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import sys
import json
import traceback
from argparse import ArgumentParser
from gn3.db_utils import database_connector
from gn3.responses.pcorrs_responses import OutputEncoder
from gn3.computations.partial_correlations import partial_correlations_with_target_db
def process_cli_arguments():
parser = ArgumentParser()
parser.add_argument(
"primary_trait",
help="The primary trait's full name",
type=str)
parser.add_argument(
"control_traits",
help="A comma-separated list of traits' full names",
type=str)
parser.add_argument(
"method",
help="The correlation method to use",
type=str)
parser.add_argument(
"target_database",
help="The target database to run the partial correlations against",
type=str)
parser.add_argument(
"--criteria",
help="Number of results to return",
type=int, default=500)
return parser.parse_args()
def cleanup_string(the_str):
return the_str.strip('"\t\n\r ')
def run_partial_corrs(args):
with database_connector() as conn:
try:
return partial_correlations_with_target_db(
conn, cleanup_string(args.primary_trait),
tuple(cleanup_string(args.control_traits).split(",")),
cleanup_string(args.method), args.criteria,
cleanup_string(args.target_database))
except Exception as exc:
print(traceback.format_exc(), file=sys.stderr)
return {
"status": "exception",
"message": traceback.format_exc()
}
def enter():
args = process_cli_arguments()
print(json.dumps(
run_partial_corrs(process_cli_arguments()),
cls = OutputEncoder))
if __name__ == "__main__":
enter()
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