def savePathsWithSecVec(currSecVec):
currSecMets = list(np.nonzero(currSecVec)[0])
augNutrientSet = currSecMets[:]
if not currSecVec.any():
return
elif not os.path.exists(saveDir + str(bool2int(currSecVec)) +
'_prebSeed_randRxnSets_core' + str(Core[-1]) +
'_' + str(NUM_PATHS - 1) + '.txt'):
for coreTBP in Core:
print('Finding paths to ' + cpd_string_dict[id_to_kegg[coreTBP]] +
'.')
coreProdRxns = (prodMat[:, coreTBP] == 1) * 1
satMetVec, satRxnVec = giveRevScope(rxnMat, prodMat, sumRxnVec,
augNutrientSet, Currency,
coreTBP)
satMets, satRxns = np.nonzero(satMetVec)[0], np.nonzero(
satRxnVec)[0]
# Randomizing pathways to coreTBP.
rMinSubnetsRxns = []
for netNum in range(NUM_PATHS):
rMinSubnetsRxns.append(
randMinSubnet(satRxnVec, rxnMat, prodMat, sumRxnVec,
coreProdRxns, coreTBP, augNutrientSet,
Currency))
# Saving the made pathway.
np.savetxt(
saveDir + str(bool2int(currSecVec)) +
'_prebSeed_randRxnSets_core' + str(coreTBP) + '_' +
str(netNum) + '.txt', rMinSubnetsRxns[-1])
currSecVec = secByproducts(currPath.astype(int), rxnMat, prodMat, Core) * 1
currSecMets = list(np.nonzero(currSecVec)[0])
augNutrientSet = currSecMets
if not currSecVec.any():
continue
elif not os.path.exists(saveDir + str(bool2int(currSecVec)) +
'_prebSeed_randRxnSets_core' + str(Core[-1]) +
'_' + str(NUM_PATHS - 1) + '.txt'):
for coreTBP in Core:
print('Finding paths to ' + cpd_string_dict[id_to_kegg[coreTBP]] +
'.')
coreProdRxns = (prodMat[:, coreTBP] == 1) * 1
satMetVec, satRxnVec = giveRevScope(rxnMat, prodMat, sumRxnVec,
augNutrientSet, Currency,
coreTBP)
satMets, satRxns = np.nonzero(satMetVec)[0], np.nonzero(
satRxnVec)[0]
# Randomizing pathways to coreTBP.
rMinSubnetsRxns = []
for netNum in range(NUM_PATHS):
rMinSubnetsRxns.append(
randMinSubnet(satRxnVec, rxnMat, prodMat, sumRxnVec,
coreProdRxns, coreTBP, augNutrientSet,
Currency))
# Saving the made pathway.
np.savetxt(
saveDir + str(bool2int(currSecVec)) +