Example #1
0
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
Example #3
0
    #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.
Example #4
0
    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)