Option to save bed file.

create_metagene_profile.py

@@ -72,6 +72,7 @@ import sys
 import warnings
 from copy import deepcopy
 from pathlib import Path
+from shutil import copyfile
 from tempfile import NamedTemporaryFile
 from collections import defaultdict
 # from itertools import chain
@@ -310,6 +311,10 @@ def main():
         help="Path to a file containing one gene identifier per line.\n"
         "The metagene profile will only take into account those genes.\n"
         "This should not be used at the same time as option -c")
+    parser.add_argument(
+        "-k", "--keep_bed",
+        help="Path to a file where bed coordinates of the genes "
+        "listed whith option -g are to be saved.")
     parser.add_argument(
         "-c", "--bed_coordinates",
         help="Path to a file containing the coordinates of the features "
@@ -380,6 +385,9 @@ def main():
             args.bigwig_files, bed_filename,
             plot_filename=args.profile_plot, **extra_parameters)
         if args.gene_list:
+            if args.keep_bed:
+                copyfile(bed_filename, args.keep_bed)
+                print(f"bed coordinates saved in: {args.keep_bed}")
             os.unlink(bed_filename)
     return 0