--- a/gene_family_classifier.py	Mon Feb 27 10:56:03 2017 -0500
+++ b/gene_family_classifier.py	Mon Feb 27 11:07:43 2017 -0500
@@ -25,8 +25,11 @@
 parser.add_argument('--save_hmmscan_log', dest='save_hmmscan_log', default=None, help='Flag to save the hmmscan log')
 parser.add_argument('--hmmscan_log', dest='hmmscan_log', default=None, help='hmmscan log file')
 parser.add_argument('--output_ptortho', dest='output_ptortho', default=None, help='Output for orthogroups')
+parser.add_argument('--output_ptortho_dir', dest='output_ptortho_dir', default=None, help='output_ptortho.files_path')
 parser.add_argument('--output_ptorthocs', dest='output_ptorthocs', default=None, help='Output for orthogroups with corresponding coding sequences')
+parser.add_argument('--output_ptorthocs_dir', dest='output_ptorthocs_dir', default=None, help='output_ptorthocs.files_path')
 parser.add_argument('--output_ptsco', dest='output_ptsco', default=None, help='Output for single copy orthogroups')
+parser.add_argument('--output_ptsco_dir', dest='output_ptsco_dir', default=None, help='output_ptsco.files_path')
 
 args = parser.parse_args()
 
@@ -139,18 +142,19 @@
 if create_ortho_sequences:
     if create_corresponding_coding_sequences:
         out_file = args.output_ptorthocs
+        orthogroups_fasta_dest_dir = args.output_ptorthocs_dir
         title = 'Orthogroups with corresponding coding sequences'
     else:
         out_file = args.output_ptortho
+        orthogroups_fasta_dest_dir = args.output_ptortho_dir
         title = 'Orthogroups'
     orthogroups_fasta_src_dir = os.path.join(OUTPUT_DIR, 'orthogroups_fasta')
-    orthogroups_fasta_dest_dir = out_file.files_path
     move_directory_files(orthogroups_fasta_src_dir, orthogroups_fasta_src_dir)
     write_html_output(out_file, title, orthogroups_fasta_dest_dir)
 # Handle single copy orthogroup outputs.
 if args.output_ptsco is not None:
     single_copy_fasta_src_dir = os.path.join(OUTPUT_DIR, 'single_copy_fasta')
-    single_copy_fasta_dest_dir = args.output_ptsco.files_path
+    single_copy_fasta_dest_dir = args.output_ptsco_dir
     title = 'Single copy orthogroups'
     move_directory_files(single_copy_fasta_src_dir, single_copy_fasta_dest_dir)
     write_html_output(args.output_ptsco, title, single_copy_fasta_dest_dir)