def main(rdir, eqnfn, molfn, outfn):
print ("Loading molecule names... ")
# dictionary where keys are mol ids (C00001) and
# items are names from second column of kegg-compounds file
mol2name = common.parse_molecule_names(molfn)
print "Loading reconstruction: %s/%s" % (rdir, common.NETWORK_REACTION_FILE)
f = open("%s/%s" % (rdir, common.NETWORK_REACTION_FILE))
bf = open(eqnfn)
reco = common.read_reconstruction(f)
eqns = read_balanced_reactions(bf)
print "%d reactions" % (len(reco))
write_matrix(reco, eqns, mol2name, outfn)
def main(rdir, eqnfn, molfn, taxon, modelid, modelname, species, outfn, sbmlversion, boundsfile, rxnnamefile=None, pathwayfile=None):
print("Loading molecule names... ")
# dictionary where keys are mol ids (C00001) and
# items are names from second column of kegg-compounds file
mol2name = common.parse_molecule_names(molfn)
print "Loading reconstruction: %s/%s" % (rdir, common.NETWORK_REACTION_FILE)
f = open("%s/%s" % (rdir, common.NETWORK_REACTION_FILE))
bf = open(eqnfn)
reco = common.read_reconstruction(f)
eqns = read_balanced_reactions(bf)
if pathwayfile is not None:
fp = open(pathwayfile)
pathways={};
pathwayasnames={};
for s in fp:
#print s
sisalto = s.strip().split("\t")
#print len(sisalto)
if len(sisalto)>1:
pathways[sisalto[0]]=sisalto[1]
if len(sisalto)>2:
pathwayasnames[sisalto[0]]=sisalto[2]
if len(pathwayasnames) == 0:
pathwayasnames = None
else:
pathways = None
if rxnnamefile is not None:
fp = open(rxnnamefile)
rxnnames={};
for s in fp:
sisalto = s.strip().split("\t")
if len(sisalto)>1:
rxnnames[sisalto[0]]=sisalto[1]
#print ("rxnnames[%s] = %s" % (sisalto[0],sisalto[1]))
else:
rxnnames = None
bounds={};
if boundsfile is not None:
fp = open(boundsfile)
for s in fp:
sisalto = s.strip().split("\t")
if len(sisalto)>1:
bounds[sisalto[0].strip()]=sisalto[3] +","+ sisalto[4]
# print "%d reactions" % (len(reco))
sbml = convert_to_SBML(reco, eqns, mol2name, taxon, modelid, modelname, species, sbmlversion, bounds, rxnnames, pathways, pathwayasnames)
libsbml.writeSBMLToFile(sbml, outfn)