Adding edge attributes in networkx

Question

I'm trying to add edge labels to my edges in networkx. I will use nx.write_dot() to convert it into a dot file. How can I do this? When I do this: G.add_edge("ATC", "TCG", label = "ATCG"), nx.write_dot() throws an error. I like networkx, but if it can't label edges then I think I'll have to use another library.

Specifically, I get this error:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/local/lib/python3.3/site-packages/networkx/drawing/nx_agraph.py", line 180, in write_dot
    A.clear()
  File "/usr/local/lib/python3.3/site-packages/pygraphviz/agraph.py", line 907, in clear
    self.edge_attr.clear()
  File "/usr/local/Cellar/python3/3.3.3/Frameworks/Python.framework/Versions/3.3/lib/python3.3/collections/abc.py", line 553, in clear
    self.popitem()
  File "/usr/local/Cellar/python3/3.3.3/Frameworks/Python.framework/Versions/3.3/lib/python3.3/collections/abc.py", line 542, in popitem
    key = next(iter(self))
  File "/usr/local/lib/python3.3/site-packages/pygraphviz/agraph.py", line 1692, in __iter__
    for (k,v) in self.iteritems():
  File "/usr/local/lib/python3.3/site-packages/pygraphviz/agraph.py", line 1700, in iteritems
    yield (gv.agattrname(ah).decode(self.encoding),
AttributeError: 'str' object has no attribute 'decode'

Answer 1

Should work something like this:

In [1]: import networkx as nx

In [2]: G = nx.Graph()

In [3]: G.add_edge(1,2,label='one-two')

In [4]: import sys

In [5]: nx.write_dot(G,sys.stdout)
strict graph  {
    1 -- 2   [label="one-two"];
}