def load_associations_from_file(self, associations_type: DataType,
associations_url: str,
associations_cache_path: str,
config: GenedescConfigParser) -> None:
"""load go associations from file
Args:
associations_type (DataType): the type of associations to set
associations_url (str): url to the association file
associations_cache_path (str): path to cache file for the associations
config (GenedescConfigParser): configuration object where to read properties
"""
assoc_config = AssocParserConfig(remove_double_prefixes=True,
paint=True)
if associations_type == DataType.GO:
logger.info("Loading GO associations from file")
self.go_associations = AssociationSetFactory().create_from_assocs(
assocs=GafParser(config=assoc_config).parse(
file=self._get_cached_file(
cache_path=associations_cache_path,
file_source_url=associations_url),
skipheader=True),
ontology=self.go_ontology)
self.go_associations = self.remove_blacklisted_annotations(
association_set=self.go_associations,
ontology=self.go_ontology,
terms_blacklist=config.get_module_property(
module=Module.GO, prop=ConfigModuleProperty.EXCLUDE_TERMS))
elif associations_type == DataType.DO:
logger.info("Loading DO associations from file")
self.do_associations = AssociationSetFactory().create_from_assocs(
assocs=GafParser(config=assoc_config).parse(
file=self._get_cached_file(
cache_path=associations_cache_path,
file_source_url=associations_url),
skipheader=True),
ontology=self.do_ontology)
self.do_associations = self.remove_blacklisted_annotations(
association_set=self.do_associations,
ontology=self.do_ontology,
terms_blacklist=config.get_module_property(
module=Module.DO_EXP_AND_BIO,
prop=ConfigModuleProperty.EXCLUDE_TERMS))
elif associations_type == DataType.EXPR:
logger.info("Loading Expression associations from file")
self.expression_associations = AssociationSetFactory(
).create_from_assocs(assocs=GafParser(config=assoc_config).parse(
file=self._get_cached_file(cache_path=associations_cache_path,
file_source_url=associations_url),
skipheader=True),
ontology=self.expression_ontology)
self.expression_associations = self.remove_blacklisted_annotations(
association_set=self.expression_associations,
ontology=self.expression_ontology,
terms_blacklist=config.get_module_property(
module=Module.EXPRESSION,
prop=ConfigModuleProperty.EXCLUDE_TERMS))
def __init__(self, config=None):
"""
Arguments:
---------
config : a AssocParserConfig object
"""
if config is None:
config = AssocParserConfig()
self.config = config
self.report = Report()
def load_associations_from_file(self, associations_type: DataType,
associations_url: str,
associations_cache_path: str,
config: GenedescConfigParser) -> None:
"""load go associations from file
Args:
associations_type (DataType): the type of associations to set
associations_url (str): url to the association file
associations_cache_path (str): path to cache file for the associations
config (GenedescConfigParser): configuration object where to read properties
"""
logger.info("Loading associations from file")
assoc_config = AssocParserConfig(remove_double_prefixes=True,
paint=True)
assocs = AssociationSetFactory().create_from_assocs(
assocs=GafParser(config=assoc_config).parse(
file=self._get_cached_file(cache_path=associations_cache_path,
file_source_url=associations_url),
skipheader=True),
ontology=self.get_ontology(associations_type))
self.set_associations(associations_type=associations_type,
associations=assocs,
config=config)
def __init__(self):
# Needed to retain IBA annotations
config = AssocParserConfig()
config.paint = True
GafParser.__init__(self, config=config)