feat: netmix2 #225
feat: netmix2 #225
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| @@ -24,7 +24,7 @@ container_registry: | |||
| base_url: docker.io | |||
| # The owner or project of the registry | |||
| # For example, "reedcompbio" if the image is available as docker.io/reedcompbio/allpairs | |||
| owner: reedcompbio | |||
| owner: pubtristanf | |||
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This will go once I undraft this PR.
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please update the file to have include: true for all that were turned to false
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Hi! Apologies for the late response on these reviews - this PR is a draft PR, so I didn't mean for anyone to do a deep review of its contents 😅
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It's okay, I'm going through each PR in waiting.
| scores_file, | ||
| '-o', mapped_out_prefix + '/v-output.txt'] | ||
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| # Add optional arguments |
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These parameters are not currently in the example config.yaml file. Please add them as parameters a user can set.
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Is there a goal to allow for the other families other than the propagation family?
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Not at the moment.
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| @staticmethod | ||
| def run(network=None, scores=None, output_file=None, delta=None, num_edges=None, density=None, | ||
| time_limit=None, |
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Should we preset a time_limit?
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I wasn't quite sure how to handle that, as time_limit feels like another option that should really be global to algorithms.
| output_vertices.rename(output_file) | ||
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| @staticmethod | ||
| def parse_output(raw_pathway_file, standardized_pathway_file): |
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Netmix2 will not work with the ML post processing and possibly some of the other post processing. I'm not sure how to fix this at the moment, but this is something that will need to be considered.
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Please add the expected-pathway file and input raw-pathway file
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Please add the expected input file
| required_inputs = ['network', 'scores'] | ||
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| @staticmethod | ||
| def generate_inputs(data: Dataset, filename_map): |
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For directionality and edges, I just wanted to confirm that NetMix2 deals with only undirected inputs and can handle duplicate edges?
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Unsure, I've only tested it on undirected inputs so far.
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Netmix itself could either interpret the network as fully directed, fully undirected, or mixed. From what I can tell it only deals with undirected graphs based on the code. It's not based on the universal input SPRAS/user is giving.
test/NetMix2/test_nm2.py
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Please add test cases that includes the required parameters only, required + all optional parameters, missing any required parameters, and singularity test case.
WIP - need to actually handle gurobi from https://github.com/raphael-group/netmix2. Everything else is laid out.
Closes #157.