--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/domestication.py	Mon May 12 10:21:24 2025 +0000
@@ -0,0 +1,135 @@
+import os
+import argparse
+import pandas
+import zipfile
+import genedom
+import dnacauldron
+import proglog
+import shutil
+#proglog.notebook()
+from Bio.SeqRecord import SeqRecord
+from Bio.Seq import Seq
+from Bio import SeqIO
+
+def domestication(files_to_domestication, csv_file,file_name_mapping, use_file_names_as_id, 
+                               allow_edits, output_dom):
+
+    file_to_domestication = files_to_domestication.split(',')
+
+    records_to_domesticate = dnacauldron.biotools.load_records_from_files(
+        files=file_to_domestication,  
+        folder=None, 
+        use_file_names_as_ids=use_file_names_as_id
+    )
+
+    #refine the real record name dict
+    if isinstance(file_name_mapping, str):
+        file_name_mapping = dict(
+            item.split(":") for item in file_name_mapping.split(",")
+        )
+    real_names = {
+        os.path.splitext(os.path.basename(k))[0]: v.replace(".gb", "")
+        for k, v in file_name_mapping.items()
+    } 
+    updated_records = []
+    for record in records_to_domesticate:
+        original_id = record.id
+        if original_id in real_names:
+            new_id = real_names[original_id]
+            record.id = new_id
+        updated_records.append(record)
+    ########################################################
+    
+    df=pandas.read_csv(csv_file)
+    EMMA_PLUS = genedom.GoldenGateDomesticator.standard_from_spreadsheet(dataframe=df)
+    genedom.batch_domestication(
+    records=updated_records, 
+    standard=EMMA_PLUS, 
+    allow_edits=allow_edits,
+    target=output_dom)
+
+    # Check if any names were truncated:
+    if isinstance(output_dom, str) and output_dom.endswith(".zip"):
+        with zipfile.ZipFile(output_dom, "r") as zipf:
+            with zipf.open("order_ids.csv") as f:
+                order_ids = pandas.read_csv(f)
+    else:
+        order_ids = pandas.read_csv(os.path.join(output_dom, "order_ids.csv"))
+
+    any_truncated = False
+    for index, row in order_ids.iterrows():
+        if row["sequence"] != row["order_id"]:
+            any_truncated = True
+            print("Changed names:", end=" ")
+            print(" --> ".join(row))
+    if not any_truncated:
+        print("Part names were not truncated")
+        
+    #zip compressing
+    if os.path.isdir(output_dom):
+        zip_path = output_dom.rstrip("/\\") + ".zip"
+        shutil.make_archive(output_dom, 'zip', output_dom)
+        shutil.move(zip_path, output_dom)
+
+    return output_dom
+
+def methylation_protection(domestication_target, output_methprot):
+
+    if domestication_target.endswith(".zip"):
+        extracted_dir = "extracted_genbanks"
+        with zipfile.ZipFile(domestication_target, "r") as zipf:
+            os.makedirs(extracted_dir, exist_ok=True)
+            for member in zipf.namelist():
+                if member.startswith("domesticated_genbanks/") and member.endswith(".gb"):
+                    zipf.extract(member, path=extracted_dir)
+        gb_folder = os.path.join(extracted_dir, "domesticated_genbanks")
+    else:
+        gb_folder = os.path.join(domestication_target, "domesticated_genbanks")
+    
+    records_to_protect = dnacauldron.biotools.load_records_from_files(folder=gb_folder, use_file_names_as_ids=True)
+
+    for record in records_to_protect:
+        new_seqrecord = SeqRecord("TTC") + record + SeqRecord("GAA")  # these sequences are designed to prevent Dcm recognition site formation
+        new_seqrecord.id = record.id
+        new_seqrecord.name = record.name
+        new_seqrecord.annotations = {"molecule_type": "DNA"}
+
+        target_file = os.path.join(output_methprot, new_seqrecord.id + ".gb")
+        with open(target_file, "w") as output_handle:
+            SeqIO.write(new_seqrecord, output_handle, "genbank")
+
+def parse_command_line_args():
+    parser = argparse.ArgumentParser(description="Domestication")
+
+    parser.add_argument("--files_to_domestication", required=True, 
+                        help="List of GenBank files (Comma-separated)")
+    parser.add_argument("--csv_file", required=True, 
+                        help="csv file")
+    parser.add_argument('--file_name_mapping', type=str, 
+                        help='Mapping of Galaxy filenames to original filenames')
+    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("--allow_edits", type=lambda x: x.lower() == 'true', default=True, 
+                        help="Allow sequence edits")
+    parser.add_argument("--output_dom", required=True, 
+                        help="zip output for domestication results")
+    parser.add_argument("--output_methprot", required=False, 
+                        help="gb output for methylation protection")
+    parser.add_argument("--methylation_protection", type=lambda x: x.lower() == 'true', default=False,
+                        help="Enable methyl protection (true/false)")
+ 
+    return parser.parse_args()
+
+if __name__ == "__main__":
+    args = parse_command_line_args()
+
+    domestication(
+        args.files_to_domestication, args.csv_file,
+        args.file_name_mapping, args.use_file_names_as_id, 
+        args.allow_edits, args.output_dom
+    )
+
+    if args.methylation_protection:
+        methylation_protection(
+            args.output_dom, args.output_methprot
+        )