def coreFromReactions(sources, reactionSet):
avrxns = [rxn_kegg_to_id[e] for e in reactionSet]
scopeMets, avScopeRxn = giveScope(rxnMat[avrxns], prodMat[avrxns],
giveSeedVec(sources), sumRxnVec[avrxns])
scopeRxns = np.nonzero(avrxns * avScopeRxn)[0]
return set([id_to_kegg[e]
for e in set(np.where(scopeMets)[0])]) & set(Core)
def give_ind_degree(org):
# Getting all the reactions performable by this organism.
can = set(np.genfromtxt('organism_reactions/' + org + '.txt').astype(int))
can = ['R' + (5 - len(str(int(e)))) * '0' + str(int(e)) for e in can]
can = list((set(can)) & set(rxns))
avrxns = [rxn_kegg_to_id[e] for e in can]
# Calculating the metabolites within the scope of
# this organism's reaction network.
scopeMets = giveScope(rxnMat[avrxns], prodMat[avrxns], seedVec,
sumRxnVec[avrxns])[0]
# Finding how much of the core is within the network's scope.
return list(
set([id_to_kegg[e] for e in set(np.where(scopeMets)[0])]) & set(Core))
def propagate_rxns_for_medium(orgrxns, medium):
# Defining the seed set to be the medium and the currency,
seedVec = np.zeros(len(rxnMat.T))
seedVec[[kegg_to_id[e] for e in Currency + medium]] = 1
# Getting all the reactions performable by this organism.
avrxns = orgrxns[:]
# Calculating the metabolites within the scope of
# this organism's reaction network.
scopeMets = giveScope(rxnMat[avrxns], prodMat[avrxns], seedVec,
sumRxnVec[avrxns])[0]
# Finding how much of the core is within the network's scope.
return uniqify([id_to_kegg[e] for e in np.where(scopeMets)[0]])
def propagate_core_for_medium(corerxns, medium):
# Defining the seed set to be the medium and the currency,
seedVec = np.zeros(len(rxnMat.T))
seedVec[[kegg_to_id[e] for e in Currency + medium]] = 1
# Getting all the reactions performable by these corerxns.
can = ['R' + (5 - len(str(int(e)))) * '0' + str(int(e)) for e in corerxns]
can = list((set(can)) & set(rxns))
avrxns = [rxn_kegg_to_id[e] for e in can]
# Calculating the metabolites within the scope of
# this organism's reaction network.
scopeMets = giveScope(rxnMat[avrxns], prodMat[avrxns], seedVec, sumRxnVec[avrxns])[0]
# Finding how much of the core is within the network's scope.
return uniqify([id_to_kegg[e] for e in np.where(scopeMets)[0]])
def propagate_single_for_medium(org, medium):
# Defining the seed set to be the medium and the currency,
seedVec = np.zeros(len(rxnMat.T))
seedVec[[kegg_to_id[e] for e in Currency + medium]] = 1
# Getting all the reactions performable by this organism.
can = ''.join(open('strain_reactions/' + org + '.txt', 'r').readlines()).split()
can = list((set(can)) & set(rxns))
avrxns = [rxn_kegg_to_id[e] for e in can]
# Calculating the metabolites within the scope of
# this organism's reaction network.
scopeMets = giveScope(rxnMat[avrxns], prodMat[avrxns], seedVec, sumRxnVec[avrxns])[0]
# Finding how much of the core is within the network's scope.
return uniqify([id_to_kegg[e] for e in np.where(scopeMets)[0]])
def inferProducible(genotype, sources=defaultSeedVec):
"""
Given a genotype, infers what reactions it can perform, and then calculates
all producible metabolites in a given environment.
If no environment is supplied, assumes a rich environment with all single
carbon source enrichments.
"""
# Getting all reactions that the genotype can perform.
can = genotypeToRxns(genotype)
# Generating the seed vector from the environmental sources.
currSeedVec = giveSeedVec(sources)
avrxns = [rxn_kegg_to_id[e] for e in can]
scopeMets = giveScope(rxnMat[avrxns], prodMat[avrxns], currSeedVec,
sumRxnVec[avrxns])[0]
return set([id_to_kegg[e] for e in np.where(scopeMets)[0]])
def inferIndDegree(genotype):
kos = [pos_to_gene_map[i] for i in np.where((genotype > 0.5) * 1)[0]]
refDF = pd.read_csv('KOREF.txt',
delimiter='\t',
sep='delimiter',
header=None,
names=['id', 'rid'])
def give_number(string):
return int(string[-5:])
refDF['id'] = refDF['id'].apply(give_number)
refDF['rid'] = refDF['rid'].apply(give_number)
can = refDF.loc[refDF['id'].isin(kos), :]['rid'].values
can = ['R' + (5 - len(str(int(e)))) * '0' + str(int(e)) for e in can]
can = list((set(can)) & set(rxns))
avrxns = [rxn_kegg_to_id[e] for e in can]
scopeMets = giveScope(rxnMat[avrxns], prodMat[avrxns], seedVec,
sumRxnVec[avrxns])[0]
return list(
set([id_to_kegg[e] for e in set(np.where(scopeMets)[0])]) & set(Core))
