--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/velvetg_wrapper.py	Tue Oct 13 16:38:28 2015 -0400
@@ -0,0 +1,46 @@
+#!/usr/bin/env python
+
+"""
+Classes encapsulating decypher tool.
+James E Johnson - University of Minnesota
+"""
+import os
+import sys
+import subprocess
+
+assert sys.version_info[:2] >= ( 2, 4 )
+
+def stop_err( msg ):
+    sys.stderr.write( "%s\n" % msg )
+    sys.exit()
+
+
+def __main__():
+    #Parse Command Line
+    working_dir = sys.argv[1]
+    inputs = ' '.join(sys.argv[2:])
+    for _ in ('Roadmaps', 'Sequences'):
+        os.symlink(os.path.join(working_dir, _), _)
+    cmdline = 'velvetg . %s' % (inputs)
+    print "Command to be executed: %s" % cmdline
+    try:
+        proc = subprocess.Popen( args=cmdline, shell=True, stderr=subprocess.PIPE )
+        returncode = proc.wait()
+        # get stderr, allowing for case where it's very large
+        stderr = ''
+        buffsize = 1048576
+        try:
+            while True:
+                stderr += proc.stderr.read( buffsize )
+                if not stderr or len( stderr ) % buffsize != 0:
+                    break
+        except OverflowError:
+            pass
+        if returncode != 0:
+            raise Exception, stderr
+    except Exception, e:
+        stop_err( 'Error running velvetg ' + str( e ) )
+
+
+if __name__ == "__main__":
+    __main__()