def compdistcomplete(rawfluxvector,model, debug = False):
if debug:
print('compdistcomplete: Calculating distance...')
import loadData as load
import extractflux
#print 'Loading experimental data...'
expdata = load.ExpFluxesfromXML('expdata.xml','Perrenoud','Batch','aerobe')
#print 'Loading reaction map...'
rmap = load.ReactionMapfromXML('reactionmaps.xml','Perrenoud','SCHUETZR')
tup = zip([reaction.id for reaction in model.reactions],rawfluxvector,) #
rawfluxdict = {reactionid:fluxvalue for reactionid,fluxvalue in tup}
extractfluxdict = extractflux.extractfluxdict(rawfluxdict,rmap)
fluxvector = []
fluxvalues = []
for key in extractfluxdict:
if (key in expdata):
fluxvector.append(extractfluxdict[key])
fluxvalues.append(float(expdata[key]))
dist = np.linalg.norm(np.array(fluxvector)-np.array(fluxvalues))
return dist
cobramodel = create_cobra_model_from_sbml_file('../SBML/SCHUETZR.xml')
import loadData as load
rmap = load.ReactionMapfromXML('reactionmaps.xml','Perrenoud','SCHUETZR')
optreq = 0.0
fluxvalues = load.ExpFluxesfromXML('expdata.xml','Perrenoud','Batch','aerobe')
gurobimodel = QPmindist(cobramodel,fluxvalues,rmap,optreq)
QPsolutionvector = getgurobisolutionvector(gurobimodel)
QPsolutiondict = getgurobisolutiondict(gurobimodel)
QPFBAobjval = computeFBAobjval(QPsolutionvector,cobramodel)
import extractflux
extractfluxdict = extractflux.extractfluxdict(QPsolutiondict,rmap)
import fluxreport
#fluxreport.fluxreport(extractedfluxes,fluxvalarray)
import compdist
dist = compdist.compdistdict(extractfluxdict)
#print 'Optimality requirement:',optreq
print 'Optreq = 0:'
print 'compdist distance:',dist
#print 'gurobimomdel gurobi objective value:',gurobimodel.ObjVal
import math
#print 'square root of gurobi objective value:',math.sqrt(gurobimodel.ObjVal)
print "QP solution FBA objective value:",QPFBAobjval
#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]))
#Commenting out above line for the moment, as not sure how the Pythn 3 syntax for this is.
return diff_dict
#TEST CODE START:
if __name__ == "__main__":
from cobra.io.sbml import read_sbml_model
SCHUETZR = read_sbml_model('../SBML/SCHUETZR.xml')
solution = SCHUETZR.optimize()
#FBAresult = solution.x_dict #x_dict is deprecated. Use "fluxes" instead.
FBAresult = solution.fluxes
import extractflux
rmap = load.ReactionMapfromXML('reactionmaps.xml', 'Perrenoud', 'SCHUETZR')
expfluxes = load.ExpFluxesfromXML('expdata.xml', 'Perrenoud', 'Batch',
'aerobe')
fluxresult = extractflux.extractfluxdict(FBAresult, rmap)
t = fluxreport(fluxresult)
#TEST CODE END.
import loadData as load
rmap = load.ReactionMapfromXML('reactionmaps.xml', 'Perrenoud', 'SCHUETZR')
optreq = 0.0
fluxvalues = load.ExpFluxesfromXML('expdata.xml', 'Perrenoud', 'Batch',
'aerobe')
gurobimodel = QPmindist(cobramodel, fluxvalues, rmap, optreq)
QPsolutionvector = getgurobisolutionvector(gurobimodel)
QPsolutiondict = getgurobisolutiondict(gurobimodel)
QPFBAobjval = computeFBAobjval(QPsolutionvector, cobramodel)
import extractflux
extractfluxdict = extractflux.extractfluxdict(QPsolutiondict, rmap)
import fluxreport
#fluxreport.fluxreport(extractedfluxes,fluxvalarray)
import compdist
dist = compdist.compdistdict(extractfluxdict)
#print 'Optimality requirement:',optreq
print('Optreq = 0:')
print('compdist distance:', dist)
#print 'gurobimomdel gurobi objective value:',gurobimodel.ObjVal
import math
#print 'square root of gurobi objective value:',math.sqrt(gurobimodel.ObjVal)
print("QP solution FBA objective value:", QPFBAobjval)