def load_data(organism, conf_parser: GenedescConfigParser):
logger = logging.getLogger("WB Gene Description Pipeline - Data loader")
sister_df = None
df_agr = None
organisms_info = conf_parser.get_wb_organisms_info()
df = WBDataManager(species=organism, do_relations=None, go_relations=["subClassOf", "BFO:0000050"],
config=conf_parser)
if organism == "c_elegans":
df_agr = DataManager(go_relations=["subClassOf", "BFO:0000050"], do_relations=None)
df_agr.load_ontology_from_file(ontology_type=DataType.GO,
ontology_url=conf_parser.get_wb_human_orthologs_go_ontology(),
ontology_cache_path=os.path.join(conf_parser.get_cache_dir(),
"wormbase_agr_human", "go_ontology.obo"),
config=conf_parser)
df_agr.load_associations_from_file(associations_type=DataType.GO,
associations_url=conf_parser.get_wb_human_orthologs_go_associations(),
associations_cache_path=os.path.join(
conf_parser.get_cache_dir(), "wormbase_agr_human", "go_assoc.daf.gz"),
config=conf_parser)
if "main_sister_species" in organisms_info[organism] and organisms_info[organism]["main_sister_species"]:
sister_df = WBDataManager(species=organisms_info[organism]["main_sister_species"],
do_relations=None, go_relations=["subClassOf", "BFO:0000050"], config=conf_parser)
logger.info("Loading GO data for sister species")
sister_df.load_ontology_from_file(ontology_type=DataType.GO, ontology_url=sister_df.go_ontology_url,
ontology_cache_path=sister_df.go_ontology_cache_path,
config=conf_parser)
sister_df.load_associations_from_file(associations_type=DataType.GO,
associations_url=sister_df.go_associations_url,
associations_cache_path=sister_df.go_associations_cache_path,
config=conf_parser)
logger.info("Loading all data for main species")
df.load_all_data_from_file()
return df, sister_df, df_agr
class TestGOModule(unittest.TestCase):
def setUp(self):
logging.basicConfig(
filename=None,
level="ERROR",
format='%(asctime)s - %(name)s - %(levelname)s: %(message)s')
logger.info("Starting DataManager tests")
self.this_dir = os.path.split(__file__)[0]
self.conf_parser = GenedescConfigParser(
os.path.join(self.this_dir, "config_test_wb.yml"))
self.df = WBDataManager(do_relations=None,
go_relations=["subClassOf", "BFO:0000050"],
config=self.conf_parser,
species="c_elegans")
def test_load_expression_data(self):
self.df.load_ontology_from_file(
ontology_type=DataType.EXPR,
ontology_url="file://" +
os.path.join(self.this_dir, "data", "anatomy_gd_test.obo"),
ontology_cache_path=os.path.join(self.this_dir, "cache",
"anatomy_gd_test.obo"),
config=self.conf_parser)
self.df.load_associations_from_file(
associations_type=DataType.EXPR,
associations_url="file://" +
os.path.join(self.this_dir, "data", "anatomy_gd_test.wb"),
associations_cache_path=os.path.join(self.this_dir, "cache",
"anatomy_gd_test.wb"),
config=self.conf_parser)
self.assertTrue(self.df.expression_ontology is not None)
self.assertTrue('WB:WBGene00000001' in
self.df.expression_associations.associations_by_subj)
for annotations in self.df.expression_associations.associations_by_subj.values(
):
for annotation in annotations:
self.assertTrue(annotation["evidence"]["type"] == "IDA")
class TestGOModule(unittest.TestCase):
def setUp(self):
logging.basicConfig(
filename=None,
level="ERROR",
format='%(asctime)s - %(name)s - %(levelname)s: %(message)s')
logger.info("Starting DataManager tests")
self.this_dir = os.path.split(__file__)[0]
self.conf_parser = GenedescConfigParser(
os.path.join(self.this_dir, "config_test_wb.yml"))
self.df = WBDataManager(do_relations=None,
go_relations=["subClassOf", "BFO:0000050"],
config=self.conf_parser,
species="c_elegans")
def test_load_expression_data(self):
self.df.load_ontology_from_file(
ontology_type=DataType.EXPR,
ontology_url="file://" +
os.path.join(self.this_dir, "data", "anatomy_gd_test.obo"),
ontology_cache_path=os.path.join(self.this_dir, "cache",
"anatomy_gd_test.obo"),
config=self.conf_parser)
self.df.load_associations_from_file(
associations_type=DataType.EXPR,
associations_url="file://" +
os.path.join(self.this_dir, "data", "anatomy_gd_test.wb"),
associations_cache_path=os.path.join(self.this_dir, "cache",
"anatomy_gd_test.wb"),
config=self.conf_parser)
self.assertTrue(self.df.expression_ontology is not None)
self.assertTrue('WB:WBGene00000001' in
self.df.expression_associations.associations_by_subj)
for annotations in self.df.expression_associations.associations_by_subj.values(
):
for annotation in annotations:
self.assertTrue(annotation["evidence"]["type"] == "IDA")
def test_load_disease_data(self):
self.df.load_ontology_from_file(
ontology_type=DataType.DO,
ontology_url="file://" +
os.path.join(self.this_dir, os.pardir, "data", "doid.obo"),
ontology_cache_path=os.path.join(self.this_dir, "cache",
"doid.obo"),
config=self.conf_parser)
self.df.load_associations_from_file(
associations_type=DataType.DO,
associations_url=self.df.do_associations_url,
associations_cache_path=os.path.join(self.this_dir, "cache",
"do_ann.gaf"),
association_additional_cache_path=os.path.join(
self.this_dir, "cache", "do_ann.daf"),
association_additional_url=self.df.do_associations_new_url,
config=self.conf_parser)
self.assertTrue(
any([
annotation["evidence"]["type"] == "IMP" for annotations in
self.df.expression_associations.associations_by_subj.values()
for annotation in annotations
]))
def test_load_orthology_data(self):
df = WBDataManager(do_relations=None,
go_relations=["subClassOf", "BFO:0000050"],
config=self.conf_parser,
species="c_remanei")
df.load_orthology_from_file()
self.assertTrue(len(df.orthologs) > 0)
def test_load_protein_domain_data(self):
df = WBDataManager(do_relations=None,
go_relations=["subClassOf", "BFO:0000050"],
config=self.conf_parser,
species="c_elegans")
df.load_protein_domain_information()
self.assertTrue(True)
def test_expression_the_cell_renaming_to_widely(self):
self.df.load_ontology_from_file(
ontology_type=DataType.EXPR,
ontology_url=self.df.expression_ontology_url,
ontology_cache_path=self.df.expression_ontology_cache_path,
config=self.conf_parser)
self.df.load_associations_from_file(
associations_type=DataType.EXPR,
associations_url=self.df.expression_associations_url,
associations_cache_path=self.df.expression_associations_cache_path,
config=self.conf_parser)
gene_desc = GeneDescription(gene_id="WB:WBGene00007352",
gene_name="cdc-48.1",
add_gene_name=False)
expr_sentence_generator = OntologySentenceGenerator(
gene_id=gene_desc.gene_id,
module=Module.EXPRESSION,
data_manager=self.df,
config=self.conf_parser)
expression_module_sentences = expr_sentence_generator.get_module_sentences(
config=self.conf_parser,
aspect='A',
qualifier="Verified",
merge_groups_with_same_prefix=True,
keep_only_best_group=False)
gene_desc.set_or_extend_module_description_and_final_stats(
module_sentences=expression_module_sentences,
module=Module.EXPRESSION)
self.assertTrue("is expressed widely" in gene_desc.description)