--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cmFinder.py	Fri Dec 16 07:34:34 2016 -0500
@@ -0,0 +1,43 @@
+import os
+import sys
+from shutil import copyfile
+from os import system
+
+
+def sh(script):
+    system("bash -c '%s'" % script)
+
+
+model_tree_stk = sys.argv[1]
+cmfinder_fa = sys.argv[2]
+path = sys.argv[3]
+
+gapCmd = ""
+gapVal = ""
+if len(sys.argv) > 4:
+    gapCmd = sys.argv[4]
+    gapVal = sys.argv[5]
+
+
+cmd = " cp -f %s model.cmfinder.stk" % (model_tree_stk)
+sh(cmd)
+
+alifoldCmd = "%salifold.pl -file  %s" % (path, model_tree_stk)
+# alifoldCmd = "perl " + path + "/alifold.pl -file " + model_tree_stk
+sh(alifoldCmd)
+
+cmd_stk = "%smloc2stockholm.pl -file model.cmfinder.stk  -split_input yes --con_struct %s.alifold" % (path, model_tree_stk)
+# cmd_stk = "perl " + path + "/mloc2stockholm.pl -file model.cmfinder.stk  -split_input yes --con_struct " + model_tree_stk + ".alifold"
+sh(cmd_stk)
+
+model_tree_stk_sth = "model.cmfinder.stk.sth"
+x = "cat " + model_tree_stk_sth
+sh("mv model.cmfinder.stk.sth model.tree.stk")
+
+sh("cmfinder %s %s -a model.tree.stk %s output > model.cmfinder.stk" % (gapCmd, gapVal, cmfinder_fa))
+# sh("cmfinder " + gapCmd + " " + gapVal + " -a model.tree.stk" + " " + cmfinder_fa + " " + " output > model.cmfinder.stk")
+
+if os.path.isfile('output'):
+    sh("rm output")
+else:
+    copyfile("model.tree.stk", "model.cmfinder.stk")