return dist if __name__ == "__main__": #If the module is executed as a program, run a test. from cobra.io.sbml import read_sbml_model cobramodel = read_sbml_model('../SBML/SCHUETZR.xml') import loadData as load fluxvalues = load.ExpFluxesfromXML('expdata.xml', 'Perrenoud', 'Batch', 'aerobe') rmap = load.ReactionMapfromXML('reactionmaps.xml', 'Perrenoud', 'SCHUETZR') optreq = 1.0 import QPmindist as qp gurobimodel = qp.QPmindist(cobramodel, fluxvalues, rmap, optreq) QPsolutiondict = qp.getgurobisolutiondict(gurobimodel) import extractflux2 as extract extractfluxdict = extract.extractfluxdict(QPsolutiondict, rmap) dictdist = compdistdict(extractfluxdict) print('dist:', dictdist) simple1 = {"A": 1, "B": 2, "C": 3} simple2 = {"A": 1, "B": 2, "C": 4} simpledist = compdistdict(simple1, expdata=simple2)
#print exp_errordict[key] #print uncertfrac_dict[key] #print uncertfrac_dict print "%s %15.1f %15.1f %15.1f %15.1f %15.1f" % (key,float(fluxdict[key]),float(expfluxdict[key]),float(diff_dict[key]),float(exp_errordict[key]),float(uncertfrac_dict[key])) return diff_dict #TEST CODE START: if __name__ == "__main__": from cobra.io.sbml import create_cobra_model_from_sbml_file SCHUETZR = create_cobra_model_from_sbml_file('../SBML/SCHUETZR.xml') SCHUETZR.optimize(solver='gurobi') FBAresult = SCHUETZR.solution.x_dict import extractflux2 rmap = load.ReactionMapfromXML('reactionmaps.xml','Perrenoud','SCHUETZR') expfluxes = load.ExpFluxesfromXML('expdata.xml','Perrenoud','Batch','aerobe') fluxresult = extractflux2.extractfluxdict(FBAresult,rmap) t = fluxreport(fluxresult) #TEST CODE END.
if __name__ == "__main__": #If the module is executed as a program, run a test. from cobra.io.sbml import create_cobra_model_from_sbml_file cobramodel = create_cobra_model_from_sbml_file('../SBML/SCHUETZR.xml') import loadData as load fluxvalues = load.ExpFluxesfromXML('expdata.xml','Perrenoud','Batch','aerobe') rmap = load.ReactionMapfromXML('reactionmaps.xml','Perrenoud','SCHUETZR') optreq = 1.0 import QPmindist as qp gurobimodel = qp.QPmindist(cobramodel,fluxvalues,rmap,optreq) QPsolutiondict = qp.getgurobisolutiondict(gurobimodel) import extractflux2 as extract extractfluxdict = extract.extractfluxdict(QPsolutiondict,rmap) dictdist = compdistdict(extractfluxdict) print('dist:',dictdist) simple1 = {"A":1,"B":2,"C":3} simple2 = {"A":1,"B":2,"C":4} simpledist = compdistdict(simple1, expdata = simple2)