generate_network.py error

[agcmartins]

Hi,
I'm using the follow command but it didn't working

:$ /home/user/programs/kinfin/scripts/generate_network.py -m -m kinfin_results/TAXON/TAXON.cluster_summary.txt -c config.txt

[+] Parsing SpeciesClassification file: config.simple.txt ...
[+] Parsing kinfin_results/TAXON/TAXON.cluster_summary.txt ...
[+] Max edge weight is 26312, ...
[+] Building graphs
Traceback (most recent call last):
File "/home/user/programs/kinfin/scripts/generate_network.py", line 189, in
construct_graphs(weighted_edges, proteomeObj_by_proteome_id, attributes)
File "/home/user/programs/kinfin/scripts/generate_network.py", line 111, in construct_graphs
G.add_node(proteomeObj.proteome_id, {k :v for k, v in proteomeObj.level_by_attribute.items()})
TypeError: add_node() takes exactly 2 arguments (3 ###given)

[clydeandforth]

Hi André,

I had the same problem with this script. It requires an older version of the python networkx module.

You can check what verison of the module you have:
pip freeze | grep networkx
networkx==2.2

I know it works with networkx 1.11 so I installed that:
pip install --force-reinstall networkx==1.11

and then ran the script:

generate_network.py -c config_VFDB.txt -m TAXON/TAXON.cluster_summary.txt
[+] Parsing SpeciesClassification file: config_VFDB.txt ...
[+] Parsing JD_kinfin_Oct_revised.kinfin_results/TAXON/TAXON.cluster_summary.txt ...
[+] Max edge weight is 3423, ...
[+] Building graphs
Name: Graph
Type: Graph
Number of nodes: 29
Number of edges: 406
Average degree: 28.0000
[+] Saving network graph.graphml
[+] Saving network graph.gexf

Cheers,

James

[Yixiangzhang1996]

Hi,
I'm using the follow command but it didn't working
(python27) [zyx@node01 TAXON]$ python ~/my_kinfin/kinfin-1.0.3/scripts/generate_network.py -m TAXON.cluster_summary.txt -c config.txt [+] Parsing SpeciesClassification file: config.txt ... [+] Parsing TAXON.cluster_summary.txt ... [+] Max edge weight is 9918, ... [+] Building graphs Traceback (most recent call last): File "/home1/zyx/my_kinfin/kinfin-1.0.3/scripts/generate_network.py", line 190, in <module> construct_graphs(weighted_edges, proteomeObj_by_proteome_id, attributes) File "/home1/zyx/my_kinfin/kinfin-1.0.3/scripts/generate_network.py", line 111, in construct_graphs G.add_node(proteomeObj.proteome_id, {k :v for k, v in proteomeObj.level_by_attribute.items()}) TypeError: add_node() takes exactly 2 arguments (3 given)