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66 lines
2.2 KiB
Python
66 lines
2.2 KiB
Python
#!/usr/bin/env python
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"""
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Classes encapsulating decypher tool.
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James E Johnson - University of Minnesota
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"""
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import pkg_resources
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import logging, os, string, sys, tempfile, glob, shutil, types, urllib
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import shlex, subprocess
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from optparse import OptionParser, OptionGroup
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from stat import *
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log = logging.getLogger( __name__ )
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assert sys.version_info[:2] >= ( 2, 4 )
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def stop_err( msg ):
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sys.stderr.write( "%s\n" % msg )
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sys.exit()
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def __main__():
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#Parse Command Line
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s = 'velveth_wrapper.py: argv = %s\n' % (sys.argv)
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argcnt = len(sys.argv)
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html_file = sys.argv[1]
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working_dir = sys.argv[2]
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try: # for test - needs this done
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os.makedirs(working_dir)
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except Exception, e:
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stop_err( 'Error running velveth ' + str( e ) )
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hash_length = sys.argv[3]
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inputs = string.join(sys.argv[4:],' ')
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cmdline = 'velveth %s %s %s > /dev/null' % (working_dir, hash_length, inputs)
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try:
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proc = subprocess.Popen( args=cmdline, shell=True, stderr=subprocess.PIPE )
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returncode = proc.wait()
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# get stderr, allowing for case where it's very large
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stderr = ''
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buffsize = 1048576
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try:
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while True:
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stderr += proc.stderr.read( buffsize )
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if not stderr or len( stderr ) % buffsize != 0:
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break
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except OverflowError:
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pass
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if returncode != 0:
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raise Exception, stderr
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except Exception, e:
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stop_err( 'Error running velveth ' + str( e ) )
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sequences_path = os.path.join(working_dir,'Sequences')
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roadmaps_path = os.path.join(working_dir,'Roadmaps')
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rval = ['<html><head><title>Velvet Galaxy Composite Dataset </title></head><p/>']
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rval.append('<div>%s<p/></div>' % (cmdline) )
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rval.append('<div>This composite dataset is composed of the following files:<p/><ul>')
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rval.append( '<li><a href="%s" type="text/plain">%s </a>%s</li>' % (sequences_path,'Sequences','Sequences' ) )
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rval.append( '<li><a href="%s" type="text/plain">%s </a>%s</li>' % (roadmaps_path,'Roadmaps','Roadmaps' ) )
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rval.append( '</ul></div></html>' )
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f = file(html_file,'w')
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f.write("\n".join( rval ))
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f.write('\n')
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f.close()
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if __name__ == "__main__": __main__()
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