Some tiny scripts involving padmet to hack metabolic networks

subnetwork.py

Inputs:

• an empty padmet data/empty.padmet
• a list of reactions
• a padmet file with the reactions data
• an output SBML file
• option to remove cofactors (defined in the script) from the reactions

python subnetwork.py --help

extract_pathways.py

Inputs:

• an empty padmet data/empty.padmet
• a pathway name
• a padmet file with the reactions data
• an output SBML file

python extract_pathways.py --help

cpd_ontology.py and pwy_ontology.py build a tree with all parent/children relationships used to describe metabolites and metabolic pathways in Metacyc.

get_high_lvl_cpds.py and get_high_lvl_pwys.py use the previous ontology (nw file) to get the high level parents of a list of compounds/pathways. padmet_cpd_to_highlevel_onto.py and padmet_pwys_to_highlevel_onto.py use the previous ontology (nw file) to get the high level parents of all compounds/pathways from a padmet file.

get_family_metabolites.py retrieves the families of given compounds and pathways using families ontology (json file).

analyse_all_mn_cpds.py and analyse_all_mn_pwys.py analyse the pathways or metabolites of directory of metabolic networks and retrieve for each of them the representation of each category of compounds/pathway using a json ontology of Metacyc.

onto_json_to_long_format create tabulated files out of the json ontologies of pathways.