mini.reactions.get_by_id(i).lower_bound = mini.reactions.PGI.lower_bound # set names and annotation for g in mini.genes: try: tg = textbook.genes.get_by_id(g.id) except KeyError: continue g.name = tg.name g.annotation = tg.annotation mini.reactions.sort() mini.genes.sort() mini.metabolites.sort() # output to various formats with open("mini.pickle", "wb") as outfile: dump(mini, outfile, protocol=2) save_matlab_model(mini, "mini.mat") save_json_model(mini, "mini.json", pretty=True) write_sbml_model(mini, "mini_fbc2.xml") write_sbml_model(mini, "mini_fbc2.xml.bz2") write_sbml_model(mini, "mini_fbc2.xml.gz") write_sbml2(mini, "mini_fbc1.xml", use_fbc_package=True) write_sbml_model(mini, "mini_cobra.xml", use_fbc_package=False) # fva results fva_result = cobra.flux_analysis.flux_variability_analysis(textbook) clean_result = OrderedDict() for key in sorted(fva_result): clean_result[key] = {k: round(v, 5) for k, v in fva_result[key].items()} with open("textbook_fva.json", "w") as outfile: json_dump(clean_result, outfile)
except KeyError: continue g.name = tg.name g.annotation = tg.annotation mini.reactions.sort() mini.genes.sort() mini.metabolites.sort() # output to various formats with open("mini.pickle", "wb") as outfile: dump(mini, outfile, protocol=2) save_matlab_model(mini, "mini.mat") save_json_model(mini, "mini.json", pretty=True) write_sbml_model(mini, "mini_fbc2.xml") write_sbml_model(mini, "mini_fbc2.xml.bz2") write_sbml_model(mini, "mini_fbc2.xml.gz") write_sbml2(mini, "mini_fbc1.xml", use_fbc_package=True) write_sbml_model(mini, "mini_cobra.xml", use_fbc_package=False) raven = load_matlab_model("raven.mat") with open("raven.pickle", "wb") as outfile: dump(raven, outfile, protocol=2) # fva results fva_result = cobra.flux_analysis.flux_variability_analysis(textbook) clean_result = OrderedDict() for key in sorted(fva_result): clean_result[key] = {k: round(v, 5) for k, v in fva_result[key].items()} with open("textbook_fva.json", "w") as outfile: json_dump(clean_result, outfile) # textbook solution # TODO: this needs a reference solution rather than circular solution checking!