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| author | Frederick Muriuki Muriithi | 2022-06-20 11:17:11 +0300 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2022-06-20 11:17:11 +0300 |
| commit | 7f66bb029322a06b52359abf8836e158afaa6755 (patch) | |
| tree | 573566c634552d345f166eb7cdf4834c43b434a4 | |
| parent | 4d0d77ad005f0832a14c4bc050fad77ec727d476 (diff) | |
| download | genenetwork3-7f66bb029322a06b52359abf8836e158afaa6755.tar.gz | |
Restrict partial correlation method choices
- Have "Pearson's r" and "Spearman's rho" as the only valid choices for the
partial correlations
| -rw-r--r-- | gn3/commands.py | 2 | ||||
| -rw-r--r-- | scripts/partial_correlations.py | 3 |
2 files changed, 3 insertions, 2 deletions
diff --git a/gn3/commands.py b/gn3/commands.py index 41418b0..0a74b7d 100644 --- a/gn3/commands.py +++ b/gn3/commands.py @@ -69,7 +69,7 @@ def compose_pcorrs_command( """Compose the command to run partias correlations""" prefix_cmd = ( f"{sys.executable}", "-m", "scripts.partial_correlations", - primary_trait, ",".join(control_traits), f'"{method}"') + primary_trait, ",".join(control_traits), method) if ( kwargs.get("target_database") is not None and kwargs.get("target_traits") is None): diff --git a/scripts/partial_correlations.py b/scripts/partial_correlations.py index de364dc..d28a17a 100644 --- a/scripts/partial_correlations.py +++ b/scripts/partial_correlations.py @@ -106,7 +106,8 @@ def process_cli_arguments(): parser.add_argument( "method", help="The correlation method to use", - type=str) + type=str, + choices=("Pearson's r", "Spearman's rho")) against_db_parser(against_traits_parser( parser.add_subparsers( title="subcommands", |