refactor: remove command line interface

Author: JoshLoecker

main/como/proteomics_gen.py

@@ -218,80 +218,5 @@ async def proteomics_gen(
         to_bool_context(context_name, group_ratio, hi_group_ratio, groups)
 
 
-def _main():
-    parser = argparse.ArgumentParser(
-        prog="proteomics_gen.py",
-        description="Description goes here",
-        epilog="For additional help, please post questions/issues in the MADRID GitHub repo at "
-        "https://github.com/HelikarLab/MADRID or email babessell@gmail.com",
-    )
-    parser.add_argument(
-        "-c",
-        "--config-file",
-        type=str,
-        required=True,
-        dest="config_file",
-        help="The configuration file for proteomics",
-    )
-    parser.add_argument(
-        "-r",
-        "--replicate-ratio",
-        type=float,
-        required=False,
-        default=0.5,
-        dest="rep_ratio",
-        help="Ratio of replicates required for a gene to be considered active in that group",
-    )
-    parser.add_argument(
-        "-b",
-        "--batch-ratio",
-        type=float,
-        required=False,
-        default=0.5,
-        dest="group_ratio",
-        help="Ratio of groups (batches or studies) required for a gene to be considered active in a context",
-    )
-    parser.add_argument(
-        "-hr",
-        "--high-replicate-ratio",
-        type=float,
-        required=False,
-        default=0.5,
-        dest="hi_rep_ratio",
-        help="Ratio of replicates required for a gene to be considered high-confidence in that group",
-    )
-    parser.add_argument(
-        "-hb",
-        "--high-batch-ratio",
-        type=float,
-        required=False,
-        default=0.5,
-        dest="hi_group_ratio",
-        help="Ratio of groups (batches or studies) required for a gene to be considered high-confidence in a context",
-    )
-
-    parser.add_argument(
-        "-q",
-        "--quantile",
-        type=int,
-        required=False,
-        default=25,
-        dest="quantile",
-        help="The quantile of genes to accept. This should be an integer from 0% (no proteins pass) "
-        "to 100% (all proteins pass).",
-    )
-    args = parser.parse_args()
-    asyncio.run(
-        proteomics_gen(
-            args.config_file,
-            args.rep_ratio,
-            args.group_ratio,
-            args.hi_rep_ratio,
-            args.hi_group_ratio,
-            args.quantile,
         )
     )
-
-
-if __name__ == "__main__":
-    _main()