def set_ontology(self,
ontology_type: DataType,
ontology: Ontology,
config: GenedescConfigParser,
slim_cache_path: str = None) -> None:
"""set the go ontology and apply terms renaming
Args:
ontology_type (DataType): the type of ontology to set
ontology (Ontology): an ontology object to set as go ontology
config (GenedescConfigParser): configuration object where to read properties
slim_cache_path (str): path to slim file to use
"""
if ontology_type == DataType.GO:
logger.info("Setting GO ontology")
if self.go_relations:
self.go_ontology = ontology.subontology(
relations=self.go_relations)
else:
self.go_ontology = ontology
elif ontology_type == DataType.DO:
logger.info("Setting DO ontology")
if self.do_relations:
self.do_ontology = ontology.subontology(
relations=self.do_relations)
else:
self.do_ontology = ontology
elif ontology_type == DataType.EXPR:
logger.info("Setting Expression ontology")
if self.expr_relations:
self.expression_ontology = ontology.subontology(
relations=self.expr_relations)
else:
self.expression_ontology = ontology
module = get_module_from_data_type(ontology_type)
ontology = self.get_ontology(data_type=ontology_type)
terms_replacement_regex = config.get_module_property(
module=module, prop=ConfigModuleProperty.RENAME_TERMS)
if terms_replacement_regex:
self.rename_ontology_terms(
ontology=ontology,
terms_replacement_regex=terms_replacement_regex)
set_all_depths(ontology=ontology,
relations=self.get_relations(ontology_type))
if config.get_module_property(
module=module,
prop=ConfigModuleProperty.TRIMMING_ALGORITHM) == "ic":
set_ic_ontology_struct(ontology=ontology,
relations=self.get_relations(ontology_type))
if slim_cache_path:
slim_url = config.get_module_property(
module=module, prop=ConfigModuleProperty.SLIM_URL)
self.load_slim(module=module,
slim_url=slim_url,
slim_cache_path=slim_cache_path)
def set_ontology(self,
ontology_type: DataType,
ontology: Ontology,
terms_replacement_regex: Dict[str, str] = None) -> None:
"""set the go ontology and apply terms renaming
Args:
ontology_type (DataType): the type of ontology to set
ontology (Ontology): an ontology object to set as go ontology
terms_replacement_regex (Dict[str, str]): a dictionary containing the regular expression to be applied for
renaming terms. Each key must be a regular expression to search for terms and the associated value
another regular expression that defines the final result
"""
new_ontology = None
if ontology_type == DataType.GO:
logger.info("Setting GO ontology")
self.go_ontology = ontology.subontology(
relations=self.go_relations)
new_ontology = self.go_ontology
elif ontology_type == DataType.DO:
logger.info("Setting DO ontology")
self.do_ontology = ontology.subontology(
relations=self.do_relations)
new_ontology = self.do_ontology
elif ontology_type == DataType.EXPR:
logger.info("Setting Expression ontology")
self.expression_ontology = ontology.subontology()
DataManager.add_article_to_expression_nodes(
self.expression_ontology)
new_ontology = self.expression_ontology
self.rename_ontology_terms(
ontology=new_ontology,
terms_replacement_regex=terms_replacement_regex)
for root_id in new_ontology.get_roots():
set_all_depths_in_subgraph(ontology=new_ontology,
root_id=root_id,
relations=None)