def parse_dot(args, files):
if len(files) == 0:
return None
content = files[0].read()
g = pydotplus.parse_dot_data(content)
nodes = [_to_node(n) for n in g.get_nodes()]
edges = [_to_edge(e) for e in g.get_edges()]
return dict(name=_resolve_name(args, files[0]), nodes=nodes, edges=edges)
def parse_dot(args, files):
if len(files) == 0:
return None
content = files[0].read()
g = pydotplus.parse_dot_data(content)
nodes = [_to_node(n) for n in g.get_nodes()]
edges = [_to_edge(e) for e in g.get_edges()]
return dict(name=_resolve_name(args, files[0]), nodes=nodes, edges=edges)
def import_file(file):
importer.delete_all()
# fix dot file: don't like =\n -> replace by =""\n
with open(file, 'r') as f:
content = f.read()
g = pydotplus.parse_dot_data(content)
for n in g.get_nodes():
id = clean(n.get_name())
attrs = n.get_attributes()
targetclass = clean(attrs['targetclass'])
geneids = clean(attrs['geneids'])
color = clean(attrs['color'])
label = clean(attrs['label'])
labels = ['_Network_Node']
if len(targetclass) > 0:
labels.append(targetclass.replace(' ', '_'))
importer.add_node(labels, id, dict(color=color, name=label, geneids=geneids))
importer.done_nodes()
for link in g.get_edges():
source = clean(link.get_source())
target = clean(link.get_destination())
attrs = n.get_attributes()
distance = float(attrs.get('distance', 0))
weight = float(attrs.get('weight', 0))
importer.add_edge('LinkTo', source, target, dict(_isNetworkEdge=True, distance=distance, weight=weight))
# add reverse edge
if args.undirected:
importer.add_edge('LinkTo', target, source, dict(_isNetworkEdge=True, distance=distance, weight=weight))
if args.sets:
# create set relationship by targetclass
for k, g in itertools.groupby(sorted(g.get_nodes(), key=lambda x: x.get_label('targetclass')),
lambda x: x.get_label('targetclass')):
importer.add_node(['_Set_Node'], k, {'name': k})
groups = list(g)
for node in groups:
id = clean(node.get_name())
importer.add_edge('ConsistsOf', k, id, dict(), '_Set_Node')
# for node2 in groups:
# id2 = node2.get_name()
# if id != id2:
# importer.add_edge('Edge', id, id2, dict(_isSetEdge=True,targetclass=k))
importer.finish()
def import_file(file):
importer.delete_all()
#fix dot file: don't like =\n -> replace by =""\n
with open(file,'r') as f:
content = f.read()
g = pydotplus.parse_dot_data(content)
for n in g.get_nodes():
id = clean(n.get_name())
attrs = n.get_attributes()
targetclass = clean(attrs['targetclass'])
geneids = clean(attrs['geneids'])
color = clean(attrs['color'])
label = clean(attrs['label'])
labels = ['_Network_Node']
if len(targetclass) > 0:
labels.append(targetclass.replace(' ','_'))
importer.add_node(labels, id, dict(color=color,name=label,geneids=geneids))
importer.done_nodes()
for link in g.get_edges():
source = clean(link.get_source())
target = clean(link.get_destination())
attrs = n.get_attributes()
distance = float(attrs.get('distance',0))
weight = float(attrs.get('weight',0))
importer.add_edge('LinkTo', source, target, dict(_isNetworkEdge=True,distance=distance,weight=weight))
#add reverse edge
if args.undirected:
importer.add_edge('LinkTo', target, source, dict(_isNetworkEdge=True,distance=distance,weight=weight))
if args.sets:
#create set relationship by targetclass
for k, g in itertools.groupby(sorted(g.get_nodes(),key=lambda x : x.get_label('targetclass')), lambda x : x.get_label('targetclass')):
importer.add_node(['_Set_Node'], k, {'name': k})
groups = list(g)
for node in groups:
id = clean(node.get_name())
importer.add_edge('ConsistsOf', k, id, dict(),'_Set_Node')
#for node2 in groups:
# id2 = node2.get_name()
# if id != id2:
# importer.add_edge('Edge', id, id2, dict(_isSetEdge=True,targetclass=k))
importer.finish()
