def cntxtAnalysis(path, outpath, level=.8, cutoff=.8):
dataPaths = tuple([file.rstrip() for file in os.popen("ls "+path+"*.tsv")])
print dataPaths
outputFile = open(outpath, 'w').close()
outputFile = open(outpath, 'a')
model_path = '../../work/HumanFBA/validHumanFBAmodel.lp'
stdFBAfluxDist = metabolism.Metabolism(util.ImportCplex(model_path)).fba()
print "Standard FBA fluxDist: ", stdFBAfluxDist.getActiveFluxDist()
print 2*"\n"
reactionSets = list()
lp = util.ImportCplex(model_path)
cntxtFBA = ContextFBA(lp, rmfID='R("R_Obj")', level=level)
for path in dataPaths:
(cntxtFluxDist, incon) = cntxtFBA.contextFBA(loadReactionData(path), \
cutoff=cutoff)
print "results for: ", path
print "ContextFBA fluxDist: ", cntxtFluxDist.getActiveFluxDist()
print "Inconsistency Score: ", incon
print 2*'\n'
stuff = "\t".join(cntxtFluxDist.getActiveReactions())
outputFile.write(path + '\t'+ str(incon) + "\t" + stuff + "\n")
outputFile.close()
def checkInconsistencyForAllReactions(data, level=.8, cutoff=.8):
model_path = '../../work/HumanFBA/validHumanFBAmodel.lp'
lp = util.ImportCplex(model_path)
reacs = metabolism.Metabolism(lp).getReactions()
print reacs
print 2*"\n"
testReacs =reacs[0:5]
testReacs.append('R("R_Obj")')
for r in testReacs:
print r
lp = util.ImportCplex(model_path)
cntxtFBA = ContextFBA(lp, rmfID=r, level=.8)
if cntxtFBA.getObjVal() > 0:
for path in data:
print path
(cntxtFluxDist, incon) = cntxtFBA.contextFBA(loadReactionData(path), \
cutoff=cutoff)
print "results for: ", path
print "ContextFBA fluxDist: ", cntxtFluxDist.getActiveFluxDist()
print "Inconsistency Score: ", incon
print 2*'\n'
stuff = "\t".join(cntxtFluxDist.getActiveReactions())
else:
print "no rmfID flux!"
