--- a/reverse.py	Sat Apr 12 07:25:47 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,48 +0,0 @@
-#!/usr/bin/env python
-from os.path import join
-import sys
-from optparse import OptionParser
-from ConfigParser import SafeConfigParser
-import subprocess
-
-DEBUG = False
-
-def main():
-    (options, args) = _parse_args()
-    _run_shell("cat '%s' > '%s'" % (options.input, options.output))
-    _run_dbtoolkit("com.compomics.dbtoolkit.toolkit.ReverseFASTADB", "'%s' | head --lines -4 >> '%s'" % (options.input, options.output), options)
-
-
-def _run_shell(command):
-    if DEBUG:
-        print "Running shell command %s" % command
-    _exec(command)
-
-
-def _run_dbtoolkit(java_class, command, args):
-    command_prefix = "java -cp %s" % _dbtoolkit_jar_path( args.script_path )
-    _exec("%s %s %s" % (command_prefix, java_class, command))
-
-
-def _dbtoolkit_jar_path( script_path ):
-    jar_path = join(script_path, "dbtoolkit-4.2", "dbtoolkit-4.2.jar")
-    return jar_path
-
-def _exec(command):
-    proc = subprocess.Popen(args=command, shell=True)
-    return_code = proc.wait()
-    if return_code != 0:
-        print "Error executing command [%s], return code is %d" % (command, return_code)
-        sys.exit(return_code)
-
-
-def _parse_args():
-    parser = OptionParser()
-    parser.add_option("-i", "--input")
-    parser.add_option("-o", "--output")
-    parser.add_option("-s", "--script_path")
-    return parser.parse_args()
-
-
-if __name__ == "__main__":
-    main()