def merge_models(worm_m, wol_m, out_name, out_file):
rxn_pref_remove = ('TEST_', )
worm_m += wol_m
rxns_to_remove = []
for rxn in worm_m.reactions:
if rxn.id.startswith(rxn_pref_remove):
rxns_to_remove.append(rxn.id)
worm_m.remove_reactions(rxns_to_remove)
worm_m.id = out_name
write_excel(worm_m, out_file)
print('%s saved to %s' % (worm_m, out_file))
def compare_reaction_mtbs(model1, model2, missing_mtb, outfile):
rxn_mtbs = set()
exchanges, transports = set(), set()
for rxn in model1.reactions:
rs = tuple(sorted(m.id.strip()[1:] for m in rxn.reactants))
ps = tuple(sorted(m.id.strip()[1:] for m in rxn.products))
if any(m[0].isalpha() for m in rs + ps): # Using a custom metabolite.
continue
if rs == ps:
transports.add(rs)
elif not rs:
exchanges.add(ps)
elif not ps:
exchanges.add(rs)
else:
rxn_mtbs.add((rs, ps))
print('\nParsed %i reactions, %i transports, and %i exchanges.' %
(len(rxn_mtbs), len(transports), len(exchanges)))
missed_exs = set()
bad_ids = set()
missing_mtb_ids = set()
for rxn in model2.reactions:
rs = tuple(sorted(m.id.strip()[1:] for m in rxn.reactants))
ps = tuple(sorted(m.id.strip()[1:] for m in rxn.products))
if not rs or not ps:
ms = rs if rs else ps
if ms not in exchanges:
missed_exs.add(ms)
else:
if (rs, ps) in rxn_mtbs or (ps, rs) in rxn_mtbs:
pass
else:
coef = check_rxn_missing_mtb(missing_mtb, rs, ps, rxn_mtbs)
if coef:
missing_mtb_ids.add(rxn.id)
rxn.add_metabolites({missing_mtb: coef})
else:
bad_ids.add(rxn.id)
print(
'%s is missing %i exchanges present in %s, with %i inconsistencies.' %
(model2, len(missed_exs), model1, len(bad_ids)))
write_excel(model2, outfile)
print('%i reactions were missing %s; modified and saved as %s' %
(len(missing_mtb_ids), missing_mtb, outfile))
old_directions.append('blocked')
else:
old_directions.append('missing')
agreed = False
if len(set(old_directions)) == 1 and old_directions[0] == 'missing':
continue # No matching reactions found in old_m
elif 'blocked' in old_directions or 'missing' in old_directions:
broken += 1 # Part of the reaction set exists in old_m, but part is missing or blocked.
elif cel_direction == 'reversible':
if 'irreversible' not in old_directions:
agreed = True
else:
rvsb += 1
else: # Should be irreversible
if 'irreversible' in old_directions:
agreed = True
else:
irrvsb += 1
if not agreed:
disagreements.append((', '.join(r_ids), cel_direction,
', '.join(old_directions), products))
disagreements.sort(key=lambda d: d[0])
disagreements.sort(key=lambda d: d[1])
print('\n%i should have been reversible, %i irreversible, and %i were broken' %
(rvsb, irrvsb, broken))
unresolved = use_directionalities(old_m, disagreements)
print('\n'.join('%s should be %s, but is: %s' % (d[:3]) for d in unresolved))
print len(unresolved)
write_excel(old_m, model_out_file)
% (wm, wm.solution.f))
if test_removed_wol_rxns:
for m, fva, r_ids in zip(in_models, fvas, unique_wol_ids):
print('\nEvaluating %i reactions from %s. Initial flux: %.1f.' %
(len(r_ids), m, m.solution.f))
diffs = test_changed_constraints(r_ids,
m,
fva,
bounds_deltas=None,
cumulative=False)
for d in diffs:
print('%i loss [%s]: %s' %
(d[0], d[1][0], ', '.join(x for x in d[3])))
if save_wol_models:
out_wol_model_files = [
os.path.join(files_dir, '%s-sep.xlsx' % m_name)
for m_name in wol_model_names
]
for wm, m_file in zip(wol_models, out_wol_model_files):
write_excel(wm, m_file)
# add in common reactions.
if save_nem_models:
out_nem_model_files = [
os.path.join(files_dir, '%s-sep.xlsx' % m_name)
for m_name in out_nem_model_names
]
for m, m_file in zip(in_models, out_nem_model_files):
write_excel(m, m_file)
model_files = ['model_o_vol_3.xlsx', 'model_b_mal_3.xlsx']
out_files = ['model_o_vol_3.5-wip.xlsx', 'model_b_mal_3.5-wip.xlsx']
do_deletions = True
cel_m = read_excel(os.path.join(files_dir, 'iCEL1273.xlsx'), verbose=False)
#cel_m.reactions.BIO0101.objective_coefficient = 1.0 # # # TESTING ONLY
#cobra.flux_analysis.parsimonious.optimize_minimal_flux(cel_m)
models = [
read_excel(os.path.join(files_dir, m_file), verbose=False)
for m_file in model_files
]
for m, out_file in zip(models, out_files):
if do_deletions:
modify_model(m, cel_m, do_deletions)
write_excel(m, os.path.join(files_dir, out_file))
else:
print('Obj before modifications: %.1f' % (m.optimize().f))
rxns_to_delete = modify_model(m, cel_m, do_deletions)
diffs = []
cur_f = m.optimize().f
for rxn in rxns_to_delete:
rxn.delete()
diff_f = m.optimize().f - cur_f
diffs.append((diff_f, rxn))
cur_f += diff_f
if cur_f < 1.0:
break
diffs.sort()
for d in diffs:
print('%.1f by %s' % (d[0], d[1].id))
"""
import os
from read_excel import read_excel, write_excel
files_dir = '/mnt/hgfs/win_projects/brugia_project'
in_model_names = ['model_o_vol_3.5', 'model_b_mal_3.5']
in_model_files = [os.path.join(files_dir, m_file+'.xlsx') for m_file in in_model_names]
out_model_files = [os.path.join(files_dir, m_file+'-wip.xlsx') for m_file in in_model_names]
in_models = [read_excel(m_file, verbose=False) for m_file in in_model_files]
for m in in_models:
for mtb in m.metabolites:
if mtb.id == 'FA_storage_mix': continue
elif mtb.id[0] == 'C':
mtb.compartment = 'c'
if mtb.id[1] == 'C': continue
elif mtb.id[0] == 'M':
mtb.compartment = 'm'
if mtb.id[1] == 'C' or mtb.name: continue
c_id = 'C' + mtb.id[1:]
if c_id in m.metabolites and m.metabolites.get_by_id(c_id).name:
mtb.name = m.metabolites.get_by_id(c_id).name
elif mtb.id[0] == 'G':
pass
for m, out_file in zip(in_models, out_model_files):
write_excel(m, out_file)