problem with 'DiGraph' object has no attribute 'in_degree_iter'

[juliana...@hotmail.com]

Hi everyone

My name is Juliana Eschholz and I have a problem with this: 'DiGraph' object has no attribute 'in_degree_iter'

I use Mix-Master and I need of Networkx working together.... When I ran this command (in Mix Master) :
serv@Serv:~$ /home/serv/MIX-master/bin/Mix.py -a /home/serv/MIX-master/alignments.coords -c /home/serv/MIX-master/contigs.fa -o /home/serv/MIX-master/results -C 300 -A 200
I received this error:

Traceback (most recent call last):
  File "/home/serv/MIX-master/bin/Mix.py", line 958, in <module>
    main()
  File "/home/serv/MIX-master/bin/Mix.py", line 708, in main
    processing(cleaned_alignments, ctg_adr, output_repository, ctg_threshold, aln_threshold, display_dot, display_cytoscape, contigs, contigs_included_in_other)
  File "/home/serv/MIX-master/bin/Mix.py", line 544, in processing
    selected_paths,selected_contigs=lower_duplication(paths,selected_single_contigs)
  File "/home/serv/MIX-master/bin/Mix.py", line 781, in lower_duplication
    for (n,d_in),(n,d_out) in zip(D.in_degree_iter(),D.out_degree_iter()):
AttributeError: 'DiGraph' object has no attribute 'in_degree_iter'


I made tests with Networkx, and I put this command:
serv@Serv:~$ sudo python -c "import networkx as nx; nx.test()"

ERROR: test suite for <class 'test_agraph.TestAGraph'>
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/serv/.local/lib/python2.7/site-packages/nose/suite.py", line 209, in run
    self.setUp()
  File "/home/serv/.local/lib/python2.7/site-packages/nose/suite.py", line 292, in setUp
    self.setupContext(ancestor)
  File "/home/serv/.local/lib/python2.7/site-packages/nose/suite.py", line 315, in setupContext
    try_run(context, names)
  File "/home/serv/.local/lib/python2.7/site-packages/nose/util.py", line 471, in try_run
    return func()
  File "/usr/local/lib/python2.7/dist-packages/networkx-2.0-py2.7.egg/networkx/drawing/tests/test_agraph.py", line 16, in setupClass
    import pygraphviz
  File "/home/serv/.local/lib/python2.7/site-packages/pygraphviz/__init__.py", line 58, in <module>
    from .agraph import AGraph, Node, Edge, Attribute, ItemAttribute, DotError
  File "/home/serv/.local/lib/python2.7/site-packages/pygraphviz/agraph.py", line 26, in <module>
    from . import graphviz as gv
  File "/home/serv/.local/lib/python2.7/site-packages/pygraphviz/graphviz.py", line 293, in <module>
    AGRAPH = _graphviz.AGRAPH
AttributeError: 'module' object has no attribute 'AGRAPH'

----------------------------------------------------------------------
Ran 3172 tests in 94.947s

FAILED (SKIP=3, errors=1)



So, I need a help! I don't know what's happening!

Best Regards

Juliana

[Dan Schult]

It looks like your Mix code works with older versions of NetworkX. Perhaps Mix has already released a new version to work with NetworkX2.0 (or maybe is working on it). You could also try installing a version of networkx before v2.0, like v1.11.

Dan

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