement + ('[&&NHX:%s]' % ':'.join(nhx_to_print))
node_comment_str = self.compose_comment_string(node)
statement += node_comment_str
return statement
def write_trees_block(self, tree_list, stream):
block = []
newick_writer = newick.NewickWriter(
suppress_rooting=self.suppress_rooting,
suppress_edge_lengths=self.suppress_edge_lengths,
unquoted_underscores=self.unquoted_underscores,
preserve_spaces=self.preserve_spaces,
store_tree_weights=self.store_tree_weights,
suppress_annotations=self.suppress_annotations,
annotations_as_nhx=self.annotations_as_nhx,
suppress_item_comments=self.suppress_item_comments,
suppress_leaf_taxon_labels=self.suppress_leaf_taxon_labels,
suppress_leaf_node_labels=self.suppress_leaf_node_labels,
suppress_internal_taxon_labels=self.suppress_internal_taxon_labels,
suppress_internal_node_labels=self.suppress_internal_node_labels,
node_label_element_separator=self.node_label_element_separator,
node_label_compose_func=self.node_label_compose_func,
edge_label_compose_func=self.edge_label_compose_func,
)
block.append('BEGIN TREES;')
if not self.suppress_annotations:
block.append(
nexustokenizer.format_annotation_as_comments(
tree_list, nhx=self.annotations_as_nhx))
if self._link_blocks():
title = self.compose_block_title(tree_list)
if title:
block.append(' %s;' % title)
if tree_list.taxon_set.labels:
block.append(
' LINK TAXA = %s;' % textutils.escape_nexus_token(
tree_list.taxon_set.label,
preserve_spaces=self.preserve_spaces,
quote_underscores=not self.unquoted_underscores))
for treeidx, tree in enumerate(tree_list):
if tree.label:
tree_name = tree.label
else:
tree_name = str(treeidx)
newick_str = newick_writer.compose_tree(tree)
block.append(' TREE %s = %s' % (textutils.escape_nexus_token(
tree_name,
preserve_spaces=self.preserve_spaces,
quote_underscores=not self.unquoted_underscores), newick_str))
block.append('END;\n\n')
stream.write('\n'.join(block))