--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dotplot_runner.py	Fri Jan 29 09:57:31 2016 -0500
@@ -0,0 +1,57 @@
+#######################################################################################
+# Python-code: Dotplot Runner
+# Author: Adam L Borne
+# Contributers: Paul A Stewart, Brent Kuenzi
+#######################################################################################
+# This script runs the dotplot program found at http://prohitstools.mshri.on.ca/.
+#######################################################################################
+# Copyright (C)  Adam Borne.
+# Permission is granted to copy, distribute and/or modify this document
+# under the terms of the GNU Free Documentation License, Version 1.3
+# or any later version published by the Free Software Foundation;
+# with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts.
+# A copy of the license is included in the section entitled "GNU
+# Free Documentation License".
+#######################################################################################
+## REQUIRED INPUT ##
+
+# 1) list_file: SaintExpress output file.
+# 2) FDR1: Primary false discovery rate. (default = 0.01)
+# 3) FDR2: Secondary false discovery rate. (default = 0.025)
+# 4) spec_max: Maximum spectral count. (default = 50)
+#######################################################################################
+
+
+import os
+import sys
+
+
+dirs_list = []
+for (dirpath, dirnames, filename) in os.walk(str(ins_path)):
+    dirs_list.extend(dirnames)
+    break
+if r"Dotplot_Release" in dirs_list:
+    pass
+else:
+    cmd = r"tar -xvf /Dotplot_Release.tar.gz " + str(ins_path) + "/Dotplot_Release.tar.gz" 
+    os.system(cmd)
+
+
+FDR1 = sys.argv[2]
+FDR2 = sys.argv[3]
+spec_max = sys.argv[4]
+os.rename(sys.argv[1], "saint_input.txt")
+ins_path = sys.argv[9]
+
+cmd = (str(ins_path) + r"Dotplot_Release/dotplot.bash -f saint_input.txt" + r" -c b -s " + str(FDR1) +
+    r" -t " + str(FDR2) + " -m " + str(spec_max))
+os.system(cmd)
+
+cmd1 = r"cp -a ./Output_saint_input/. ."
+os.system(cmd1)
+
+os.rename("saint_input.txt", str(sys.argv[1]))
+os.rename('dotplot.pdf', str(sys.argv[5]))
+os.rename('bait2bait.pdf', str(sys.argv[6]))
+os.rename('estimated.pdf', str(sys.argv[7]))
+os.rename('stats.pdf', str(sys.argv[8]))