--- a/sculpt_sequences.py	Mon Jul 07 13:11:42 2025 +0000
+++ b/sculpt_sequences.py	Thu Jul 17 13:24:49 2025 +0000
@@ -1,4 +1,6 @@
 import argparse
+import json
+import sys
 import os
 import re
 import dnacauldron
@@ -175,16 +177,20 @@
     parser.add_argument("--outdir_unscul", required=True, help="unscul file dir")
     parser.add_argument("--use_file_names_as_id", type=lambda x: x.lower() == 'true', default=True,
                         help="Use file names as IDs (True/False)")
-    parser.add_argument("--avoid_patterns", required=True,
+    parser.add_argument("--avoid_patterns", required=False,
                         help="List of patterns to avoid (comma-separated, e.g., 'BsaI_site,BsmBI_site')")
-    parser.add_argument("--gc_constraints", required=True,
+    parser.add_argument("--gc_constraints", required=False,
                         help="GC content constraints as 'min;max;window' (space-separated, e.g., '0.3;0.7;100 0.1;0.3;100')")
-    parser.add_argument("--DnaOptimizationProblemClass", required=True,
+    parser.add_argument("--DnaOptimizationProblemClass", required=False,
                         help="the class to use for DnaOptimizationProblem")
-    parser.add_argument("--hairpin_constraints", required=True,
+    parser.add_argument("--hairpin_constraints", required=False,
                         help="Hairpin constraints as 'stem_size;window_size' (space-separated, e.g., '20;200 30;250')")
-    parser.add_argument("--kmer_size", required = True,
+    parser.add_argument("--kmer_size", required = False,
                         help="K-mer uniqueness size (e.g., '15')")
+    parser.add_argument("--json_params", required=False,
+                        help="JSON params for the tool")
+    parser.add_argument("--use_json_param", required=True,
+                            help="If use JSON as param source")
 
     return parser.parse_args()
 
@@ -206,19 +212,78 @@
     # 4. k-mer size: single value or list
     kmer_size = [int(k.strip()) for k in args.kmer_size.strip().split(',') if k.strip()] if args.kmer_size.strip() else []
     
-    return avoid_patterns, hairpin_constraints, gc_constraints, kmer_size
+    # 5. DnaOptimizationProblemClass (as string)
+    DnaOptimizationProblemClass = args.DnaOptimizationProblemClass if args.DnaOptimizationProblemClass else None
+    
+    return avoid_patterns, hairpin_constraints, gc_constraints, kmer_size, DnaOptimizationProblemClass
 
 
+def load_constraints_from_json(json_path):
+    with open(json_path, 'r') as f:
+        params = json.load(f)
+
+    def split_lines(val):
+        if isinstance(val, str):
+            return [line.strip() for line in val.strip().split('\n') if line.strip()]
+        return val
+
+    avoid_patterns = split_lines(params.get("avoid_patterns", ""))
+    hairpin_constraints = split_lines(params.get("hairpin_constraints", ""))
+    gc_constraints = split_lines(params.get("gc_constraints", ""))
+    kmer_size = [int(k.strip()) for k in str(params.get("kmer_size", "")).split(',') if k.strip()]
+    DnaOptimizationProblemClass = params.get("DnaOptimizationProblemClass", None)
+
+    return {
+        "avoid_patterns": avoid_patterns,
+        "hairpin_constraints": hairpin_constraints,
+        "gc_constraints": gc_constraints,
+        "kmer_size": kmer_size,
+        "DnaOptimizationProblemClass": DnaOptimizationProblemClass
+    }
 
 if __name__ == "__main__":
     args = parse_command_line_args()
 
-    avoid_patterns, hairpin_constraints, gc_constraints, kmer_size, = extract_constraints_from_args(args)
+    avoid_patterns, hairpin_constraints, gc_constraints, kmer_size, DnaOptimizationProblemClass = extract_constraints_from_args(args)
+
+    # Check if the flag --use_json_param is present and set to true
+    if "--use_json_param" in sys.argv:
+        use_json_index = sys.argv.index("--use_json_param") + 1
+        use_json = sys.argv[use_json_index].lower() == "true"
+    else:
+        use_json = False
+
+    # Now only check --json_params if use_json is True
+    if use_json:
+        if "--json_params" in sys.argv:
+            json_index = sys.argv.index("--json_params") + 1
+            json_file = sys.argv[json_index]
+            if json_file.lower() != "none":
+                json_constraints = load_constraints_from_json(json_file)
+                avoid_patterns = json_constraints["avoid_patterns"]
+                hairpin_constraints = json_constraints["hairpin_constraints"]
+                gc_constraints = json_constraints["gc_constraints"]
+                kmer_size = json_constraints["kmer_size"]
+                DnaOptimizationProblemClass = json_constraints["DnaOptimizationProblemClass"]
+
+    params = {
+        "files_to_sculpt": args.files_to_sculpt,
+        "file_name_mapping": args.file_name_mapping,
+        "outdir_unscul": args.outdir_unscul,
+        "outdir_scul": args.outdir_scul,
+        "use_file_names_as_id": args.use_file_names_as_id,
+        "avoid_patterns": avoid_patterns,
+        "hairpin_constraints": hairpin_constraints,
+        "gc_constraints": gc_constraints,
+        "kmer_size": kmer_size,
+        "DnaOptimizationProblemClass": DnaOptimizationProblemClass
+    }
+
 
     sculpt_sequances(
         args.files_to_sculpt, args.file_name_mapping,
         args.outdir_scul, args.outdir_unscul,
         args.use_file_names_as_id, avoid_patterns,
-        gc_constraints, args.DnaOptimizationProblemClass,
+        gc_constraints, DnaOptimizationProblemClass,
         kmer_size, hairpin_constraints
     )