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, outfn):
mol2name = {}
f = open(molfn)
for s in f:
molid, name, name2 = s.strip().split("\t")
mol2name[molid] = name
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):
mol2name = {}
f = open(molfn)
for s in f:
molid, name, name2 = s.strip().split("\t")
mol2name[molid] = name
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))
sbml = convert_to_SBML(reco, eqns, mol2name, taxon, modelid, modelname, species)
libsbml.writeSBMLToFile(sbml, outfn)
def main():
if len(sys.argv) == 3:
ddir = sys.argv[1] # reconstruction result directory
ofn = sys.argv[2] # output
reco = common.read_reconstruction(open("%s/%s" % (ddir, common.NETWORK_REACTION_FILE)))
convert(reco, open(ofn, "w"))
elif len(sys.argv) == 2:
pdir = sys.argv[1] # project dir, reconstruction dirs as subdirs
convert_multiple_dirs(pdir)
else:
print """Usage:
%s reco-dir output
%s project-dir
""" % (sys.argv[0], sys.argv[0])
def main(rdir, eqnfn, molfn, outfn):
mol2name = {}
f = open(molfn)
for s in f:
molid, name, name2 = s.strip().split("\t")
mol2name[molid] = name
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():
if len(sys.argv) == 3:
ddir = sys.argv[1] # reconstruction result directory
ofn = sys.argv[2] # output
reco = common.read_reconstruction(
open("%s/%s" % (ddir, common.NETWORK_REACTION_FILE)))
convert(reco, open(ofn, "w"))
elif len(sys.argv) == 2:
pdir = sys.argv[1] # project dir, reconstruction dirs as subdirs
convert_multiple_dirs(pdir)
else:
print """Usage:
%s reco-dir output
%s project-dir
""" % (sys.argv[0], sys.argv[0])
def main(rdir, eqnfn, molfn, taxon, modelid, modelname, species, outfn):
mol2name = {}
f = open(molfn)
for s in f:
molid, name, name2 = s.strip().split("\t")
mol2name[molid] = name
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))
sbml = convert_to_SBML(reco, eqns, mol2name, taxon, modelid, modelname,
species)
libsbml.writeSBMLToFile(sbml, 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)
def main(inputdir, ecfile):
ec2r, r2ec = common.read_ec_list(open(ecfile))
reactions = common.read_stoichiometry(open(STOICHIOMETRY)).reactions
reco = common.read_reconstruction(open("%s/%s" % (inputdir, common.NETWORK_REACTION_FILE)))
cofactors = common.read_set(open(COFACTORS))
o = open("%s/%s" % (inputdir, common.FILE_EC_GRAPH), "w")
R = set()
for r in reco:
baser = r.split("_")[0].replace("#","_")
#baser = r.split("_")[0]
R.add(baser)
E = {}
for r in R:
if r in reactions:
re = reactions[r]
if r not in E:
E[r] = {}
for m in re.substrates:
if m not in E:
E[m] = {}
E[m][r] = 1
E[r][m] = 1
for m in re.products:
if m not in E:
E[m] = {}
E[r][m] = 1
E[m][r] = 1
ecg = {}
for r in E:
if r not in r2ec:
continue
ec1 = r2ec[r]
for m in E[r]:
if m in E:
for r2 in E[m]:
if r == r2:
continue
if r2 not in r2ec:
continue
ec2 = r2ec[r2]
for e1 in ec1:
if e1 not in ecg:
ecg[e1] = {}
for e2 in ec2:
if e2 not in ecg[e1]:
ecg[e1][e2] = set()
ecg[e1][e2].add(m)
o.write("#Output of \"%s\" on %s\n" % (" ".join(sys.argv), datetime.datetime.now()))
cofs = list(cofactors)
cofs.sort()
o.write("#Cofactors: %s\n" % (",".join(cofs)))
o.write("#EC1 EC2 SharedMetabolites AllCofactors\n")
k1 = ecg.keys()
k1.sort()
for ec1 in k1:
k2 = ecg[ec1].keys()
k2.sort()
for ec2 in k2:
cofactor = 1
for m in ecg[ec1][ec2]:
if m not in cofactors:
cofactor = 0
if cofactor and REMOVE_COFACTORS:
continue
o.write("%s\t%s\t%s\t%s\n" % (ec1, ec2, ",".join(ecg[ec1][ec2]), cofactor))
def convert_dir(ddir):
reco = common.read_reconstruction(open("%s/%s" % (ddir, common.NETWORK_REACTION_FILE)))
convert(reco, open("%s/%s" % (ddir, common.NETWORK_ECLIST_FILE), "w"))
def main(inputdir):
ec2r, r2ec = common.read_ec_list(open(common.FILE_EC_MAP))
reactions = common.read_stoichiometry(open(STOICHIOMETRY)).reactions
reco = common.read_reconstruction(open("%s/%s" % (inputdir, common.NETWORK_REACTION_FILE)))
cofactors = common.read_set(open(COFACTORS))
o = open("%s/%s" % (inputdir, common.FILE_EC_GRAPH), "w")
R = set()
for r in reco:
baser = r.split("_")[0]
R.add(baser)
E = {}
for r in R:
if r in reactions:
re = reactions[r]
if r not in E:
E[r] = {}
for m in re.substrates:
if m not in E:
E[m] = {}
E[m][r] = 1
E[r][m] = 1
for m in re.products:
if m not in E:
E[m] = {}
E[r][m] = 1
E[m][r] = 1
ecg = {}
for r in E:
if r not in r2ec:
continue
ec1 = r2ec[r]
for m in E[r]:
if m in E:
for r2 in E[m]:
if r == r2:
continue
if r2 not in r2ec:
continue
ec2 = r2ec[r2]
for e1 in ec1:
if e1 not in ecg:
ecg[e1] = {}
for e2 in ec2:
if e2 not in ecg[e1]:
ecg[e1][e2] = set()
ecg[e1][e2].add(m)
o.write("#Output of \"%s\" on %s\n" % (" ".join(sys.argv), datetime.datetime.now()))
cofs = list(cofactors)
cofs.sort()
o.write("#Cofactors: %s\n" % (",".join(cofs)))
o.write("#EC1 EC2 SharedMetabolites AllCofactors\n")
k1 = ecg.keys()
k1.sort()
for ec1 in k1:
k2 = ecg[ec1].keys()
k2.sort()
for ec2 in k2:
cofactor = 1
for m in ecg[ec1][ec2]:
if m not in cofactors:
cofactor = 0
if cofactor and REMOVE_COFACTORS:
continue
o.write("%s\t%s\t%s\t%s\n" % (ec1, ec2, ",".join(ecg[ec1][ec2]), cofactor))
def convert_dir(ddir):
reco = common.read_reconstruction(
open("%s/%s" % (ddir, common.NETWORK_REACTION_FILE)))
convert(reco, open("%s/%s" % (ddir, common.NETWORK_ECLIST_FILE), "w"))