changeset 0:46a582eb1ea9 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nsaf_scoring.py	Wed May 11 10:50:52 2016 -0400
@@ -0,0 +1,40 @@
+#######################################################################################
+# Python-code: NSAF scoring wrapper
+# Author: Adam L Borne
+# Contributers: Paul A Stewart, Brent Kuenzi
+#######################################################################################
+# This program runs the R script that generates a nsaf scoring table. 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) listfile: SaintExpress output file.
+# 2) preyfile: Prey file listing gene name, sequence legnth, and gene id.
+# 3) crapfile: Crapome file can be created at http://crapome.org. (default = "None")
+# 4) interfile: inter file from preprocessing script.
+#######################################################################################
+import os 
+import sys
+import time
+
+
+listfile = sys.argv[1]
+preyfile = sys.argv[2]
+crapfile = sys.argv[3]
+interfile = sys.argv[4]
+ins_path = sys.argv[6]
+
+
+cmd = (r"Rscript "+ str(ins_path) + r"/nsaf_scoring.R " + str(listfile) + r" "
+    + str(preyfile) + r" " + str(crapfile) + r" " + str(inter_file))
+os.system(cmd)
+
+os.rename("SaintTable.txt", sys.argv[5])