--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gene_family_integrator.py	Thu Apr 06 13:34:02 2017 -0400
@@ -0,0 +1,31 @@
+#!/usr/bin/env python
+import argparse
+import subprocess
+
+import utils.py
+
+OUTPUT_DIR = 'integratedGeneFamilies_dir'
+
+parser = argparse.ArgumentParser()
+parser.add_argument('--orthogroup_faa', dest='orthogroup_faa', help="Directory of input fasta datasets")
+parser.add_argument('--scaffold', dest='scaffold', default='mode', 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")
+
+args = parser.parse_args()
+
+# Build the command line.
+cmd = 'GeneFamilyIntegrator'
+cmd += ' --orthogroup_faa %s' % args.orthogroup_fasta
+cmd += ' --scaffold %s' % args.scaffold
+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.move_directory_files(OUTPUT_DIR, args.output_dir)
+utils.write_html_output(args.output, 'Integrated gene family sequences', args.output_dir)