--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/viral_assembly_annotation/VIGOR.py	Thu Jan 31 13:41:35 2013 -0500
@@ -0,0 +1,42 @@
+#!/usr/bin/env python
+
+"""
+Runs VIGOR3 on given input fasta file.
+"""
+
+import os, sys, subprocess, tempfile, shutil
+
+def __main__():
+	# Parse the command line options
+	(inputFasta,outputALN,outputCDS,outputFS,outputPEP,outputRPT,outputSTATS,outputTBL) = sys.argv[1:]
+	
+	# Set up output variables
+	outputDir = "/usr/local/VIGOR/tools/vigor/test"
+	outputName = "output"
+	outputLog = "%s/%s_log.txt"      % (outputDir,outputName)
+	vigorOutputALN = "%s/%s.aln"     % (outputDir,outputName)
+	vigorOutputCDS = "%s/%s.cds"     % (outputDir,outputName)
+	vigorOutputFS = "%s/%s.fs"       % (outputDir,outputName)
+	vigorOutputPEP = "%s/%s.pep"     % (outputDir,outputName)
+	vigorOutputRPT = "%s/%s.rpt"     % (outputDir,outputName)
+	vigorOutputSTATS = "%s/%s.stats" % (outputDir,outputName)
+	vigorOutputTBL = "%s/%s.tbl"     % (outputDir,outputName)
+	
+	# Create empty output log file (cannot be created by VIGOR command alone).
+	os.system("sudo touch %s" % outputLog)
+	os.system("sudo chmod 777 %s" % outputLog)
+	
+	# Run command
+	command = "/usr/local/VIGOR/tools/vigor/prod3/VIGOR3.pl -A -i %s -O %s/%s > %s" % (inputFasta,outputDir,outputName,outputLog)
+	os.system("sudo %s" % command)
+	os.system("sudo chmod 777 %s/%s.*" % (outputDir,outputName))
+	os.system("sudo cp %s %s" % (vigorOutputALN,outputALN))
+	os.system("sudo cp %s %s" % (vigorOutputCDS,outputCDS))
+	os.system("sudo cp %s %s" % (vigorOutputFS,outputFS))
+	os.system("sudo cp %s %s" % (vigorOutputPEP,outputPEP))
+	os.system("sudo cp %s %s" % (vigorOutputRPT,outputRPT))
+	os.system("sudo cp %s %s" % (vigorOutputSTATS,outputSTATS))
+	os.system("sudo cp %s %s" % (vigorOutputTBL,outputTBL))
+
+if __name__=="__main__": 
+	__main__()