Update summary.py to include parameter combinations #194
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spras/analysis/summary.py
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| # algorithm parameters have format { algo : { hashcode : { parameter combos } } } | ||
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| filepath = nw_name.split("/") | ||
| filename = filepath[1].split("-") |
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Will this work for outputs stored in subfolders within the main output folder?
example output/example/data#-algo-params-hashcode/pathway.txt"
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Can get the list of algorithm-params-hashcode from algorithms_with_params in the Snakefile and then pass it to the function so you don't have to extract it
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For the test cases, we discussed dropping the toy summarization example because it does not have corresponding algorithm-parameter combinations that generated those graphs. We will summarize only the example data and EGFR data that correspond to actual SPRAS runs. |
warning: in the working copy of 'test/analysis/input/example/data0-allpairs-params-BEH6YB2_pathway.txt', LF will be replaced by CRLF the next time Git touches it
spras/analysis/summary.py
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| cur_nw_info.append(params) | ||
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| # Prepare column names | ||
| col_names = ["Name", "Number of nodes", "Number of undirected edges", "Number of connected components"] |
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Should the header be updated to “Number of edges" instead of "Number of undirected edges"?
Even though we’re treating all graphs as undirected (on line 43), directionality doesn’t seem to be considered in any of the statistics being calculated in summary.py at the moment.
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I believe the original intention of this header was to convey that even a directed or mixed graph would be parsed and summarized as an undirected graph here. I can see how that could instead be interpreted as only counting the undirected edges in a mixed graph though. Which do you think is more precise?
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I was looking at the summary file and got confused on why we were only counting the undirected edges (then I looked through the code and realized we weren't doing that). So, I think renaming it to "Number of edges" is more intuitive and putting a comment above line 43 to say that "directed or mixed graph are parsed and summarized as an undirected graph"
| graphspace: | ||
| include: false | ||
| # Create Cytoscape session file with all pathway graphs for each dataset | ||
| cytoscape: |
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the test for cytoscape might be failing because the include is set to false.
test/analysis/test_cytoscape.py
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| @@ -6,17 +6,23 @@ | |||
| import spras.config as config | |||
| from spras.analysis.cytoscape import run_cytoscape | |||
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| config.init_from_file("config/config.yaml") | |||
| config.init_from_file("input/config.yaml") | |||
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if using the config file in the input folder in analysis, make sure to set cytoscape include to true incase
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