Closed pax6pax6 closed 4 years ago
I am not immediately sure what the problem is, but two possibilities:
Your networkx version might be old, try doing
pip install -U networkx
(in a way that works in your Anaconda environment)
There is some issue with the input file that GeneWalk is loading. Check if your ~/genewalk/resources/PathwayCommons11.All.hgnc.sif
file is around 57 MB in size, if not, delete it, to have it be re-downloaded.
Updating networkx solved the problem! It seems to be running now. Should've thought to double check the dependencies. Thanks a lot for your help!
Is there any additional inputs required for running GeneWalk on a list of human gene IDs? I am running the following command, which has about 80 gene names from a DE experiment.
genewalk --project test --genes /results.txt --id_type hgnc_symbol
Which returned this:
INFO: [2019-09-11 12:01:29] genewalk.nx_mg_assembler - Adding gene edges from Pathway Commons to graph. Traceback (most recent call last): File "/anaconda3/lib/python3.6/site-packages/networkx/convert.py", line 46, in _prep_create_using create_using.clear() TypeError: clear() missing 1 required positional argument: 'self'
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/anaconda3/bin/genewalk", line 11, in
sys.exit(main())
File "/anaconda3/lib/python3.6/site-packages/genewalk/cli.py", line 151, in main
resource_manager=rm)
File "/anaconda3/lib/python3.6/site-packages/genewalk/nx_mg_assembler.py", line 38, in load_network
mg = PcNxMgAssembler(genes, resource_manager=resource_manager)
File "/anaconda3/lib/python3.6/site-packages/genewalk/nx_mg_assembler.py", line 196, in init
self.add_pc_edges()
File "/anaconda3/lib/python3.6/site-packages/genewalk/nx_mg_assembler.py", line 214, in add_pc_edges
create_using=nx.MultiGraph)
File "/anaconda3/lib/python3.6/site-packages/networkx/convert_matrix.py", line 313, in from_pandas_edgelist
g = _prep_create_using(create_using)
File "/anaconda3/lib/python3.6/site-packages/networkx/convert.py", line 48, in _prep_create_using
raise TypeError("Input graph is not a networkx graph type")
Any insight?