42 lines
557 B
Tcsh
42 lines
557 B
Tcsh
#!/bin/csh -f
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#
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# clip-seqs
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#
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# clip all sequences in a file of file names on quality
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#
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# Usage:
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# clip-seqs fof
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#
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onintr abort
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if ( $#argv != 1 ) then
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echo Usage: clip-seqs fof
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exit 2
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endif
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if (! -f "$1") then
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echo clip-seqs: file "$1" does not exist
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exit 1
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endif
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foreach file ( `cat "$1"`)
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/bin/rm -f tmp.$$
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awk -f clip-seq.awk $file > tmp.$$
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if ( $status ) then
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echo clip-seqs: error while clipping $file
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goto abort
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endif
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/bin/mv $file ${file}~
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/bin/mv tmp.$$ $file
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end
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exit 0
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abort:
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echo aborted `date`
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/bin/rm -f tmp.$$
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exit 1 |