added template code for calling identify interactions function with D…

…IALECT w/o implementation yet

src/dialect/__main__.py

@@ -10,6 +10,9 @@
     generate_bmr_and_counts,
 )  # TODO: export function from generate.py
 
+from dialect.utils.identify import (
+    identify_pairwise_interactions,
+)  # TODO: export function from identify.py
 
 configure_logging()
 
@@ -27,6 +30,13 @@ def main():
         os.makedirs(args.out, exist_ok=True)  # create output directory if nonexistent
         generate_bmr_and_counts(maf=args.maf, out=args.out, reference=args.reference)
 
+    elif args.command == "identify":
+        os.makedirs(args.out, exist_ok=True)  # create output directory if nonexistent
+        identify_pairwise_interactions(
+            maf=args.maf, bmr=args.bmr, out=args.out, k=args.top_k
+        )
+        pass
+
 
 if __name__ == "__main__":
     main()

src/dialect/utils/identify.py

@@ -0,0 +1,29 @@
+import logging
+
+from dialect.utils.helpers import *
+
+# ---------------------------------------------------------------------------- #
+#                               Helper Functions                               #
+# ---------------------------------------------------------------------------- #
+
+
+# ---------------------------------------------------------------------------- #
+#                                 Main Function                                #
+# ---------------------------------------------------------------------------- #
+def identify_pairwise_interactions(maf, bmr, out, k):
+    """
+    Main function to identify pairwise interactions between genetic drivers in tumors using DIALECT.
+    ! Not Yet Implemented
+
+    @param maf: Path to the input MAF (Mutation Annotation Format) file containing mutation data.
+    @param bmr: Path to the file with background mutation rate (BMR) distributions.
+    @param out: Directory where outputs will be saved.
+    @param k: Top k genes according to count of mutations will be used.
+    """
+    check_file_exists(maf)
+    check_file_exists(bmr)
+    if k <= 0:
+        logging.error("k must be a positive integer")
+        raise ValueError("k must be a positive integer")
+    logging.info("Identifying pairwise interactions using DIALECT")
+    logging.info("Functionality not yet implemented")