Update code to use networkx objects (incomplete)#1
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willu47 wants to merge 5 commits intoscripts_developmentfrom
Open
Update code to use networkx objects (incomplete)#1willu47 wants to merge 5 commits intoscripts_developmentfrom
willu47 wants to merge 5 commits intoscripts_developmentfrom
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willu47
commented
Oct 9, 2020
| # Write out the graph to a new file | ||
| nx.write_graphml(RES, 'glucoseRES_modified,noDUMMY,v4_202010.graphml') | ||
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| # %% |
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This line here allows you to run the file from the command line and pass in a variable e.g.
python GLUCOSE_VisualizingRES.py glucoseRES_modified,noDUMMY,v2_202010.graphmlI'd recommend using shorter file names (because it's easier to type shorter names).
…Frame with networkx data structure
willu47
commented
Oct 12, 2020
willu47
commented
Oct 12, 2020
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Hi @AgnesBelt - I've had a look at your code and simplified it. I removed use of the pandas DataFrames as it was making the code very complicated. Everything you need is provided by networkx, but understanding the data structure of the networkx Graph isn't that easy.
I believe It is now working, and adds labels from the list of input_edges to the relevant nodes. I've left the output and emission edges an exercise for you to complete!
I'll add some comments below in the text, and you can ask questions below too.
I suggest you pull down this branch and then push your commits to the same branch. Then we can track progress and I can help if needed here too.