def __init__(self, amp, cdir):
"""amp AtomMappingParser"""
self.amp = amp
self.separate_mols = common.read_set(open("%s/%s" % (cdir, DRAW_SEPARATELY_LIST)))
self.sep_id = 1
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 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))