--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/toolshed_version/saint_wrapper.py	Tue Mar 15 16:06:51 2016 -0400
@@ -0,0 +1,107 @@
+#######################################################################################
+# Python-code: Dotplot Runner
+# Author: Adam L Borne
+# Contributers: Paul A Stewart, Brent Kuenzi
+#######################################################################################
+# This runs SAINTexpress found at http://saint-apms.sourceforge.net/Main.html in
+# galaxy. 
+#######################################################################################
+# 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
+
+
+inter_file = sys.argv[1]
+prey_file = sys.argv[2]
+bait_file = sys.argv[3]
+num_of_rep = sys.argv[4]
+vc_bool = sys.argv[5]
+vc_num = sys.argv[6]
+go_bool = sys.argv[7]
+go_file = sys.argv[8]
+output_file = sys.argv[9]
+ins_path = sys.argv[10]
+
+
+def first_run_check():
+    dirs_list = []
+    for (dirpath, dirnames, filename) in os.walk(str(ins_path)):
+        dirs_list.extend(dirnames)
+        break
+    if r"SAINTexpress_v3.6.1__2015-05-03" in dirs_list:
+        pass
+    else:
+        cmd = r"unzip " + str(ins_path) + "/SAINTexpress_v3.6.1__2015-05-03.zip -d " + str(ins_path)
+        os.system(cmd)
+        os.chdir(str(ins_path) + "/SAINTexpress_v3.6.1__2015-05-03")
+        cmd1 = r"make -j"
+        os.system(cmd1)
+
+
+def default_run(inter_file1, prey_file1, bait_file1, output_file1, num_of_rep1):
+    # Default is no virtual controls through purification and set replicates number.
+    cmd = (str(ins_path) + r"/SAINTexpress_v3.6.1__2015-05-03/bin/SAINTexpress-spc " + r"-R"
+           + str(num_of_rep1) + " " + str(inter_file1) + " " + str(prey_file1) +
+           " " + str(bait_file1))
+    os.system(cmd) 
+    open('list.txt')
+    os.rename('list.txt', str(output_file1)) 
+
+
+def with_L(inter_file1, prey_file1, bait_file1, output_file1, vc_num1, num_of_rep1):
+    # L is the flag for Virtual Controls through Purification.
+    cmd = (str(ins_path) + r"/SAINTexpress_v3.6.1__2015-05-03/bin/SAINTexpress-spc "+ r"-R"
+           + str(num_of_rep1) + " " + r"-L" + str(vc_num1) + " " + str(inter_file1) + " " +
+           str(prey_file1) + " " + str(bait_file1))
+    os.system(cmd) 
+    open('list.txt')
+    os.rename('list.txt', str(output_file1)) 
+
+
+def external_data_no_L(inter_file1, prey_file1, bait_file1, output_file1, go_file1, num_of_rep1):
+    # Uses external data in the GO file format and no Virtual Controls.
+    cmd = (str(ins_path) + r"/SAINTexpress_v3.6.1__2015-05-03/bin/SAINTexpress-spc "+ r"-R"
+           + str(num_of_rep1) + " " + str(inter_file1) + " " + str(prey_file1) + " " +
+           str(bait_file1) + " " + str(go_file1))
+    os.system(cmd) 
+    open('list.txt')
+    os.rename('list.txt', str(output_file1)) 
+
+
+def external_data_with_L(inter_file1, prey_file1, bait_file1, output_file1, go_file1, num_of_rep1, vc_num1):
+    # Uses external data in the GO file format and Virtual Controls.
+    cmd = (str(ins_path) + r"/SAINTexpress_v3.6.1__2015-05-03/bin/SAINTexpress-spc "+ r"-R"
+           + str(num_of_rep1) + " " + r"-L" + str(vc_num1) + " " + str(inter_file1) + " " +
+           str(prey_file1) + " " + str(bait_file1) + " " + str(go_file1))
+    os.system(cmd) 
+    open('list.txt')
+    os.rename('list.txt', str(output_file1)) 
+
+
+first_run_check()
+if vc_bool == "true":
+    if go_bool == "false":
+        with_L(inter_file, prey_file, bait_file, output_file, vc_num, num_of_rep)
+    elif go_bool == "true":
+        external_data_with_L(inter_file, prey_file, bait_file, output_file, go_file, num_of_rep, vc_num)
+elif vc_bool == "false":
+    if go_bool == "false":
+        default_run(inter_file, prey_file, bait_file, output_file, num_of_rep)
+    elif go_bool == "true":
+        external_data_no_L(inter_file, prey_file, bait_file, output_file, go_file, num_of_rep)