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annotate velveth_wrapper.py @ 0:08256557922f draft

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