Add --with_sequence_edits option to script

The optionannotates the Genbank file with edits.

scripts/dnachisel

@@ -4,17 +4,20 @@
 DNA Chisel Command Line Interface
 
 Usage:
-  dnachisel <source> <target> [--circular] [--mute]
+  dnachisel <source> <target> [--circular] [--mute] [--with_sequence_edits]
 
 Where ``source`` is a fasta or Genbank file, and target can be one of:
 - A folder name or a zip name (extension .zip). In this case a complete report
   along with the sequence will be generated.
+- A Genbank file. In this case, only the optimized sequence file is created.
+  The with_sequence_edits option specifies that edits are also annotated in the
+  Genbank file. Note that the filename must end with '.gb'.
 
 Note: this CLI will be developed on a per-request basis, so don't hesitate to
 ask for more handles and options on Github
 (https://github.com/Edinburgh-Genome-Foundry/DnaChisel/issues)
 
-Example to output the result to a genbank (filename must end with '.gb'):
+Example to output the result to a genbank:
 
 >>> dnachisel annotated_record.gb optimized_record.gb
 
@@ -57,11 +60,15 @@ if __name__ == "__main__":
     )
 
     if target.lower().endswith(".gb"):  # save genbank
+        if params["--with_sequence_edits"]:
+            annotate_edits=True
+        else:
+            annotate_edits=False
         verbose_print("Resolving Constraints...")
         problem.resolve_constraints()
         verbose_print("Optimizing...")
         problem.optimize()
-        problem.to_record(filepath=target, with_sequence_edits=True)
+        problem.to_record(filepath=target, with_sequence_edits=annotate_edits)
 
     else:  # save into zip or folder
         project_name = os.path.basename(source)