def get(self, object_category, taxon):
"""
Bulk download of gene associations.
NOTE: this route has a limiter on it, you may be restricted in the number of downloads per hour. Use carefully.
"""
assocs = bulk_fetch(subject_category='gene',
object_category=object_category,
taxon=taxon)
return assocs
def main():
"""
Wrapper for OGR
"""
parser = argparse.ArgumentParser(
description='Command line interface to python-ontobio.golr library'
"""
Provides command line interface onto the ontobio.golr python library, a high level
abstraction layer over Monarch and GO solr indices.
""",
formatter_class=argparse.RawTextHelpFormatter)
parser.add_argument('-o', '--outfile', type=str, required=False,
help='Path to output file')
parser.add_argument('-C', '--category', nargs=2, type=str, required=True,
help='Category pair. E.g. disease gene')
parser.add_argument('-s', '--species', type=str, required=True,
help='NCBITaxon ID')
parser.add_argument('-S', '--slim', nargs='*', type=str, required=False,
help='Slim IDs')
parser.add_argument('-L', '--limit', type=int, default=100000, required=False,
help='Limit on number of rows')
parser.add_argument('-u', '--url', type=str, required=False,
help='Solr URL. E.g. http://localhost:8983/solr/golr')
parser.add_argument('-v', '--verbosity', default=0, action='count',
help='Increase output verbosity')
parser.add_argument('ids',nargs='*')
args = parser.parse_args()
if args.verbosity >= 2:
logging.basicConfig(level=logging.DEBUG)
elif args.verbosity == 1:
logging.basicConfig(level=logging.INFO)
else:
logging.basicConfig(level=logging.WARNING)
logging.info("Welcome!")
[subject_category, object_category] = args.category
assocs = bulk_fetch(subject_category,
object_category,
args.species,
rows=args.limit,
slim=args.slim,
url=args.url)
for a in assocs:
print("{}\t{}\t{}".format(a['subject'],
a['relation'],
";".join(a['objects'])))
def get(self, taxon1, taxon2):
"""
Bulk download of orthologs
"""
assocs = bulk_fetch(subject_category='gene',
object_category='gene',
relation=ortholog_rel,
taxon=taxon1,
object_taxon=taxon2,
user_agent=USER_AGENT)
return assocs
def get(self, object_category, taxon):
"""
Bulk download of disease associations.
NOTE: this route has a limiter on it, you may be restricted in the number of downloads per hour. Use carefully.
"""
# TODO temporary workaround
if taxon == "NCBITaxon:9606":
taxon = None
assocs = bulk_fetch(subject_category='disease',
object_category=object_category,
taxon=taxon)
return assocs
def get(self, object_category, taxon):
"""
Bulk download of disease associations.
NOTE: this route has a limiter on it, you may be restricted in the number of downloads per hour. Use carefully.
"""
# TODO temporary workaround for # https://github.com/monarch-initiative/monarch-app/issues/1448
if taxon == "NCBITaxon:9606":
taxon = None
assocs = bulk_fetch(subject_category='disease',
object_category=object_category,
taxon=taxon,
user_agent=USER_AGENT)
return assocs
def bulk_fetch_cached(**args):
logging.info("Fetching assocs from store (will be cached)")
return bulk_fetch(**args)
