[2] | 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 | assert sys.version_info[:2] >= ( 2, 4 ) |
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| 6 | |
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| 7 | if sys.version_info[:2] >= ( 2, 5 ): |
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| 8 | import xml.etree.cElementTree as cElementTree |
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| 9 | else: |
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| 10 | import cElementTree |
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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 = cElementTree.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 contains tags that are not recognizable by the tool." ) |
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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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