82 lines
2.1 KiB
Tcsh
82 lines
2.1 KiB
Tcsh
#! /bin/csh -f
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#
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# script to make a free text index for the genbank library
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#
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# NOTE only active for primate file
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#
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echo "genbfreetext.script Version 1.0"
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echo ""
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set RM = "echo /bin/rm -f"
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set SORT = "sort -T tmp"
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set UNIQ = uniq
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#
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#
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#
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set WORDS = $STADENROOT/seqman/stopwords
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genbfreetext gbpri.seq gbpri.list
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if ( $status ) goto abort
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genbfreetext gbrod.seq gbrod.list
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if ( $status ) goto abort
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genbfreetext gbmam.seq gbmam.list
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if ( $status ) goto abort
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genbfreetext gbvrt.seq gbvrt.list
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if ( $status ) goto abort
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genbfreetext gbinv.seq gbinv.list
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if ( $status ) goto abort
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genbfreetext gbpln.seq gbpln.list
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if ( $status ) goto abort
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genbfreetext gborg.seq gborg.list
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if ( $status ) goto abort
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genbfreetext gbbct.seq gbbct.list
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if ( $status ) goto abort
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genbfreetext gbrna.seq gbrna.list
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if ( $status ) goto abort
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genbfreetext gbvrl.seq gbvrl.list
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if ( $status ) goto abort
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genbfreetext gbphg.seq gbphg.list
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if ( $status ) goto abort
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genbfreetext gbsyn.seq gbsyn.list
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if ( $status ) goto abort
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genbfreetext gbuna.seq gbuna.list
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if ( $status ) goto abort
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${SORT} -b +1 gbpri.list gbrod.list gbmam.list gbvrt.list gbinv.list gbpln.list gborg.list gbbct.list gbrna.list gbvrl.list gbphg.list gbsyn.list gbuna.list | ${UNIQ} | excludewords ${WORDS} | ${SORT} >! freetext.sorted
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if ( $status ) goto abort
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${RM} gbpri.list gbrod.list gbmam.list gbvrt.list gbinv.list gbpln.list gborg.list gbbct.list gbrna.list gbvrl.list gbphg.list gbsyn.list gbuna.list
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# sort on words, remove dumplicates, remove stopwords, resort on entry name
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#${SORT} -b +1 gbpri.list | ${UNIQ} | excludewords ${WORDS} | ${SORT} >! freetext.sorted
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#if ( $status ) goto abort
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#${RM} gbpri.list
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# include entry numbers in the file
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freetext2 freetext.sorted freetext.entry
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if ( $status ) goto abort
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${RM} freetext.sorted
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# sort on text
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${SORT} -b +2 freetext.entry >! freetext.sorted2
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if ( $status ) goto abort
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${RM} freetext.entry
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# create the index
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freetext4 freetext.sorted2 freetext.trg freetext.hit
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if ( $status ) goto abort
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${RM} freetext.sorted2
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echo "Completion successful"
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echo ""
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exit 0
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#
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# Abort
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#
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abort:
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echo "genbfreetext.script: aborting due to serious error"
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exit 2
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