PyGNA
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Entering edit mode
7 weeks ago

I ran a functional enrichment analysis using g:Profiler and now want to perform geneset network analysis using PyGNA.

!pygna build-rwr-diffusion ../input/meth-gprofiler/meth_gProfiler.gem.txt --output-file meth_interactome_RWR.hdf5

Traceback:

Traceback (most recent call last):
  File "/opt/conda/bin/pygna", line 11, in <module>
    sys.exit(main())
  File "/opt/conda/lib/python3.7/site-packages/pygna/cli.py", line 53, in main
    bm.generate_sbm2_network,
  File "/opt/conda/lib/python3.7/site-packages/argh/dispatching.py", line 328, in dispatch_commands
    dispatch(parser, *args, **kwargs)
  File "/opt/conda/lib/python3.7/site-packages/argh/dispatching.py", line 174, in dispatch
    for line in lines:
  File "/opt/conda/lib/python3.7/site-packages/argh/dispatching.py", line 277, in _execute_command
    for line in result:
  File "/opt/conda/lib/python3.7/site-packages/argh/dispatching.py", line 260, in _call
    result = function(*positional, **keywords)
  File "/opt/conda/lib/python3.7/site-packages/pygna/command.py", line 727, in build_rwr_diffusion
    network = rc.ReadTsv(network_file).get_network()
  File "/opt/conda/lib/python3.7/site-packages/pygna/reading_class.py", line 53, in __init__
    self.graph = self._convert_to_graph()
  File "/opt/conda/lib/python3.7/site-packages/pygna/reading_class.py", line 82, in _convert_to_graph
    graph.remove_edges_from(graph.selfloop_edges())
AttributeError: 'Graph' object has no attribute 'selfloop_edges'

Did I feed the wrong input into PyGNA? What type of input should I use?

PyGNA network analysis geneset • 116 views
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