[2] | 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__() |
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