--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/garli_wrapper.py	Fri Dec 02 17:07:27 2011 -0500
@@ -0,0 +1,48 @@
+#!/usr/bin/env python
+
+"""
+Runs Garli-2.0 on a sequence file.
+For use with Garli version 2.0
+
+usage: garli_wrapper.py config_file best_tree all_trees run_log screen_log out_conf
+"""
+import os, shutil, subprocess, sys
+
+def stop_err(msg):
+    sys.stderr.write("%s\n" % msg)
+    sys.exit()
+
+def __main__():
+    usage = "usage: %prog input conf btree balltree runlog scrlog outconf"
+    conf = sys.argv[1]
+    balltree = 'garli.best.all.tre'
+    btree = 'garli.best.tre'
+    runlog = 'garli.log00.log'
+    scrlog = 'garli.screen.log'
+    cmd = []
+    cmd.append('Garli-2.0')
+    cmd.append(os.path.basename(conf))
+    try:
+        proc = subprocess.Popen(args=cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+    except Exception, err:
+        sys.stderr.write("Error invoking command: \n%s\n\n%s\n" % (cmd, err))
+        sys.exit(1)
+    stdout, stderr = proc.communicate()
+    return_code = proc.returncode
+    if return_code:
+        sys.stdout.write(stdout)
+        sys.stderr.write(stderr)
+        sys.stderr.write("Return error code %i from command:\n" % return_code)
+        sys.stderr.write("%s\n" % cmd)
+    else:
+        sys.stdout.write(stdout)
+        sys.stdout.write(stderr)
+    try:
+        shutil.copyfile(os.path.basename(conf), 'garli.conf')
+        if not os.path.exists(balltree):
+            bat = open(balltree,'w')
+            bat.write('Only a single tree was found, so this file does not have any output')
+            bat.close()
+    except Exception, err:
+        sys.stderr.write("Error copying output files: \n%s\n" % err)
+if __name__=="__main__": __main__()