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 --helpextract_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 --helpcpd_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.