repare 0.0.2__py3-none-any.whl

repare/__init__.py

@@ -0,0 +1,4 @@
+from .pedigree import Pedigree
+from .pedigree_reconstructor import PedigreeReconstructor
+
+__all__ = ["Pedigree", "PedigreeReconstructor"]

repare/main.py

@@ -0,0 +1,64 @@
+import argparse
+import logging
+import os
+
+from tqdm.contrib.logging import logging_redirect_tqdm
+
+from repare.pedigree_reconstructor import PedigreeReconstructor
+
+
+def parse_arguments():
+    parser = argparse.ArgumentParser(description="Build and analyze pedigrees.")
+    parser.add_argument("-n", "--nodes", type=str, required=True, help="Path to the nodes CSV file.")
+    parser.add_argument("-r", "--relations", type=str, required=True, help="Path to the relations CSV file.")
+    parser.add_argument(
+        "-o",
+        "--output",
+        type=str,
+        default=".",
+        help="Directory to save the output files. Defaults to the current directory.",
+    )
+    parser.add_argument(
+        "-m",
+        "--max_candidate_pedigrees",
+        type=int,
+        default=1000,
+        help="Number of pedigrees to keep after each iteration. Default is 100.",
+    )
+    parser.add_argument(
+        "-e", "--epsilon", type=float, default=0.2, help="Epsilon value for the simulation. Default is 0.2."
+    )
+    parser.add_argument("-s", "--seed", type=int, default=42, help="Random seed for reproducibility. Default is 42.")
+    parser.add_argument("-d", "--do_not_plot", action="store_false", help="Do not plot reconstructed pedigree(s).")
+    parser.add_argument(
+        "-w", "--write_alternates", action="store_true", help="Write outputs of alternate pedigrees to disk."
+    )
+    parser.add_argument("-v", "--verbose", action="store_true", help="Enable verbose output (INFO-level logging).")
+    return parser.parse_args()
+
+
+def main():
+    args = parse_arguments()
+    logging_level = logging.INFO if args.verbose else logging.WARNING
+    logging.basicConfig(level=logging_level, format="%(levelname)s - %(message)s")
+
+    output_dir = args.output
+    if not os.path.exists(output_dir):
+        os.makedirs(output_dir, exist_ok=True)
+
+    with logging_redirect_tqdm():
+        pedigree_reconstructor = PedigreeReconstructor(
+            relations_path=args.relations,
+            nodes_path=args.nodes,
+            outputs_dir=output_dir,
+            max_candidate_pedigrees=args.max_candidate_pedigrees,
+            epsilon=args.epsilon,
+            plot=args.do_not_plot,
+            write_alternate_pedigrees=args.write_alternates,
+            random_seed=args.seed,
+        )
+        pedigree_reconstructor.find_best_pedigree()
+
+
+if __name__ == "__main__":
+    main()