diff options
| -rw-r--r-- | gn3/commands.py | 3 | ||||
| -rw-r--r-- | scripts/partial_correlations.py | 10 |
2 files changed, 10 insertions, 3 deletions
diff --git a/gn3/commands.py b/gn3/commands.py index 3598e2f..697db42 100644 --- a/gn3/commands.py +++ b/gn3/commands.py @@ -77,7 +77,8 @@ def compose_pcorrs_command_for_database( criteria: int = 500) -> Tuple[str, ...]: """Build command for partial correlations against an entire dataset.""" return prefix_cmd + ( - "against-db", f"{target_database}", f"--criteria={criteria}") + "against-db", f"{target_database}", "--criteria", str(criteria), + "--textdir", current_app.config["TEXTDIR"]) def compose_pcorrs_command( diff --git a/scripts/partial_correlations.py b/scripts/partial_correlations.py index aab8f08..f47d9d6 100644 --- a/scripts/partial_correlations.py +++ b/scripts/partial_correlations.py @@ -1,7 +1,7 @@ """Script to run partial correlations""" - import json import traceback +from pathlib import Path from argparse import ArgumentParser from gn3.db_utils import database_connection @@ -48,7 +48,8 @@ def pcorrs_against_traits(dbconn, args): def pcorrs_against_db(dbconn, args): """Run partial correlations agaist the entire dataset provided.""" - return partial_correlations_with_target_db(dbconn, **process_db_args(args)) + return partial_correlations_with_target_db( + dbconn, **process_db_args(args), textdir=args.textdir) def run_pcorrs(dbconn, args): """Run the selected partial correlations function.""" @@ -89,6 +90,11 @@ def against_db_parser(parent_parser): "--criteria", help="Number of results to return", type=int, default=500) + parser.add_argument( + "--textdir", + help="Directory to read text files from", + type=Path, + default=Path("/tmp/")) parser.set_defaults(func=pcorrs_against_db) return parent_parser |