Mercurial > repos > devteam > velvet
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__()