--- a/dotplot_runner.py	Fri Jan 29 09:57:59 2016 -0500
+++ b/dotplot_runner.py	Fri Jan 29 10:00:21 2016 -0500
@@ -26,6 +26,13 @@
 import sys
 
 
+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]
+
+
 dirs_list = []
 for (dirpath, dirnames, filename) in os.walk(str(ins_path)):
     dirs_list.extend(dirnames)
@@ -37,12 +44,6 @@
     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)