def compdist(fluxvector,
expdata=None,
options=None,
sense=None,
extract=True,
rmap='Default'):
rmap = load.ReactionMapfromXML('reactionmaps.xml', 'Perrenoud', 'SCHUETZR')
if extract:
fluxvector = extractflux.extractfluxvector(fluxvector, rmap)
if expdata == None:
expdata = load.ExpFluxesfromXML('expdata.xml',
'Perrenoud',
'Batch',
'aerobe',
vector=True)
dist = np.linalg.norm(np.array(fluxvector) - np.array(expdata))
return dist
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
experimental_r_id = linkdict['exprxns'][0]['rxid']
token_id = 't_{exprxnid}'.format(exprxnid = experimental_r_id)
new_token_reaction = Reaction(token_id)
new_token_reaction.name = 'Token exchange reaction for experimental reaction {exprxnid}'.format(exprxnid = experimental_r_id)
new_token_reaction.lower_bound = -1000
new_token_reaction.upper_bound = 1000
new_token_metabolite = Metabolite(token_id,name = 'Token metabolite for experimental reaction {exprxnid}'.format(exprxnid = experimental_r_id),compartment='c')
new_token_reaction.add_metabolites({new_token_metabolite: -1.0})
model.add_reactions(new_token_reaction)
for dictionary in linkdict['modrxns']:
modelreaction = model.reactions.get_by_id(dictionary['rxid'])
modelreaction.add_metabolites({new_token_metabolite: float(dictionary['coef'])})
return model
if __name__ == "__main__":
from cobra.io.sbml import create_cobra_model_from_sbml_file
from cobra.io.sbml import write_cobra_model_to_sbml_file
import loadData as load
notokenmodel = create_cobra_model_from_sbml_file('../SBML/SCHUETZR_notokens.xml')
notokenmap = load.ReactionMapfromXML('reactionmaps_notokens.xml','Perrenoud','SCHUETZR')
tokenmodel = createTokens(notokenmodel,notokenmap)
sbml_out_file = 'SCHUETZR_withtokens.xml'
sbml_level = 2
sbml_version = 1
write_cobra_model_to_sbml_file(tokenmodel, sbml_out_file, sbml_level,sbml_version, print_time=False)