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gpertea |
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#!/bin/tcsh -f |
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if ( $2'x' == 'x' ) then |
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echo "Usage: \nrun_pexonerate <prot_fasta> <genomic_seq_fasta> [<output_gff>]" |
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exit |
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endif |
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set excmd='exonerate -V 0 --model p2g --percent 20 -n 11 --showalignment no --showtargetgff yes --showvulgar no' |
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set excmd="$excmd --maxintron 450000 --seedrepeat 2 --ryo "'%ti\t%qi\tmap_end\t%r\t%ql|%qab-%qae\t%ps\t%g\t%qd\n' |
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set excmd="$excmd --geneseed 60 -x 50 --proteinwordlen 4 --saturatethreshold 80 $1 $2" |
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if ( $3'x' == 'x' ) then |
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$excmd |
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else |
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$excmd | fltexonerate -c70 -p70 > $3 |
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endif |
