--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/saint_wrapper.py	Tue Nov 17 13:32:05 2015 -0500
@@ -0,0 +1,63 @@
+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():
+	os.chdir(ins_path)
+	dirs_list = []
+	for (dirpath, dirnames, filename) in os.walk("./"):
+		dirs_list.extend(dirnames)
+		break
+	if r"SAINTexpress_v3.6.1__2015-05-03" in dirs_list:
+		pass
+	else: 
+		cmd = r"unzip SAINTexpress_v3.6.1__2015-05-03.zip"
+		os.system(cmd)
+		os.chdir("./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):
+	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):
+	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):
+	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):
+	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)) 
+
+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)