diff velveth_wrapper.py @ 0:08256557922f draft

planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
author devteam
date Tue, 13 Oct 2015 16:38:28 -0400
parents
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/velveth_wrapper.py	Tue Oct 13 16:38:28 2015 -0400
@@ -0,0 +1,65 @@
+#!/usr/bin/env python
+
+"""
+Classes encapsulating decypher tool.
+James E Johnson - University of Minnesota
+"""
+import pkg_resources
+import logging, os, string, sys, tempfile, glob, shutil, types, urllib
+import shlex, subprocess
+from optparse import OptionParser, OptionGroup
+from stat import *
+
+
+log = logging.getLogger( __name__ )
+
+assert sys.version_info[:2] >= ( 2, 4 )
+
+def stop_err( msg ):
+    sys.stderr.write( "%s\n" % msg )
+    sys.exit()
+
+def __main__():
+    #Parse Command Line
+    s = 'velveth_wrapper.py:  argv = %s\n' % (sys.argv)
+    argcnt = len(sys.argv)
+    html_file = sys.argv[1]
+    working_dir = sys.argv[2]
+    try: # for test - needs this done
+        os.makedirs(working_dir)
+    except Exception, e:
+        stop_err( 'Error running velveth ' + str( e ) )
+    hash_length = sys.argv[3]
+    inputs = string.join(sys.argv[4:],' ')
+    cmdline = 'velveth %s %s %s > /dev/null' % (working_dir, hash_length, inputs)
+    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 velveth ' + str( e ) )
+    sequences_path = os.path.join(working_dir,'Sequences')
+    roadmaps_path = os.path.join(working_dir,'Roadmaps')
+    rval = ['<html><head><title>Velvet Galaxy Composite Dataset </title></head><p/>']
+    rval.append('<div>%s<p/></div>' % (cmdline) )
+    rval.append('<div>This composite dataset is composed of the following files:<p/><ul>')
+    rval.append( '<li><a href="%s" type="text/plain">%s </a>%s</li>' % (sequences_path,'Sequences','Sequences' ) )
+    rval.append( '<li><a href="%s" type="text/plain">%s </a>%s</li>' % (roadmaps_path,'Roadmaps','Roadmaps' ) )
+    rval.append( '</ul></div></html>' )
+    f = file(html_file,'w')
+    f.write("\n".join( rval ))
+    f.write('\n')
+    f.close()
+
+if __name__ == "__main__": __main__()