Commit 8a1a6202 authored by Martin Preusse's avatar Martin Preusse
Browse files

add GOA

parent 1af4efd2
Pipeline #914 passed with stage
in 55 seconds
......@@ -8,8 +8,8 @@ from datetime import datetime
from multiprocessing import Pool
from graphpipeline.parser import ParserSet
from biomedgraph.datasources import OboFoundry
from biomedgraph.parser import OboFoundryParser
from biomedgraph.datasources import OboFoundry, GeneOntology
from biomedgraph.parser import OboFoundryParser, GeneOntologyAssociationParser
logging.basicConfig(level=logging.INFO)
logging.getLogger('biomedgraph').setLevel(level=logging.DEBUG)
......@@ -54,10 +54,13 @@ if __name__ == '__main__':
sleep(sleep_time)
obofoundry = OboFoundry(ROOT_DIR)
geneontology = GeneOntology(ROOT_DIR)
obofoundry.pull_latest_from_remote(REMOTE_URL, 'ftp', user=REMOTE_USER, password=REMOTE_PASSWORD)
geneontology.pull_latest_from_remote(REMOTE_URL, 'ftp', user=REMOTE_USER, password=REMOTE_PASSWORD, argument_check=False)
obofoundry_local = obofoundry.latest_local_instance()
geneontology_local = geneontology.latest_local_instance(taxids=['9606', '10090'])
parserset = ParserSet()
......@@ -67,6 +70,14 @@ if __name__ == '__main__':
go_parser.ontology_name = ontology_abbreviation
parserset.add(go_parser)
for taxid in ['9606', '10090']:
log.info(f'Run for {taxid}')
go_annotation_parser = GeneOntologyAssociationParser()
go_annotation_parser.datasource_instances.append(geneontology_local)
go_annotation_parser.taxid = taxid
parserset.add(go_annotation_parser)
output_path = os.path.join(ROOT_DIR, 'run_serial')
if not os.path.exists(output_path):
os.mkdir(output_path)
......
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