from __future__ import absolute_import from __future__ import print_function # #START_LICENSE########################################################### # # # This file is part of the Environment for Tree Exploration program # (ETE). http://etetoolkit.org # # ETE is free software: you can redistribute it and/or modify it # under the terms of the GNU General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # ETE is distributed in the hope that it will be useful, but WITHOUT # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY # or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public # License for more details. # # You should have received a copy of the GNU General Public License # along with ETE. If not, see . # # # ABOUT THE ETE PACKAGE # ===================== # # ETE is distributed under the GPL copyleft license (2008-2015). # # If you make use of ETE in published work, please cite: # # Jaime Huerta-Cepas, Joaquin Dopazo and Toni Gabaldon. # ETE: a python Environment for Tree Exploration. Jaime BMC # Bioinformatics 2010,:24doi:10.1186/1471-2105-11-24 # # Note that extra references to the specific methods implemented in # the toolkit may be available in the documentation. # # More info at http://etetoolkit.org. Contact: huerta@embl.de # # # #END_LICENSE############################################################# import sys from ._nexml import MixedContainer, FloatTree, TreeFloatEdge, TreeNode, LiteralMeta from .. import PhyloTree from ..phylo.phylotree import _parse_species from ..parser.newick import read_newick class Children(list): def append(self, item): list.append(self, item) item.nexml_edge.source = self.node.nexml_node.id item.nexml_edge.target = item.nexml_node.id class NexmlTree(PhyloTree): """ Special PhyloTree object with nexml support """ def __repr__(self): return "NexML ETE tree <%s>" %hex(hash(self)) def _get_dist(self): return self.nexml_edge.get_length() def _set_dist(self, value): try: self.nexml_edge.set_length(value) except ValueError: raise def _get_support(self): return self._nexml_support.content def _set_support(self, value): try: self._nexml_support.content = float(value) except ValueError: raise def _get_name(self): return self.nexml_node.get_label() def _set_name(self, value): try: self.nexml_node.set_label(value) except ValueError: raise def _get_children(self): return self._children def _set_children(self, value): if isinstance(value, Children) and \ len(set([type(n)==type(self) for n in value]))<2: self._children = value else: raise ValueError("children:wrong type") dist = property(fget=_get_dist, fset=_set_dist) support = property(fget=_get_support, fset=_set_support) children = property(fget=_get_children, fset=_set_children) name = property(fget=_get_name, fset=_set_name) def __init__(self, newick=None, alignment=None, alg_format="fasta", \ sp_naming_function=_parse_species, format=0): self.nexml_tree = FloatTree() self.nexml_tree.set_anyAttributes_({'xsi:type': 'FloatTree'}) self.nexml_node = TreeNode() self.nexml_edge = TreeFloatEdge() self.nexml_node.id = "node_%s" %hash(self) self.nexml_edge.id = "edge_%s" %hash(self) self.nexml_project = None self._nexml_support = LiteralMeta(datatype="float", property="branch_support", content=1.0) self.nexml_edge.length = 0.0 self.nexml_edge.add_meta(self._nexml_support) # Initialize empty PhyloTree super(NexmlTree, self).__init__() self._children = Children() self._children.node = self if alignment: self.link_to_alignment(alignment, alg_format) if newick: read_newick(newick, root_node=self, format=format) self.set_species_naming_function(sp_naming_function) def set_nexml_project(self, nexml_obj): self.nexml_project = nexml_obj def build(self, node): self.nexml_tree = FloatTree() tree = self.nexml_tree tree.build(node) # This detects the outgroup of the tree even if the root tag # is not set in any node rootid = set([e.source for e in tree.edge]) - set([e.target for e in tree.edge]) nodeid2node = {rootid.pop(): self} for xmledge in tree.edge: child = nodeid2node.setdefault(xmledge.target, self.__class__() ) parent = nodeid2node.setdefault(xmledge.source, self.__class__() ) child.name = xmledge.target child.nexml_node.id = xmledge.target parent.name = xmledge.source parent.nexml_node.id = xmledge.source child.nexml_edge = xmledge if xmledge.length is not None: child.dist = float(xmledge.length) parent.add_child(child) for xmlnode in tree.node: # just a warning. I don't know if this can occur if xmlnode.id not in nodeid2node: print("Unused node", xmlnode.id, file=sys.stderr) continue ete_node = nodeid2node[xmlnode.id] ete_node.nexml_node = xmlnode if xmlnode.label: ete_node.name = xmlnode.label elif xmlnode.id is not None: ete_node.name = xmlnode.id def export(self, outfile=sys.stdout, level=0, namespace_='', name_='FloatTree', namespacedef_=''): if self.nexml_tree: info = [(n.nexml_edge, n.nexml_node) for n in self.traverse()] self.nexml_node.set_root(True) self.nexml_tree.set_edge([i[0] for i in info]) self.nexml_tree.set_node([i[1] for i in info]) self.nexml_tree.export(outfile=outfile, level=level, name_=name_, namespacedef_=namespacedef_) def exportChildren(self, outfile, level, namespace_='', name_='FloatTree'): sorted_nodes = [] sorted_edges = [] for n in self.traverse(): # process node node_obj = self.mixedclass_(MixedContainer.CategoryComplex, MixedContainer.TypeNone, 'node', n.nexml_node) sorted_nodes.append(node_obj) # process edge if n.nexml_edge: edge_obj = self.mixedclass_(MixedContainer.CategoryComplex, MixedContainer.TypeNone, 'edge', n.nexml_edge) sorted_edges.append(edge_obj) # process the nodes and edges self.tree.content_ = sorted_nodes + sorted_edges for item_ in self.tree.content_: item_.export(outfile, level, item_.name, namespace_) # end class AbstractTreeSub NexmlNode = NexmlTree