--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Bubblebeam_For_SAINT_wrapper.py	Thu Nov 19 11:15:43 2015 -0500
@@ -0,0 +1,49 @@
+import os 
+import sys
+import time
+
+
+list_file = sys.argv[1]
+prey_file = sys.argv[2]
+crapome = sys.argv[3]
+color = sys.argv[4]
+label = sys.argv[5]
+cutoff = sys.argv[6]
+mq_sc = sys.argv[7]
+inc_file = sys.argv[8]
+exc_file = sys.argv[9]
+output_file_name = sys.argv[10]
+bub_zoom_NSAF = sys.argv[11]
+bub_zoom_SAINT =sys.argv[12]
+bub_SAINT = sys.argv[13]
+bub_NSAF = sys.argv[14]
+ins_path =sys.argv[15]
+
+if crapome == "None":
+	crapome = "FALSE"
+
+
+if label == "false":
+	label = "FALSE"
+elif label == "true":
+	label = "TRUE" 
+
+cmd = r"Rscript "+ str(ins_path) + r"/bubbles_v9_NSAF_natural_log.R " + str(list_file) + r" " + str(prey_file) + r" " + str(crapome) + r" " + str(color) + r" " + str(label) + r" " + str(cutoff) + r" " + str(mq_sc) + r" " + str(inc_file) + r" " + str(exc_file)
+os.system(cmd)
+time.sleep(3)
+
+open('./output.txt')
+os.rename('output.txt', str(output_file_name))
+
+open('./bubble_zoom_NSAF.png')
+os.rename('bubble_zoom_NSAF.png', str(bub_zoom_NSAF))
+
+open('./bubble_zoom_SAINT.png')
+os.rename('bubble_zoom_SAINT.png', str(bub_zoom_SAINT))
+
+open('./bubble_SAINT.png')
+os.rename('bubble_SAINT.png', str(bub_SAINT))
+
+open('./bubble_NSAF.png')
+os.rename('bubble_NSAF.png', str(bub_NSAF))
+