/tools/sr_assembly/velveth_wrapper.py

https://bitbucket.org/cistrome/cistrome-harvard/ · Python · 65 lines · 51 code · 7 blank · 7 comment · 11 complexity · f8a277dc6760ba1dc136971a772d68c2 MD5 · raw file 

    

  1. #!/usr/bin/env python
    2. 

  2. 

  3. """
    4. 

  4. Classes encapsulating decypher tool.
    5. 

  5. James E Johnson - University of Minnesota
    6. 

  6. """
    7. 

  7. import pkg_resources
    8. 

  8. import logging, os, string, sys, tempfile, glob, shutil, types, urllib
    9. 

  9. import shlex, subprocess
    10. 

  10. from optparse import OptionParser, OptionGroup
    11. 

  11. from stat import *
    12. 

  12. 

  13. 

  14. log = logging.getLogger( __name__ )
    15. 

  15. 

  16. assert sys.version_info[:2] >= ( 2, 4 )
    17. 

  17. 

  18. def stop_err( msg ):
    19. 

  19.     sys.stderr.write( "%s\n" % msg )
    20. 

  20.     sys.exit()
    21. 

  21. 

  22. def __main__():
    23. 

  23.     #Parse Command Line
    24. 

  24.     s = 'velveth_wrapper.py:  argv = %s\n' % (sys.argv)
    25. 

  25.     argcnt = len(sys.argv)
    26. 

  26.     html_file = sys.argv[1]
    27. 

  27.     working_dir = sys.argv[2]
    28. 

  28.     try: # for test - needs this done
    29. 

  29.         os.makedirs(working_dir)
    30. 

  30.     except Exception, e:
    31. 

  31.         stop_err( 'Error running velveth ' + str( e ) )
    32. 

  32.     hash_length = sys.argv[3]
    33. 

  33.     inputs = string.join(sys.argv[4:],' ')
    34. 

  34.     cmdline = 'velveth %s %s %s > /dev/null' % (working_dir, hash_length, inputs)
    35. 

  35.     try:
    36. 

  36.         proc = subprocess.Popen( args=cmdline, shell=True, stderr=subprocess.PIPE )
    37. 

  37.         returncode = proc.wait()
    38. 

  38.         # get stderr, allowing for case where it's very large
    39. 

  39.         stderr = ''
    40. 

  40.         buffsize = 1048576
    41. 

  41.         try:
    42. 

  42.             while True:
    43. 

  43.                 stderr += proc.stderr.read( buffsize )
    44. 

  44.                 if not stderr or len( stderr ) % buffsize != 0:
    45. 

  45.                     break
    46. 

  46.         except OverflowError:
    47. 

  47.             pass
    48. 

  48.         if returncode != 0:
    49. 

  49.             raise Exception, stderr
    50. 

  50.     except Exception, e:
    51. 

  51.         stop_err( 'Error running velveth ' + str( e ) )
    52. 

  52.     sequences_path = os.path.join(working_dir,'Sequences')
    53. 

  53.     roadmaps_path = os.path.join(working_dir,'Roadmaps')
    54. 

  54.     rval = ['<html><head><title>Velvet Galaxy Composite Dataset </title></head><p/>']
    55. 

  55.     rval.append('<div>%s<p/></div>' % (cmdline) )
    56. 

  56.     rval.append('<div>This composite dataset is composed of the following files:<p/><ul>')
    57. 

  57.     rval.append( '<li><a href="%s" type="text/plain">%s </a>%s</li>' % (sequences_path,'Sequences','Sequences' ) )
    58. 

  58.     rval.append( '<li><a href="%s" type="text/plain">%s </a>%s</li>' % (roadmaps_path,'Roadmaps','Roadmaps' ) )
    59. 

  59.     rval.append( '</ul></div></html>' )
    60. 

  60.     f = file(html_file,'w')
    61. 

  61.     f.write("\n".join( rval ))
    62. 

  62.     f.write('\n')
    63. 

  63.     f.close()
    64. 

  64. 

  65. if __name__ == "__main__": __main__()
    66.