def main():
cdir = sys.argv[1] # program dir (with ec-list.txt)
kdir = sys.argv[2] # kegg dir
ddir = sys.argv[3] # data dir
param_accept = float(sys.argv[4])
param_reject = float(sys.argv[5])
species = None
if len(sys.argv) > 6:
species = sys.argv[6].split(",")
if len(sys.argv) > 7 and sys.argv[7] == "yes":
odir_param_labeled = True
else:
odir_param_labeled = False
if len(sys.argv) > 8 and sys.argv[8] == "yes":
remove_partial = True
else:
remove_partial = False
print "Reading EC list..."
ec2r, r2ec = common.read_ec_list(open("%s/%s" %
(cdir, common.FILE_EC_MAP)))
do_reconstruction(cdir, kdir, ddir, r2ec, ec2r, param_accept, param_reject,
species, odir_param_labeled, remove_partial)
def main():
cdir = sys.argv[1] # program dir (with ec-list.txt)
kdir = sys.argv[2] # kegg dir
ddir = sys.argv[3] # data dir
param_accept = float(sys.argv[4])
param_reject = float(sys.argv[5])
species = None
if len(sys.argv) > 6:
species = sys.argv[6].split(",")
if len(sys.argv) > 7 and sys.argv[7] == "yes":
odir_param_labeled = True
else:
odir_param_labeled = False
if len(sys.argv) > 8 and sys.argv[8] == "yes":
remove_partial = True
else:
remove_partial = False
print "Reading EC list..."
ec2r, r2ec = common.read_ec_list(open("%s/%s" % (cdir, common.FILE_EC_MAP)))
do_reconstruction(cdir, kdir, ddir, r2ec, ec2r, param_accept, param_reject, species, odir_param_labeled, remove_partial)
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(rdir, dir_prefix, ref_model_fn, ofile, remove_partial):
ref_model_f = open(ref_model_fn)
of = open(ofile, "w")
ref_ecs = set()
for s in ref_model_f:
ec = s.strip()
if remove_partial and "-" in ec:
continue
ref_ecs.add(ec)
all_ecs = set()
f = open(common.FILE_EC_MAP)
ec2r, r2ec = common.read_ec_list(f)
all_ecs = set(ec2r.keys())
if remove_partial:
all_ecs = map(lambda x: "-" not in x, all_ecs)
fns = os.listdir(rdir)
results = {}
values = []
for fna in fns:
if fna.startswith(dir_prefix):
sys.stdout.write("Processing %s\n" % (fna))
params = fna[len(dir_prefix):]
if PLOT_PARAM == PARAM_ACCEPT:
param = float(params.split("-")[0]) # accept param
elif PLOT_PARAM == PARAM_REJECT:
param = float(params.split("-")[1]) # reject param
else:
print "Unknown parameter", PLOT_PARAM
assert (0)
#print fna, param
try:
f = open("%s/%s/%s" % (rdir, fna, common.NETWORK_EC_FILE))
#f = open("%s/%s/network.ecs.filtered" % (rdir, fna))
except:
sys.stderr.write("Unable to open %s\n" % (fna))
continue
res_ecs = set()
for s in f:
if s.startswith("#"):
continue
ec = s.strip().split()[0]
if ec == "?":
continue
if remove_partial and "-" in ec:
continue
res_ecs.add(ec)
tp = len(ref_ecs.intersection(res_ecs)) + 1
fp = len(res_ecs.difference(ref_ecs)) + 1
fn = len(ref_ecs.difference(res_ecs)) + 1
tn = len(all_ecs) - tp - fp - fn + 3
try:
tpr = 1.0 * tp / (tp + fn)
fpn = 1.0 * fp / (fp + tn)
prec = 1.0 * tp / (tp + fp)
recall = 1.0 * tp / (tp + fn)
f1 = 2 * prec * recall / (prec + recall)
results[param] = (tp, fp, fn, tn, tpr, fpn, f1)
#values.append((param, tp, fp, fn, tn, tpr, fpn, f1))
#print fpn, tpr
except:
print "Cannot process %s" % (fna)
raise
pfpr = ptpr = 1.0
auc = 0.0
keys = results.keys()
keys.sort()
of.write("#Param TP FP FN TN TPR FPN F1 AUC\n")
for param in keys:
tp, fp, fn, tn, tpr, fpr, f1 = results[param]
auc += (pfpr - fpr) * tpr + (pfpr - fpr) * (ptpr - tpr) / 2
print fpr, tpr, auc, f1
of.write("%.10f\t%d\t%d\t%d\t%d\t%f\t%f\t%s\t%f\n" %
(param, tp, fp, fn, tn, tpr, fpr, f1, auc))
pfpr = fpr
ptpr = tpr
tpr = 0.0
fpr = 0.0
auc += (pfpr - fpr) * tpr + (pfpr - fpr) * (ptpr - tpr) / 2
f1 = 0.0
of.write("NA\tNA\tNA\tNA\tNA\t%f\t%f\t%f\t%f\n" % (tpr, fpr, f1, auc))
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))
#!/usr/bin/env python
import sys
import common
kdir = sys.argv[1] # kegg dir
ofn = sys.argv[2] # output file
o = open(ofn, "w")
ec2r, r2ec = common.read_ec_list(open(common.FILE_EC_MAP))
target_species = sys.argv[3].split(",") # comma-separated list of species or "-" for all
f = open("%s/enzyme" % (kdir))
geneson = 0
ec2gene = {}
for s in f:
if s[0] != " ":
geneson = 0
if geneson == 0:
if s.startswith("ENTRY"):
ec = s.strip().split()[2]
ec2gene[ec] = {}
elif s.startswith("GENES"):
geneson = 1
species = s[12:15]
if target_species == "-" or species in target_species:
ec2gene[ec][species] = set(s[16:].strip().split())
elif s.startswith("///"):
#print ec
def main(rdir, dir_prefix, ref_model_fn, ofile, remove_partial):
ref_model_f = open(ref_model_fn)
of = open(ofile, "w")
ref_ecs = set()
for s in ref_model_f:
ec = s.strip()
if remove_partial and "-" in ec:
continue
ref_ecs.add(ec)
all_ecs = set()
f = open(common.FILE_EC_MAP)
ec2r, r2ec = common.read_ec_list(f)
all_ecs = set(ec2r.keys())
if remove_partial:
all_ecs = map(lambda x: "-" not in x, all_ecs)
fns = os.listdir(rdir)
results = {}
values = []
for fna in fns:
if fna.startswith(dir_prefix):
sys.stdout.write("Processing %s\n" % (fna))
params = fna[len(dir_prefix):]
if PLOT_PARAM == PARAM_ACCEPT:
param = float(params.split("-")[0]) # accept param
elif PLOT_PARAM == PARAM_REJECT:
param = float(params.split("-")[1]) # reject param
else:
print "Unknown parameter", PLOT_PARAM
assert(0)
#print fna, param
try:
f = open("%s/%s/%s" % (rdir, fna, common.NETWORK_EC_FILE))
#f = open("%s/%s/network.ecs.filtered" % (rdir, fna))
except:
sys.stderr.write("Unable to open %s\n" % (fna))
continue
res_ecs = set()
for s in f:
if s.startswith("#"):
continue
ec = s.strip().split()[0]
if ec == "?":
continue
if remove_partial and "-" in ec:
continue
res_ecs.add(ec)
tp = len(ref_ecs.intersection(res_ecs)) + 1
fp = len(res_ecs.difference(ref_ecs)) + 1
fn = len(ref_ecs.difference(res_ecs)) + 1
tn = len(all_ecs) - tp - fp - fn + 3
try:
tpr = 1.0 * tp / (tp + fn)
fpn = 1.0 * fp / (fp + tn)
prec = 1.0 * tp / (tp + fp)
recall = 1.0 * tp / (tp + fn)
f1 = 2 * prec * recall / (prec + recall)
results[param] = (tp, fp, fn, tn, tpr, fpn, f1)
#values.append((param, tp, fp, fn, tn, tpr, fpn, f1))
#print fpn, tpr
except:
print "Cannot process %s" % (fna)
raise
pfpr = ptpr = 1.0
auc = 0.0
keys = results.keys()
keys.sort()
of.write("#Param TP FP FN TN TPR FPN F1 AUC\n")
for param in keys:
tp, fp, fn, tn, tpr, fpr, f1 = results[param]
auc += (pfpr - fpr) * tpr + (pfpr - fpr) * (ptpr - tpr) / 2
print fpr, tpr, auc, f1
of.write("%.10f\t%d\t%d\t%d\t%d\t%f\t%f\t%s\t%f\n" % (param, tp, fp, fn, tn, tpr, fpr, f1, auc))
pfpr = fpr
ptpr = tpr
tpr = 0.0
fpr = 0.0
auc += (pfpr - fpr) * tpr + (pfpr - fpr) * (ptpr - tpr) / 2
f1 = 0.0
of.write("NA\tNA\tNA\tNA\tNA\t%f\t%f\t%f\t%f\n" % (tpr, fpr, f1, auc))
