--- a/gene_family_integrator.py	Fri May 05 09:33:00 2017 -0400
+++ b/gene_family_integrator.py	Fri May 05 09:33:06 2017 -0400
@@ -1,19 +1,18 @@
 #!/usr/bin/env python
 import argparse
 import os
-import subprocess
 
 import utils
 
 OUTPUT_DIR = 'integratedGeneFamilies_dir'
 
 parser = argparse.ArgumentParser()
-parser.add_argument('--orthogroup_faa', dest='orthogroup_faa', help="Directory of input fasta datasets")
+parser.add_argument('--orthogroup_faa', dest='orthogroup_faa', help='Directory of input fasta datasets')
 parser.add_argument('--scaffold', dest='scaffold', help='Orthogroups or gene families proteins scaffold')
 parser.add_argument('--method', dest='method', help='Protein clustering method')
 parser.add_argument('--orthogroup_fna', dest='orthogroup_fna', default=None, help='Use correspong coding sequences')
-parser.add_argument('--output', dest='output', help="Output dataset")
-parser.add_argument('--output_dir', dest='output_dir', help="Output dataset file_path directory")
+parser.add_argument('--output', dest='output', help='Output dataset')
+parser.add_argument('--output_dir', dest='output_dir', help='Output dataset file_path directory')
 
 args = parser.parse_args()
 
@@ -24,9 +23,10 @@
 cmd += ' --method %s' % args.method
 if args.orthogroup_fna is not None:
     cmd += ' --orthogroup_fna'
+
 # Run the command.
-proc = subprocess.Popen(args=cmd, stderr=subprocess.PIPE, stdout=subprocess.PIPE, shell=True)
-rc = proc.wait()
-utils.check_execution_errors(rc, proc.stderr)
+utils.run_command(cmd)
+
+# Handle outputs.
 utils.move_directory_files(os.path.join(OUTPUT_DIR, 'orthogroups_fasta'), args.output_dir)
 utils.write_html_output(args.output, 'Integrated gene family sequences', args.output_dir)