This code is useful for obtain enzyme-enzyme and metabolite-metabolite network for HMR and Recon. Is useful to print the fluxes obtained by FBA.
I use python language to write this scripts because I used other language but it was very delayed.
You can use different atributtes of the nodes and edges. To visualize the network use cytoscape (recommended).
Enzyme-enzyme network: enzyme that produce a metabolite (node) - metabolite produce (edge) - enzyme that use this metabolite (node). Metab-metab network: metabolite as reactive n reaction x (node) - enzyme of reaction x (edge) - metabolite as product in reaction x.
For reconstuction generated from HMRA:
For test this script use the example called "net_HMRA_test.txt".
Input format as txt separated by \tab:
name of rxn rxn formula ec number gene compartment subsystem.
For reconstuction generated from Recon:
For test this script use the example called "net_recon_test.txt".
Input format as txt separated by \tab:
name of rxn rxn formula ec number gene compartment(opt but with a '-' or 0 value) subs.
I used the scripts as follows:
- Net_HMRA.py
- Output_list_metabs.py (optional)
- metab_metab_network.py
- enzyme_enzyme_network.py
Net_Recon.py conatins all the scripts but settled for Recon format.
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