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gpertea |
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#!/bin/tcsh -f |
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# |
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# 1 2 3 4 5 6 7 |
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#my ($file, $numpass, $slice_num, $last, $skipped, $total, $user)=@ARGV; |
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set fq=$1 |
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set numpass=$2 |
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set slnum=$3 |
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set islast=$4 |
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set slskipped=$5 |
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set sltotal=$6 |
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set fesi=$7 |
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set esf=$fesi:t |
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set espath=$fesi:h |
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set fb=$esf:r |
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set fb=$fb:r |
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set srvlog=srv_${fb}_$slnum.log |
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set exout=$fq.exout |
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#goto TEST_LOOP |
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set sv=`ps auxwww | grep exonerate-server | grep 'port 3804'` |
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if ( $#sv > 2 ) then |
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echo "Existing server on this machine on port 3804, aborting.." |
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exit 241 |
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endif |
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# echo "Launching server.." |
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set cpath = `pwd` |
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cd $espath |
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exonerate-server --maxconnections 1 --verbosity 1 --proteinwordlen 4 --port 3804 $esf >& $cpath/$srvlog & |
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set bpid = $! |
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#echo "Background process ID= $bpid" |
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cd $cpath |
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while ( `grep listening $srvlog`"x" == "x" ) |
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sleep 2 |
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end |
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sleep 2 |
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echo "Running: pexo_slice.pl -o $exout $fq" |
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pexo_slice.pl -o $exout $fq |
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/bin/rm -f $fq |
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fltexonerate -p 75 -c 70 < $exout > $exout.p75c70.gff3 |
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echo '<Done.' >> /dev/stderr |
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sleep 2 |
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kill $bpid |
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exit 0 |
