Mercurial > repos > devteam > velvet
comparison velveth_wrapper.py @ 0:08256557922f draft
planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
| author | devteam |
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| date | Tue, 13 Oct 2015 16:38:28 -0400 |
| parents | |
| children |
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| -1:000000000000 | 0:08256557922f |
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| 1 #!/usr/bin/env python | |
| 2 | |
| 3 """ | |
| 4 Classes encapsulating decypher tool. | |
| 5 James E Johnson - University of Minnesota | |
| 6 """ | |
| 7 import pkg_resources | |
| 8 import logging, os, string, sys, tempfile, glob, shutil, types, urllib | |
| 9 import shlex, subprocess | |
| 10 from optparse import OptionParser, OptionGroup | |
| 11 from stat import * | |
| 12 | |
| 13 | |
| 14 log = logging.getLogger( __name__ ) | |
| 15 | |
| 16 assert sys.version_info[:2] >= ( 2, 4 ) | |
| 17 | |
| 18 def stop_err( msg ): | |
| 19 sys.stderr.write( "%s\n" % msg ) | |
| 20 sys.exit() | |
| 21 | |
| 22 def __main__(): | |
| 23 #Parse Command Line | |
| 24 s = 'velveth_wrapper.py: argv = %s\n' % (sys.argv) | |
| 25 argcnt = len(sys.argv) | |
| 26 html_file = sys.argv[1] | |
| 27 working_dir = sys.argv[2] | |
| 28 try: # for test - needs this done | |
| 29 os.makedirs(working_dir) | |
| 30 except Exception, e: | |
| 31 stop_err( 'Error running velveth ' + str( e ) ) | |
| 32 hash_length = sys.argv[3] | |
| 33 inputs = string.join(sys.argv[4:],' ') | |
| 34 cmdline = 'velveth %s %s %s > /dev/null' % (working_dir, hash_length, inputs) | |
| 35 try: | |
| 36 proc = subprocess.Popen( args=cmdline, shell=True, stderr=subprocess.PIPE ) | |
| 37 returncode = proc.wait() | |
| 38 # get stderr, allowing for case where it's very large | |
| 39 stderr = '' | |
| 40 buffsize = 1048576 | |
| 41 try: | |
| 42 while True: | |
| 43 stderr += proc.stderr.read( buffsize ) | |
| 44 if not stderr or len( stderr ) % buffsize != 0: | |
| 45 break | |
| 46 except OverflowError: | |
| 47 pass | |
| 48 if returncode != 0: | |
| 49 raise Exception, stderr | |
| 50 except Exception, e: | |
| 51 stop_err( 'Error running velveth ' + str( e ) ) | |
| 52 sequences_path = os.path.join(working_dir,'Sequences') | |
| 53 roadmaps_path = os.path.join(working_dir,'Roadmaps') | |
| 54 rval = ['<html><head><title>Velvet Galaxy Composite Dataset </title></head><p/>'] | |
| 55 rval.append('<div>%s<p/></div>' % (cmdline) ) | |
| 56 rval.append('<div>This composite dataset is composed of the following files:<p/><ul>') | |
| 57 rval.append( '<li><a href="%s" type="text/plain">%s </a>%s</li>' % (sequences_path,'Sequences','Sequences' ) ) | |
| 58 rval.append( '<li><a href="%s" type="text/plain">%s </a>%s</li>' % (roadmaps_path,'Roadmaps','Roadmaps' ) ) | |
| 59 rval.append( '</ul></div></html>' ) | |
| 60 f = file(html_file,'w') | |
| 61 f.write("\n".join( rval )) | |
| 62 f.write('\n') | |
| 63 f.close() | |
| 64 | |
| 65 if __name__ == "__main__": __main__() |