changeset 23:cb7223752458 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Bubblebeam_For_SAINT_wrapper.py	Fri Jan 29 09:33:15 2016 -0500
@@ -0,0 +1,80 @@
+#######################################################################################
+# Python-code: Bubblebeam wrapper
+# Author: Adam L Borne
+# Contributers: Paul A Stewart, Brent Kuenzi
+#######################################################################################
+# This program runs the R script that generates a bubble plot. Python script simply 
+# handles arguments and interacts with 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) prey_file: Prey file listing gene name, sequence legnth, and gene id.
+# 3) crapome: Crapome file can be created at http://crapome.org. (default = "None")
+# 4) color: Fill color of the bubbles, if set to crapome it shades based on crapome
+# potential. (default = "Red")
+# 5) cutoff: Lower limit saint score for generating bubble plot. (default = 0.8)
+# 6) mq_sc: MQ for MaxQuant data and SC for Scaffold data.
+# 7) inc_file: List of uniprot ids to be used exclusively. (default = "None")
+# 8) exc_file: List of uniprot ids to be excluded from plot. (default = "None")
+#######################################################################################
+
+
+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))