def get_mrna_dict(model):
mrna_dict = dict()
# Generate a mRNA dict
for x in nt_sequences.index:
try:
the_gene = model.genes.get_by_id(x)
except KeyError:
model.genes += [cobra.Gene(id=x)]
the_gene = model.genes.get_by_id(x)
# Try to get half life from Bernstein et al.
try:
t_half = bernstein_ecoli_deg_rates.loc[x.upper()]['medium, min.1'] #M9 medium
# Mean half life of mrna is 5 minutes in ecoli
# tau = t_0.5 /ln(2)
# kdeg = 1/tau [min^-1] * [min/h]
this_kdeg_mrna = (60 * np.log(2) / t_half)
except KeyError:
if x in rrna_genes:
this_kdeg_mrna = kdeg_rib # Same as ribosome
else:
this_kdeg_mrna = kdeg_mrna # Average value of 5 mins
if np.isnan(this_kdeg_mrna):
this_kdeg_mrna = kdeg_mrna # Average value of 5 mins
new_mrna = mRNA(x,
kdeg = this_kdeg_mrna,
gene_id = the_gene.id)
mrna_dict[x] = new_mrna
return mrna_dict
new_enzyme.notes['EC'] = this_ec
aggregated_coupling_dict[x.id].append(new_enzyme)
# 1/0
coupling_dict.update(aggregated_coupling_dict)
mrna_dict = dict()
# Generate a mRNA dict
for x in nt_sequences.index:
try:
the_gene = ecoli.genes.get_by_id(x)
except KeyError:
ecoli.add_genes([cobra.Gene(id=x)])
the_gene = ecoli.genes.get_by_id(x)
# Try to get half life from Bernstein et al.
try:
t_half = bernstein_ecoli_deg_rates.loc[x.upper()]['medium, min.1'] #M9 medium
# Mean half life of mrna is 5 minutes in ecoli
# tau = t_0.5 /ln(2)
# kdeg = 1-exp(1hr/tau)
this_kdeg_mrna = 1 - np.exp(-60 * np.log(2) / t_half)
except KeyError:
this_kdeg_mrna = kdeg_mrna # Average value of 5 mins
if np.isnan(this_kdeg_mrna):
this_kdeg_mrna = kdeg_mrna # Average value of 5 mins