The arguments used in the `/main/src/create_context_specific_model.py` file
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This script creates a context specific model

The default arguments for this script are as follows:

cmd = ' '.join(['python3', 'create_context_specific_model.py', 
                  '--context-name', '"{}"'.format(key),
                  '--reference-model-file', '"{}"'.format(general_model_filepath), 
                  '--active-genes-filepath', '"{}"'.format(active_genes_filepath),
                  '--objective', '"{}"'.format(objective),
                  '--boundary-reactions-filepath', '"{}"'.format(boundary_rxns_filepath),
                  #'--exclude-reactions-filepath', '"{}"'.format(exclude_rxns_file),
                  '--force-reactions-filepath', '"{}"'.format(force_rxns_filepath),
                  '--algorithm', '"{}"'.format(recon_algorithm),
                  '--low-threshold', '"{}"'.format(low_thresh),
                  '--high-threshold', '"{}"'.format(high_thresh),
                  '--solver', '"{}"'.format(solver),
                  '--output-filetypes', '"{}"'.format(output_filetypes)])

!{cmd}

Arguments

Argument Required? Default Value Description
--context-name Yes None Name of context or context used consistent with outputs of merge_xomics.py
--reference-model-filepath Yes None Name of Genome-scale metabolic model to seed the context model to.
For example, the GeneralModelUpdatedV2.mat, is a modified Recon3D model.
We also provide iMM_mouse for mouse. OT can be .mat, .xml, or .json.
--active-genes-filepath Yes None Path to logical table of active genes output from merge_xomics.py called ActiveGenes_contextName_Merged.csv.
Should be in the corresponding context/context folder inside /main/data/results/contextName/.
The json file output from the function using the context of interest as the key can be used here.
--objective No "biomass_reaction" Reaction ID of the objective function in the model. Generally a biomass function.
--boundary-reactions-filepath No None Path to file contains the exchange (media), sink, and demand reactions
     which the model should use to fulfill the reactions governed by transcriptomic and proteomics data inputs.
It must be a csv or xlsx with three columns: Rxn, Lowerbound, Upperbound.
If not specified, COMO will allow ALL BOUNDARY REACTIONS THAT ARE OPEN IN THE REFERENCE MODEL TO BE USED!
--exclude-reactions-filepath No None Filepath to file that contains reactions which will be removed from active reactions the model to use when seeding,
     even if considered active from transcriptomic and proteomics data inputs.
It must be a csv or xlsx with one column of reaction IDs consistent with the reference model
--force-reactions-filepath No None Filepath to file that contains reactions which will be added to active reactions for the model to use when seeding
     (unless it causes the model to be unsolvable),
     regardless of results of transcriptomic and proteomics data inputs.
It must be a csv or xlsx with one column of reaction IDs consistent with the reference model
--algorithm No "GIMME" Algorithm used to seed context specific model to the Genome-scale model.
Can be either GIMME, FASTCORE, iMAT, or tINIT.
--low-threshold No -5 Low to mid bin cutoff for iMAT solution
--high-threshold No -3 Mid to high bin cutoff for iMAT solution
--solver No "glpk" Solver used to seed model and attempt to solve objective.
Default is GLPK. Also takes GUROBI but you must mount a container license to the Docker to use.
An academic license can be obtained for free.
See the README on the Github or Dockerhub for information on mounting this license.
--output-filetypes "mat" Filetypes to save seeded model type.
Can be either a string with one filetype such as ‘xml’ or multiple in the format “[‘extension1’, ‘extension2’, … etc]”.
If you want to output in all 3 accepted formats, would be: “[‘mat’, ‘xml’, ‘json’]”
NOTE: Outer quotes are required to be interpreted by cmd. This a string, not a python list