def build_from_file(self, fname, index_otus=True):
""" Populate Nexml project with data in a nexml file. """
doc = _nexml.parsexml_(fname)
rootNode = doc.getroot()
rootTag, rootClass = _nexml.get_root_tag(rootNode)
if rootClass is None:
rootTag = 'Nexml'
rootClass = self.__class__
#rootObj = rootClass.factory()
self.build(rootNode)
# This keeps a pointer from all trees to the parent nexml
# project. This way I can access other parts, such as otus,
# etc...
if index_otus:
id2taxa = {}
for taxa in self.get_otus():
id2taxon = {}
for taxon in taxa.otu:
id2taxon[taxon.id] = taxon
id2taxa[taxa.id] = [taxa, id2taxon]
for trees in self.get_trees():
for t in trees.get_tree():
t.set_nexml_project(self)
if trees.otus in id2taxa:
t.nexml_otus = id2taxa[trees.otus][0]
def build_from_file(self, fname, index_otus=True):
""" Populate Nexml project with data in a nexml file. """
doc = _nexml.parsexml_(fname)
rootNode = doc.getroot()
rootTag, rootClass = _nexml.get_root_tag(rootNode)
if rootClass is None:
rootTag = 'Nexml'
rootClass = self.__class__
#rootObj = rootClass.factory()
self.build(rootNode)
# This keeps a pointer from all trees to the parent nexml
# project. This way I can access other parts, such as otus,
# etc...
if index_otus:
id2taxa = {}
for taxa in self.get_otus():
id2taxon = {}
for taxon in taxa.otu:
id2taxon[taxon.id] = taxon
id2taxa[taxa.id] = [taxa, id2taxon]
for trees in self.get_trees():
for t in trees.get_tree():
t.set_nexml_project(self)
if trees.otus in id2taxa:
t.nexml_otus = id2taxa[trees.otus][0]