def rdf2dendropyTree(file_obj=None, data=None):
'''
Parses the content (a `file_obj` file object or `data` as a) into a dendropyTree.
Uses the 'has_Parent' term in http://www.evolutionaryontology.org/cdao/1.0/cdao.owl#
to construct and return a rooted dendropy.Tree object
Relies on rdflib and dendropy.
Raises ValueError if the graph does not imply exactly 1 root node
'''
from dendropy import Node, Tree, Edge, TaxonSet, Taxon
graph = rdflib.Graph()
if file_obj:
graph.parse(file=file_obj)
else:
graph.parse(data=data, format='xml')
nd_dict = {}
has_parent_predicate = OBO_PREFIX + HAS_PARENT_PREDICATE
if _DEBUGGING:
out = open('parse_rdf.txt', 'w')
taxon_set = TaxonSet()
OBO = rdflib.Namespace(u"http://purl.obolibrary.org/obo/")
parentless = set()
for s, p, o in graph.triples((None, OBO[HAS_PARENT_PREDICATE], None)):
parent = nd_dict.get(id(o))
if parent is None:
#print 'Parent o.value = ', o.value(rdflib.RDF.nodeID)
raw_o = o
o = rdflib.resource.Resource(graph, o)
o_tu = o.value(OBO[REPRESENTS_TU_PREDICATE])
if o_tu:
o_label = o_tu.value(rdflib.RDFS.label)
t = Taxon(label=o_label)
taxon_set.append(t)
parent = Node(taxon=t)
else:
parent = Node()
nd_dict[id(raw_o)] = parent
parentless.add(parent)
child = nd_dict.get(id(s))
if child is None:
raw_s = s
s = rdflib.resource.Resource(graph, s)
s_tu = s.value(OBO[REPRESENTS_TU_PREDICATE])
if s_tu:
s_label = s_tu.value(rdflib.RDFS.label)
t = Taxon(label=s_label)
taxon_set.append(t)
child = Node(taxon=t)
else:
child = Node()
nd_dict[id(raw_s)] = child
else:
if child in parentless:
parentless.remove(child)
parent.add_child(child)
if _DEBUGGING:
out.write('%s %s %s\n' % (str(s), p, o))
out.write('%s\n' % (str(parentless)))
if _DEBUGGING:
out.close()
if len(parentless) != 1:
message = "Expecting to find exactly Node (an object of a has_Parent triple) in the graph without a parent. Found %d" % len(
parentless)
CUTOFF_FOR_LISTING_PARENTLESS_NODES = 1 + len(
parentless
) # we might want to put in a magic number here to suppress really long output
if len(parentless) > 0 and len(
parentless) < CUTOFF_FOR_LISTING_PARENTLESS_NODES:
message += ":\n "
for i in parentless:
if i.label:
message += "\n " + i.label
else:
message += "\n <unlabeled>" + str(id(i))
raise ValueError(message)
else:
return None
tree = Tree(taxon_set=taxon_set)
tree.seed_node = list(parentless)[0]
tree.is_rooted = True
return tree
def rdf2dendropyTree(file_obj=None, data=None):
'''
Parses the content (a `file_obj` file object or `data` as a) into a dendropyTree.
Uses the 'has_Parent' term in http://www.evolutionaryontology.org/cdao/1.0/cdao.owl#
to construct and return a rooted dendropy.Tree object
Relies on rdflib and dendropy.
Raises ValueError if the graph does not imply exactly 1 root node
'''
from dendropy import Node, Tree, Edge, TaxonSet, Taxon
graph = rdflib.Graph()
if file_obj:
graph.parse(file=file_obj)
else:
graph.parse(data=data, format='xml')
nd_dict = {}
has_parent_predicate = OBO_PREFIX + HAS_PARENT_PREDICATE
if _DEBUGGING:
out = open('parse_rdf.txt', 'w')
taxon_set = TaxonSet()
OBO = rdflib.Namespace(u"http://purl.obolibrary.org/obo/")
parentless = set()
for s, p, o in graph.triples((None, OBO[HAS_PARENT_PREDICATE], None)):
parent = nd_dict.get(id(o))
if parent is None:
#print 'Parent o.value = ', o.value(rdflib.RDF.nodeID)
raw_o = o
o = rdflib.resource.Resource(graph, o)
o_tu = o.value(OBO[REPRESENTS_TU_PREDICATE])
if o_tu:
o_label = o_tu.value(rdflib.RDFS.label)
t = Taxon(label=o_label)
taxon_set.append(t)
parent = Node(taxon=t)
else:
parent = Node()
nd_dict[id(raw_o)] = parent
parentless.add(parent)
child = nd_dict.get(id(s))
if child is None:
raw_s = s
s = rdflib.resource.Resource(graph, s)
s_tu = s.value(OBO[REPRESENTS_TU_PREDICATE])
if s_tu:
s_label = s_tu.value(rdflib.RDFS.label)
t = Taxon(label=s_label)
taxon_set.append(t)
child = Node(taxon=t)
else:
child = Node()
nd_dict[id(raw_s)] = child
else:
if child in parentless:
parentless.remove(child)
parent.add_child(child)
if _DEBUGGING:
out.write('%s %s %s\n' % ( str(s), p, o))
out.write('%s\n' % ( str(parentless)))
if _DEBUGGING:
out.close()
if len(parentless) != 1:
message = "Expecting to find exactly Node (an object of a has_Parent triple) in the graph without a parent. Found %d" % len(parentless)
CUTOFF_FOR_LISTING_PARENTLESS_NODES = 1 + len(parentless) # we might want to put in a magic number here to suppress really long output
if len(parentless) > 0 and len(parentless) < CUTOFF_FOR_LISTING_PARENTLESS_NODES:
message += ":\n "
for i in parentless:
if i.label:
message += "\n " + i.label
else:
message += "\n <unlabeled>" + str(id(i))
raise ValueError(message)
else:
return None
tree = Tree(taxon_set=taxon_set)
tree.seed_node = list(parentless)[0]
tree.is_rooted = True
return tree
def rdf2dendropyTree(filepath):
from rdflib.graph import Graph
from dendropy import Node, Tree, Edge, TaxonSet, Taxon
graph = Graph()
graph.parse(filepath)
nd_dict = {}
has_parent_predicate = OBO_PREFIX + HAS_PARENT_PREDICATE
if _DEBUGGING:
out = open("parse_rdf.txt", "w")
taxon_set = TaxonSet()
OBO = Namespace(u"http://purl.obolibrary.org/obo/")
parentless = set()
for s, p, o in graph.triples((None, OBO[HAS_PARENT_PREDICATE], None)):
parent = nd_dict.get(id(o))
if parent is None:
# print 'Parent o.value = ', o.value(rdflib.RDF.nodeID)
raw_o = o
o = rdflib.resource.Resource(graph, o)
o_tu = o.value(OBO[REPRESENTS_TU_PREDICATE])
if o_tu:
o_label = o_tu.value(rdflib.RDFS.label)
t = Taxon(label=o_label)
taxon_set.append(t)
parent = Node(taxon=t)
else:
parent = Node()
nd_dict[id(raw_o)] = parent
parentless.add(parent)
child = nd_dict.get(id(s))
if child is None:
raw_s = s
s = rdflib.resource.Resource(graph, s)
s_tu = s.value(OBO[REPRESENTS_TU_PREDICATE])
if s_tu:
s_label = s_tu.value(rdflib.RDFS.label)
t = Taxon(label=s_label)
taxon_set.append(t)
child = Node(taxon=t)
else:
child = Node()
nd_dict[id(raw_s)] = child
else:
if child in parentless:
parentless.remove(child)
parent.add_child(child)
if _DEBUGGING:
out.write("%s %s %s\n" % (str(s), p, o))
out.write("%s\n" % (str(parentless)))
if _DEBUGGING:
out.close()
if len(parentless) != 1:
message = (
"Expecting to find exactly Node (an object of a has_Parent triple) in the graph without a parent. Found %d"
% len(parentless)
)
CUTOFF_FOR_LISTING_PARENTLESS_NODES = 1 + len(
parentless
) # we might want to put in a magic number here to suppress really long output
if len(parentless) > 0 and len(parentless) < CUTOFF_FOR_LISTING_PARENTLESS_NODES:
message += ":\n "
for i in parentless:
if i.label:
message += "\n " + i.label
else:
message += "\n <unlabeled>" + str(id(i))
raise ValueError(message)
else:
sys.exit("no parentless")
return None
tree = Tree(taxon_set=taxon_set)
tree.seed_node = list(parentless)[0]
tree.is_rooted = True
return tree
