# HG changeset patch
# User bornea
# Date 1447948135 18000
# Node ID 9617d82034c6f290db283c2217ad2568fd9485cd
# Parent  318185488e49d4270bb3e349c362c38cfd983d55
Uploaded

diff -r 318185488e49 -r 9617d82034c6 Bubblebeam_For_SAINT_wrapper.py
--- a/Bubblebeam_For_SAINT_wrapper.py	Thu Nov 19 10:43:31 2015 -0500
+++ b/Bubblebeam_For_SAINT_wrapper.py	Thu Nov 19 10:48:55 2015 -0500
@@ -10,12 +10,14 @@
 label = sys.argv[5]
 cutoff = sys.argv[6]
 mq_sc = sys.argv[7]
-output_file_name = sys.argv[8]
-bub_zoom_NSAF = sys.argv[9]
-bub_zoom_SAINT =sys.argv[10]
-bub_SAINT = sys.argv[11]
-bub_NSAF = sys.argv[12]
-ins_path =sys.argv[13]
+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"
@@ -26,7 +28,7 @@
 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)
+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)