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1 #!/usr/bin/env python
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2
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3 import sys, os, re
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4
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5 if sys.version_info[:2] >= ( 2, 5 ):
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6 import xml.etree.cElementTree as ElementTree
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7 else:
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8 from galaxy import eggs
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9 import pkg_resources; pkg_resources.require( "elementtree" )
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10 from elementtree import ElementTree
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11
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12 def stop_err( msg ):
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13 sys.stderr.write( "%s\n" % msg )
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14 sys.exit()
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15
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16 def __main__():
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17 source = sys.argv[1]
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18 hspTags = [
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19 "Hsp_bit-score",
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20 "Hsp_evalue",
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21 "Hsp_query-from",
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22 "Hsp_query-to",
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23 "Hsp_hit-from",
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24 "Hsp_hit-to",
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25 "Hsp_query-frame",
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26 "Hsp_hit-frame",
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27 "Hsp_identity",
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28 "Hsp_align-len",
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29 "Hsp_qseq",
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30 "Hsp_hseq",
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31 "Hsp_midline"
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32 ]
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33 hspData = []
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34
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35 # get an iterable
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36 try:
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37 context = ElementTree.iterparse( source, events=( "start", "end" ) )
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38 except:
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39 stop_err( "Invalid data format." )
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40 # turn it into an iterator
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41 context = iter( context )
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42 # get the root element
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43 try:
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44 event, root = context.next()
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45 except:
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46 stop_err( "Invalid data format." )
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47
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48 outfile = open( sys.argv[2], 'w' )
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49 try:
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50 for event, elem in context:
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51 # for every <Iteration> tag
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52 if event == "end" and elem.tag == "Iteration":
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53 query = elem.findtext( "Iteration_query-def" )
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54 qLen = elem.findtext( "Iteration_query-len" )
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55 # for every <Hit> within <Iteration>
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56 for hit in elem.findall( "Iteration_hits/Hit" ):
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57 subject = hit.findtext( "Hit_id" )
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58 if re.search( '^gi', subject ):
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59 subject = subject.split('|')[1]
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60 sLen = hit.findtext( "Hit_len" )
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61 # for every <Hsp> within <Hit>
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62 for hsp in hit.findall( "Hit_hsps/Hsp" ):
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63 outfile.write( "%s\t%s\t%s\t%s" % ( query, qLen, subject, sLen ) )
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64 for tag in hspTags:
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65 outfile.write("\t%s" %(hsp.findtext( tag )))
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66 #hspData.append( hsp.findtext( tag ) )
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67 #hspData = []
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68 outfile.write('\n')
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69 # prevents ElementTree from growing large datastructure
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70 root.clear()
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71 elem.clear()
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72 except:
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73 outfile.close()
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74 stop_err( "The input data is malformed, or there is more than one dataset in the input file. Error: %s" % sys.exc_info()[1] )
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75
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76 outfile.close()
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77
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78 if __name__ == "__main__": __main__()
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