# HG changeset patch
# User greg
# Date 1491587199 14400
# Node ID 962feb5f08184576c47b08ea0fb7efce4d38f6a0
# Parent  01c08c35d05146cf44a64c37267a39d419d7c3ac
Uploaded

diff -r 01c08c35d051 -r 962feb5f0818 gene_family_aligner.py
--- a/gene_family_aligner.py	Fri Apr 07 13:19:26 2017 -0400
+++ b/gene_family_aligner.py	Fri Apr 07 13:46:39 2017 -0400
@@ -50,5 +50,9 @@
 proc = subprocess.Popen(args=cmd, stderr=subprocess.PIPE, stdout=subprocess.PIPE, shell=True)
 rc = proc.wait()
 utils.check_execution_errors(rc, proc.stderr)
-utils.move_directory_files(OUTPUT_DIR, args.output_dir)
+if args.codon_alignments is None:
+    src_output_dir = OUTPUT_DIR
+else:
+    src_output_dir = os.path.join(OUTPUT_DIR, 'orthogroups_aln')
+utils.move_directory_files(src_output_dir, args.output_dir)
 utils.write_html_output(args.output, 'Aligned gene family sequences', args.output_dir)