def define_instance_variables(self):
"""
Define instance variables
:return:
"""
self.report_material = {}
self.__compoundsAnnotationConfigs = file_utilities.read_conf_file(
COMPOUNDS_ANNOTATION_CONFIGS_PATH)
self.__reactionsAnnotationConfigs = file_utilities.read_conf_file(
REACTIONS_ANNOTATION_CONFIGS_PATH)
self.__compounds_ontology = CompoundsDBAccessor()
self.__home_path__ = ROOT_DIR
self.__configs = file_utilities.read_conf_file(TOOL_CONFIG_PATH)
self.changed_reactions = []
self.reactions_swapper = ReactionsChanger(
self.model,
self.__type,
self.__model_database,
self.__universal_model,
compounds_converter=self.__compoundsIdConverter)
def __define_instance_variables(self):
"""
Define instance variables
:return:
"""
self.__universal_model = Model("universal_model")
self.__swapped = []
self.__compounds_ontology = CompoundsDBAccessor()
self.__compoundsAnnotationConfigs = file_utilities.read_conf_file(
COMPOUNDS_ANNOTATION_CONFIGS_PATH)
self.__reactionsAnnotationConfigs = file_utilities.read_conf_file(
REACTIONS_ANNOTATION_CONFIGS_PATH)
self.__compoundsIdConverter = CompoundsIDConverter()
self.__compounds_revisor = CompoundsRevisor(self.model,
self.__universal_model)
biocyc.set_organism("meta")
self.mapper = ModelMapper(self.model,
self.__compoundsAnnotationConfigs,
self.__compoundsIdConverter)
self.__compounds_revisor.set_model_mapper(self.mapper)
self.granulator = Granulator(self.model, self.mapper,
self.__database_format,
self.__compoundsIdConverter,
self.__compoundsAnnotationConfigs)
def __init__(self):
super().__init__()
# scraper = ReactionsIDConverterScraper()
# path = scraper()
self.__database_config = file_utilities.read_conf_file(
DATABASE_CONFIGS)
path = ROOT_DIR + self.__database_config[
"path_model_seed_reactions_aliases"]
self.__configs = file_utilities.read_conf_file(TOOL_CONFIG_PATH)
self.__home_path__ = ROOT_DIR
self.construct_reactions_converter(path)
def __define_instance_variables(self):
"""
Method to define a set of instance values
:return:
"""
self.__swapped = []
self.lineage = []
# self.__compounds_ontology = CompoundsDBAccessor()
self.__compoundsAnnotationConfigs = file_utilities.read_conf_file(
COMPOUNDS_ANNOTATION_CONFIGS_PATH)
self.__reactionsAnnotationConfigs = file_utilities.read_conf_file(
REACTIONS_ANNOTATION_CONFIGS_PATH)
self.__compoundsAnnotationConfigs = file_utilities.read_conf_file(
COMPOUNDS_ANNOTATION_CONFIGS_PATH)
self.__reactionsAnnotationConfigs = file_utilities.read_conf_file(
REACTIONS_ANNOTATION_CONFIGS_PATH)
self.__compoundsIdConverter = CompoundsIDConverter()
# self.__ptw_handler_quinones = PathwayHandler(self.__modelseedCompoundsDb, self.__compoundsIdConverter)
# self.__ptw_handler_quinones.load_from_file(self.__home_path__ + self.__configs["quinones_pathways"])
self.__not_to_change_classes = ["cpd03476"]
self.__set_not_to_change_compounds()
self.__compounds_revisor = CompoundsRevisor(self.model,
self.__universal_model)
biocyc.set_organism("meta")
self.__swapper = MetaboliteSwapper(
self.model,
None,
None,
0,
self.__modelseedCompoundsDb,
model_database=self.__database_format,
compoundsIdConverter=self.__compoundsIdConverter,
universal_model=self.__universal_model,
not_to_change_compounds=self.__not_to_change_compounds)
self.__mapper = ModelMapper(self.model,
self.__compoundsAnnotationConfigs,
self.__compoundsIdConverter)
self.__swapper.set_model_mapper(self.__mapper)
self.__compounds_revisor.set_model_mapper(self.__mapper)
def __init__(self):
self.url_db = "https://raw.githubusercontent.com/ModelSEED/ModelSEEDDatabase/master/Biochemistry/Aliases/Unique_ModelSEED_Reaction_Aliases.txt"
self.__database_config = file_utilities.read_conf_file(DATABASE_CONFIGS)
up_to_date = self.__check_time()
if not up_to_date:
self.__download_modelseed_database()
def __init__(self, model, database_format):
"""
Class constructor
:param Model model: cobrapy model
:param str database_format: ModelSEED, BiGG or KEGG
"""
self.model = model
self.objective = linear_reaction_coefficients(self.model)
if self.objective:
self.objective = list(self.objective.keys())[0]
else:
raise Exception("No objective found")
self.__compounds_ontology = CompoundsDBAccessor()
self.model = model
self.__database_format = database_format
self.__configs = file_utilities.read_conf_file(TOOL_CONFIG_PATH)
self.__home_path__ = ROOT_DIR
self.__modelseedCompoundsDb = ModelSeedCompoundsDB()
self.__define_instance_variables()
self.write_in_progress_bar("mapping model... ", 1)
self.mapper.map_model(database_format)
self.write_in_progress_bar("model mapped ", 10)
def __init__(self):
self.__database_config = file_utilities.read_conf_file(DATABASE_CONFIGS)
path = ROOT_DIR + self.__database_config["path_model_seed_db_reactions"]
# scraper = ModelSeedReactionsDBScraper()
# path = scraper()
self.read_model_seed_reactions_database(path)
def read_config_file(self):
configs = file_utilities.read_conf_file(definitions.BOIMMG_DATABASE)
uri = configs["uri"]
user = configs["user"]
password = configs["password"]
return uri, user, password
def get_reaction_annotation_format_by_aliases(aliases):
reactionsAnnotationConfigs = file_utilities.read_conf_file(
REACTIONS_ANNOTATION_CONFIGS_PATH)
res = {}
for alias in aliases:
if alias in reactionsAnnotationConfigs.keys():
new_alias = reactionsAnnotationConfigs[alias]
res[new_alias] = aliases[alias]
return res
def get_compound_annotation_format_by_aliases(aliases):
compoundsAnnotationConfigs = file_utilities.read_conf_file(
COMPOUNDS_ANNOTATION_CONFIGS_PATH)
res = {}
for alias in aliases:
if alias in compoundsAnnotationConfigs.keys():
new_alias = compoundsAnnotationConfigs[alias]
res[new_alias] = aliases[alias]
return res
def __init__(self,
model: Model,
type: int,
model_database: str,
universal_model: Model,
compounds_converter=None):
"""
Class constructor
:param cobrapy.Model model: COBRApy model
:param int type: type of change (0,1,2 or 3)
:param string model_database: database format of metabolites and reactions
:param cobrapy.Model universal_model: universal model
:param (optional) ReactionsIDConverter reactions_converter: a reaction identifier converter
"""
if not compounds_converter:
self.__compoundsIDConverter = CompoundsIDConverter()
else:
self.__compoundsIDConverter = compounds_converter
if not universal_model:
self.__universal_model = Model()
else:
self.__universal_model = universal_model
self.__type = type
self.__model_database = model_database
self.__model = model
self.__modelseed_hydrogen = "cpd00067"
self.__reactionBalancer = CompoundsRevisor(self.__model)
self.__not_found_reactions_num = 0
self.__home_path__ = ROOT_DIR
self.__configs = file_utilities.read_conf_file(TOOL_CONFIG_PATH)
self.__compoundsAnnotationConfigs = file_utilities.read_conf_file(
COMPOUNDS_ANNOTATION_CONFIGS_PATH)
self.__reactionsAnnotationConfigs = file_utilities.read_conf_file(
REACTIONS_ANNOTATION_CONFIGS_PATH)
def __init__(self,model,universal_model = None,compoundsAnnotationConfigs = None):
if not universal_model:
self.__universal_model = Model()
else:
self.__universal_model=universal_model
if not compoundsAnnotationConfigs:
self.compoundsAnnotationConfigs = file_utilities.read_conf_file(COMPOUNDS_ANNOTATION_CONFIGS_PATH)
else:
self.compoundsAnnotationConfigs = compoundsAnnotationConfigs
self.__model = model
self.__get_hydrogen_from_model()
self.__changed_reaction = None
def read_config_file(self):
configs = file_utilities.read_conf_file(definitions.BOIMMG_DATABASE)
if "uri" in configs.keys() and "user" in configs.keys(
) and "password" in configs.keys():
uri = configs["uri"]
user = configs["user"]
password = configs["password"]
return uri, user, password
else:
raise Exception("Please insert the required database information")
def define_instance_variables(self):
"""
Instance variables definition
:return:
"""
self.__compounds_ontology = CompoundsDBAccessor()
self.__added_reactions_and_respective_target = {}
self.__reactionsAnnotationConfigs = file_utilities.read_conf_file(
REACTIONS_ANNOTATION_CONFIGS_PATH)
self.metabolite_report_material = {}
self.reaction_report_material = {}
self.__set_components()
def define_instance_variables(self):
"""
Instance variables definition
:return:
"""
self.__compounds_ontology = CompoundsDBAccessor()
self.__added_reactions_and_respective_target = {}
self.__reactionsAnnotationConfigs = file_utilities.read_conf_file(
REACTIONS_ANNOTATION_CONFIGS_PATH)
print("setting components...")
start = time.time()
self.__set_components()
end = time.time()
print("components set: %d" % (end - start))
def __init__(self, model: Model, database_format: str, db_accessor = CompoundsDBAccessor()):
"""
Class constructor
:param Model model: model being analysed
:param database_format: database format (ModelSEED, BiGG or KEGG)
:param modelseed_compoundsdb:
"""
self.report_material = {}
self.__universal_model = Model("universal_model")
self.model = model
self.__database_format = database_format
self.__configs = file_utilities.read_conf_file(TOOL_CONFIG_PATH)
self.__home_path__ = ROOT_DIR
self.__compounds_ontology = db_accessor
self.__modelseedCompoundsDb = ModelSeedCompoundsDB()
self.__define_instance_variables()
def get_annotation_from_cobra_annotation(compound):
compoundsAnnotationConfigs = file_utilities.read_conf_file(
COMPOUNDS_ANNOTATION_CONFIGS_PATH)
inverse = {
value: key
for key, value in compoundsAnnotationConfigs.items()
}
res = {}
for annotation_key in compound.annotation:
if annotation_key in inverse.keys():
boimmg_database = inverse[annotation_key]
aliases = compound.annotation[annotation_key]
if isinstance(aliases, list):
res[boimmg_database] = aliases
else:
res[boimmg_database] = [aliases]
return res
compoundsAnnotationConfigs,
compoundsIDConverter)
found_2 = compare_models_metabolites(model, model2)
print(len(found_1))
print(len(found_2))
for met2 in found_2:
if met2 not in found_1:
print(met2)
for reaction2 in found_reactions_2:
if reaction2 not in found_reactions_1:
print(reaction2)
if __name__ == "__main__":
import cobra
compoundsIDConverter = CompoundsIDConverter()
compoundsAnnotationConfigs = file_utilities.read_conf_file(
COMPOUNDS_ANNOTATION_CONFIGS_PATH)
model_database = "BiGG"
model1 = definitions.ROOT_DIR + "/case_studies/redundant_representation_case/iML1515_mapped.xml"
model3 = definitions.ROOT_DIR + "/case_studies/redundant_representation_case/iJR904_mapped.xml"
model2 = definitions.ROOT_DIR + "/case_studies/redundant_representation_case/granulated_gap_filled_iJR904.xml"
# compare_lipids_ecoli_granulated(model_database, compoundsAnnotationConfigs, compoundsIDConverter)
compare_models(model1, model2, model3, model_database,
compoundsAnnotationConfigs, compoundsIDConverter)
def __init__(self):
conf = file_utilities.read_conf_file(definitions.BOIMMG_DATABASE)
self.rest_uri = conf["rest_uri"]
