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annotate velveth_wrapper.py @ 0:c170448acc8a draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author devteam
date Mon, 09 Nov 2015 12:02:53 -0500
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c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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1 #!/usr/bin/env python
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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2
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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3 """
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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4 Classes encapsulating decypher tool.
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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5 James E Johnson - University of Minnesota
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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6 """
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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7 import pkg_resources
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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8 import logging, os, string, sys, tempfile, glob, shutil, types, urllib
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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9 import shlex, subprocess
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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10 from optparse import OptionParser, OptionGroup
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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11 from stat import *
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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12
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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13
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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14 log = logging.getLogger( __name__ )
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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15
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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16 assert sys.version_info[:2] >= ( 2, 4 )
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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17
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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18 def stop_err( msg ):
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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19 sys.stderr.write( "%s\n" % msg )
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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20 sys.exit()
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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21
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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22 def __main__():
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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23 #Parse Command Line
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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24 s = 'velveth_wrapper.py: argv = %s\n' % (sys.argv)
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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25 argcnt = len(sys.argv)
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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26 html_file = sys.argv[1]
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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27 working_dir = sys.argv[2]
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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28 try: # for test - needs this done
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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29 os.makedirs(working_dir)
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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30 except Exception, e:
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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31 stop_err( 'Error running velveth ' + str( e ) )
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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32 hash_length = sys.argv[3]
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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33 inputs = string.join(sys.argv[4:],' ')
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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34 cmdline = 'velveth %s %s %s > /dev/null' % (working_dir, hash_length, inputs)
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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35 try:
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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36 proc = subprocess.Popen( args=cmdline, shell=True, stderr=subprocess.PIPE )
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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37 returncode = proc.wait()
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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38 # get stderr, allowing for case where it's very large
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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39 stderr = ''
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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40 buffsize = 1048576
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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41 try:
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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42 while True:
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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43 stderr += proc.stderr.read( buffsize )
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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44 if not stderr or len( stderr ) % buffsize != 0:
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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45 break
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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46 except OverflowError:
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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47 pass
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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48 if returncode != 0:
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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49 raise Exception, stderr
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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50 except Exception, e:
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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51 stop_err( 'Error running velveth ' + str( e ) )
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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52 sequences_path = os.path.join(working_dir,'Sequences')
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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53 roadmaps_path = os.path.join(working_dir,'Roadmaps')
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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54 rval = ['<html><head><title>Velvet Galaxy Composite Dataset </title></head><p/>']
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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55 rval.append('<div>%s<p/></div>' % (cmdline) )
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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56 rval.append('<div>This composite dataset is composed of the following files:<p/><ul>')
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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57 rval.append( '<li><a href="%s" type="text/plain">%s </a>%s</li>' % (sequences_path,'Sequences','Sequences' ) )
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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58 rval.append( '<li><a href="%s" type="text/plain">%s </a>%s</li>' % (roadmaps_path,'Roadmaps','Roadmaps' ) )
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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59 rval.append( '</ul></div></html>' )
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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60 f = file(html_file,'w')
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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61 f.write("\n".join( rval ))
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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62 f.write('\n')
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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63 f.close()
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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64
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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65 if __name__ == "__main__": __main__()