/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
- #!/usr/bin/env python
-
- import sys, os, re
- if sys.version_info[:2] >= ( 2, 5 ):
- import xml.etree.cElementTree as ElementTree
- else:
- from galaxy import eggs
- import pkg_resources; pkg_resources.require( "elementtree" )
- from elementtree import ElementTree
- def stop_err( msg ):
- sys.stderr.write( "%s\n" % msg )
- sys.exit()
- def __main__():
- source = sys.argv[1]
- hspTags = [
- "Hsp_bit-score",
- "Hsp_evalue",
- "Hsp_query-from",
- "Hsp_query-to",
- "Hsp_hit-from",
- "Hsp_hit-to",
- "Hsp_query-frame",
- "Hsp_hit-frame",
- "Hsp_identity",
- "Hsp_align-len",
- "Hsp_qseq",
- "Hsp_hseq",
- "Hsp_midline"
- ]
- hspData = []
- # get an iterable
- try:
- context = ElementTree.iterparse( source, events=( "start", "end" ) )
- except:
- stop_err( "Invalid data format." )
- # turn it into an iterator
- context = iter( context )
- # get the root element
- try:
- event, root = context.next()
- except:
- stop_err( "Invalid data format." )
- outfile = open( sys.argv[2], 'w' )
- try:
- for event, elem in context:
- # for every <Iteration> tag
- if event == "end" and elem.tag == "Iteration":
- query = elem.findtext( "Iteration_query-def" )
- qLen = elem.findtext( "Iteration_query-len" )
- # for every <Hit> within <Iteration>
- for hit in elem.findall( "Iteration_hits/Hit" ):
- subject = hit.findtext( "Hit_id" )
- if re.search( '^gi', subject ):
- subject = subject.split('|')[1]
- sLen = hit.findtext( "Hit_len" )
- # for every <Hsp> within <Hit>
- for hsp in hit.findall( "Hit_hsps/Hsp" ):
- outfile.write( "%s\t%s\t%s\t%s" % ( query, qLen, subject, sLen ) )
- for tag in hspTags:
- outfile.write("\t%s" %(hsp.findtext( tag )))
- #hspData.append( hsp.findtext( tag ) )
- #hspData = []
- outfile.write('\n')
- # prevents ElementTree from growing large datastructure
- root.clear()
- elem.clear()
- except:
- outfile.close()
- stop_err( "The input data is malformed, or there is more than one dataset in the input file. Error: %s" % sys.exc_info()[1] )
- outfile.close()
- if __name__ == "__main__": __main__()