/tools/metag_tools/megablast_xml_parser.py

https://bitbucket.org/cistrome/cistrome-harvard/ · Python · 78 lines · 60 code · 8 blank · 10 comment · 13 complexity · ce64d58eceab6a8d45762afabb901377 MD5 · raw file

  1. #!/usr/bin/env python
  2. import sys, os, re
  3. if sys.version_info[:2] >= ( 2, 5 ):
  4. import xml.etree.cElementTree as ElementTree
  5. else:
  6. from galaxy import eggs
  7. import pkg_resources; pkg_resources.require( "elementtree" )
  8. from elementtree import ElementTree
  9. def stop_err( msg ):
  10. sys.stderr.write( "%s\n" % msg )
  11. sys.exit()
  12. def __main__():
  13. source = sys.argv[1]
  14. hspTags = [
  15. "Hsp_bit-score",
  16. "Hsp_evalue",
  17. "Hsp_query-from",
  18. "Hsp_query-to",
  19. "Hsp_hit-from",
  20. "Hsp_hit-to",
  21. "Hsp_query-frame",
  22. "Hsp_hit-frame",
  23. "Hsp_identity",
  24. "Hsp_align-len",
  25. "Hsp_qseq",
  26. "Hsp_hseq",
  27. "Hsp_midline"
  28. ]
  29. hspData = []
  30. # get an iterable
  31. try:
  32. context = ElementTree.iterparse( source, events=( "start", "end" ) )
  33. except:
  34. stop_err( "Invalid data format." )
  35. # turn it into an iterator
  36. context = iter( context )
  37. # get the root element
  38. try:
  39. event, root = context.next()
  40. except:
  41. stop_err( "Invalid data format." )
  42. outfile = open( sys.argv[2], 'w' )
  43. try:
  44. for event, elem in context:
  45. # for every <Iteration> tag
  46. if event == "end" and elem.tag == "Iteration":
  47. query = elem.findtext( "Iteration_query-def" )
  48. qLen = elem.findtext( "Iteration_query-len" )
  49. # for every <Hit> within <Iteration>
  50. for hit in elem.findall( "Iteration_hits/Hit" ):
  51. subject = hit.findtext( "Hit_id" )
  52. if re.search( '^gi', subject ):
  53. subject = subject.split('|')[1]
  54. sLen = hit.findtext( "Hit_len" )
  55. # for every <Hsp> within <Hit>
  56. for hsp in hit.findall( "Hit_hsps/Hsp" ):
  57. outfile.write( "%s\t%s\t%s\t%s" % ( query, qLen, subject, sLen ) )
  58. for tag in hspTags:
  59. outfile.write("\t%s" %(hsp.findtext( tag )))
  60. #hspData.append( hsp.findtext( tag ) )
  61. #hspData = []
  62. outfile.write('\n')
  63. # prevents ElementTree from growing large datastructure
  64. root.clear()
  65. elem.clear()
  66. except:
  67. outfile.close()
  68. stop_err( "The input data is malformed, or there is more than one dataset in the input file. Error: %s" % sys.exc_info()[1] )
  69. outfile.close()
  70. if __name__ == "__main__": __main__()