def load_custom_reactions_to_be_excluded():
"""A list of undesirable reactions that are specific
to the glycolysis study
Returns:
TYPE: Description
"""
NTP_involving_rxns = gams_parser.convert_set_to_list(
os.path.join(DATA_DIR, 'NTP_and_AMP_reactions.txt')
)
cofactor_only_rxns = gams_parser.convert_set_to_list(
os.path.join(DATA_DIR, 'cofactor_only_reactions.txt')
)
cofactor_only_rxns.append('R10092')
methylglyoxal_rxns = [
'R00203',
'R00205',
'R01016',
'R02260',
'R02527',
'R02528',
'R02529',
'R02530',
'R02531',
'R07183',
'R09796',
'R10049',
'R10050'
]
other_undesirable_rxns = [
# Bicarbonate and pyrrole cycle
'R09794',
'R09795',
# Undesirable glucose uptake loop
'R00305',
'R00874',
'R07359',
'R00837',
'R09749',
'R03075',
'R02985',
'R02558',
'R01555',
'R02727',
'R00010',
'R02778',
'R08946',
'R00306'
]
excluded_reactions = (NTP_involving_rxns +
methylglyoxal_rxns +
cofactor_only_rxns +
other_undesirable_rxns)
all_excluded_reactions = list(set(excluded_reactions))
return all_excluded_reactions
def load(self):
# Method 1: JSON approach
if self.dbdict_json is not None:
self.logger.debug('Reading S matrix from JSON...')
self.Sji = json.load(
open(
os.path.join(
self.data_filepath,
self.dbdict_json['Sji']),
'r+'))
self.S = self.transpose_S(self.Sji)
self.reactions = sorted(self.Sji.keys())
self.internal_rxns = copy.deepcopy(self.reactions)
self.metabolites = sorted(self.S.keys())
self.logger.debug('Reading reaction type file...')
self.rxntype = json.load(
open(
os.path.join(
self.data_filepath,
self.dbdict_json['reactiontype']),
'r+'))
# Method 2: Standard GAMS input file
else:
self.logger.debug('Reading S matrix from txt...')
self.S = gams_parser.convert_parameter_table_to_dict(
os.path.join(self.data_filepath,
self.dbdict_gams['Sji'])
)
self.Sji = self.transpose_S(self.S)
# Load reactions
self.logger.debug('Reading reaction file...')
self.reactions = gams_parser.convert_set_to_list(
os.path.join(self.data_filepath, self.dbdict_gams['reaction'])
)
# Create internal reactions list
self.internal_rxns = copy.deepcopy(self.reactions)
self.logger.debug('Reading metabolite file...')
self.metabolites = gams_parser.convert_set_to_list(
os.path.join(self.data_filepath, self.dbdict_gams['metabolite'])
)
self.logger.debug('Reading reaction type file...')
self.rxntype = gams_parser.convert_parameter_list_to_dict(
os.path.join(self.data_filepath, self.dbdict_gams['reactiontype']),
datadict=None
)
self.validate()
def load_db_v3_toy_model(user_defined_export_rxns_Sji,
reduce_model_size=True,
logger=None):
"""Load OptStoic database v3
Returns:
TYPE: Description
Args:
reduce_model_size (bool, optional): True if you want to reduce the size of the
model by removing blocked reactions from the S matrix.
user_defined_export_rxns_Sji (dict, optional): The list of export reactions that
need to be added to the model for metabolite exchange (i.e., any metabolite
that participate in the design equation)
"""
if logger is None:
logger = create_logger(name="optstoicpy.core.database.load_db_v3")
# get reactions that are manually curated to be excluded for glycolysis
# study
excluded_reactions = load_custom_reactions_to_be_excluded()
dbdict_json = {
'Sji': 'toy_model_Sji.json',
#'Nint': 'Nint_ecolicore.json',
'reactiontype': 'toy_model_reactiontype.json'
}
dbdict_gams = {
'Sji': 'optstoic_v3_Sij.txt',
'reaction': 'optstoic_v3_reactions.txt',
'metabolite': 'optstoic_v3_metabolites.txt',
'reactiontype': 'optstoic_v3_reactiontype.txt',
'loops': 'optstoic_v3_loops_nocofactor.txt',
'Nint': 'optstoic_v3_null_sij_nocofactor.txt',
'blocked_rxns': 'optstoic_v3_blocked_reactions_0to5ATP.txt',
}
logger.debug('Reading blocked reactions file...')
if 'blocked_rxns' in dbdict_gams:
blocked_rxns = gams_parser.convert_set_to_list(
os.path.join(DATA_DIR, dbdict_gams['blocked_rxns']))
else:
blocked_rxns = None
DB = Database(description='toy_model_v3',
data_filepath=DATA_DIR,
dbdict_json=dbdict_json,
dbdict_gams=dbdict_gams,
blocked_rxns=[],
excluded_reactions=excluded_reactions,
reduce_model_size=reduce_model_size)
DB.load_toy_model()
# Update reaction type
# Update reaction type = 0
irreversible_fwd_rxns = gams_parser.convert_set_to_list(
os.path.join(DATA_DIR,
'optstoic_v3_ATP_irreversible_forward_rxns.txt'))
new_reaction_type_dict = dict(
list(zip(irreversible_fwd_rxns, [0] * len(irreversible_fwd_rxns))))
# Update reaction type = 2
irreversible_bwd_rxns = gams_parser.convert_set_to_list(
os.path.join(DATA_DIR,
'optstoic_v3_ATP_irreversible_backward_rxns.txt'))
new_reaction_type_dict.update(
dict(list(zip(irreversible_bwd_rxns,
[2] * len(irreversible_bwd_rxns)))))
DB.update_rxntype(new_reaction_type_dict)
# user_defined_export_rxns = ['EX_glc', 'EX_nad', 'EX_adp',
# 'EX_phosphate', 'EX_pyruvate', 'EX_nadh',
# 'EX_atp', 'EX_h2o', 'EX_hplus', 'EX_nadp',
# 'EX_nadph']
# Add a list of export reactions and the metabolites
#if user_defined_export_rxns_Sji is not None:
user_defined_export_rxns_Sij = Database.transpose_S(
user_defined_export_rxns_Sji)
DB.set_database_export_reaction(user_defined_export_rxns_Sij)
return DB
def load_base_reaction_db_ecolicore(user_defined_export_rxns_Sji=None,
logger=None):
"""Load the base reaction database with all reactions
(i.e., no blocked reactions and no loops)
Args:
user_defined_export_rxns_Sji (None, optional): Description
Returns:
:obj:`BaseReactionDatabase`:
"""
if logger is None:
logger = create_logger(
name="optstoicpy.core.database.load_base_reaction_db")
# get reactions that are manually curated to be excluded for glycolysis
# study
excluded_reactions = load_custom_reactions_to_be_excluded()
dbdict_json = {
'Sji': 'Sji_dict_ecolicore.json',
'reactiontype': 'ecolicore_reactiontype.json'
}
dbdict_gams = {
'Sji': 'optstoic_v3_Sij.txt',
'reaction': 'optstoic_v3_reactions.txt',
'metabolite': 'optstoic_v3_metabolites.txt',
'reactiontype': 'optstoic_v3_reactiontype.txt'
}
DB = BaseReactionDatabase(data_filepath=DATA_DIR,
dbdict_json=dbdict_json,
dbdict_gams=dbdict_gams)
DB.load_ecolicore()
# Update reaction type
# Update reaction type = 0
irreversible_fwd_rxns = gams_parser.convert_set_to_list(
os.path.join(DATA_DIR,
'optstoic_v3_ATP_irreversible_forward_rxns.txt'))
new_reaction_type_dict = dict(
list(zip(irreversible_fwd_rxns, [0] * len(irreversible_fwd_rxns))))
# Update reaction type = 2
irreversible_bwd_rxns = gams_parser.convert_set_to_list(
os.path.join(DATA_DIR,
'optstoic_v3_ATP_irreversible_backward_rxns.txt'))
new_reaction_type_dict.update(
dict(list(zip(irreversible_bwd_rxns,
[2] * len(irreversible_bwd_rxns)))))
DB.update_rxntype(new_reaction_type_dict)
# Add a list of export reactions and the metabolites
if user_defined_export_rxns_Sji is not None:
user_defined_export_rxns_Sij = Database.transpose_S(
user_defined_export_rxns_Sji)
DB.set_database_export_reaction(user_defined_export_rxns_Sij)
return DB
def load_toy_model(self):
# Method 1: JSON approach
if self.dbdict_json is not None:
self.logger.debug('Reading S matrix from JSON...')
self.Sji = json.load(
open(os.path.join(self.data_filepath, self.dbdict_json['Sji']),
'r+'))
self.S = self.transpose_S(self.Sji)
self.reactions = sorted(self.Sji.keys())
self.internal_rxns = copy.deepcopy(self.reactions)
self.metabolites = sorted(self.S.keys())
self.logger.debug('Reading reaction type file...')
self.rxntype = json.load(
open(
os.path.join(self.data_filepath,
self.dbdict_json['reactiontype']), 'r+'))
self.logger.debug('Reading Nint(loop, j) from JSON...')
#no hay loops en el toy_model
#self.Ninternal = json.load(
# open(
# os.path.join(
# self.data_filepath,
# self.dbdict_json['Nint']),
# 'r+'))
#self.loops = sorted(self.Ninternal.keys())
# Method 2: Standard GAMS input file
else:
self.logger.debug('Reading S matrix from txt...')
self.S = gams_parser.convert_parameter_table_to_dict(
os.path.join(self.data_filepath, self.dbdict_gams['Sji']))
self.Sji = self.transpose_S(self.S)
self.logger.debug('Reading metabolite file...')
self.metabolites = gams_parser.convert_set_to_list(
os.path.join(self.data_filepath,
self.dbdict_gams['metabolite']))
# Load reactions
self.logger.debug('Reading reaction file...')
self.reactions = gams_parser.convert_set_to_list(
os.path.join(self.data_filepath, self.dbdict_gams['reaction']))
self.internal_rxns = copy.deepcopy(self.reactions)
self.logger.debug('Reading reaction type file...')
self.rxntype = gams_parser.convert_parameter_list_to_dict(
os.path.join(self.data_filepath,
self.dbdict_gams['reactiontype']),
datadict=None)
self.logger.debug('Reading Nint(loop, j) from txt...')
self.Ninternal = gams_parser.convert_parameter_table_to_dict(
os.path.join(self.data_filepath, self.dbdict_gams['Nint']))
self.logger.debug('Reading loop file...')
self.loops = gams_parser.convert_set_to_list(
os.path.join(self.data_filepath, self.dbdict_gams['loops']))
if self.excluded_reactions is not None:
self.all_excluded_reactions = list(
set(self.excluded_reactions + self.blocked_rxns))
else:
self.all_excluded_reactions = self.blocked_rxns
#self.validate()
if self.reduce_model_size:
self.remove_blocked_reactions()
self.validate()
