| 1 |
#!/bin/tcsh -f |
| 2 |
if ( $2'x' == 'x' ) then |
| 3 |
echo "Usage: \nrun_pexonerate <prot_fasta> <genomic_seq_fasta> [<output_gff>]" |
| 4 |
exit |
| 5 |
endif |
| 6 |
|
| 7 |
set excmd='exonerate -V 0 --model p2g --percent 20 -n 11 --showalignment no --showtargetgff yes --showvulgar no' |
| 8 |
set excmd="$excmd --maxintron 450000 --seedrepeat 2 --ryo "'%ti\t%qi\tmap_end\t%r\t%ql|%qab-%qae\t%ps\t%g\t%qd\n' |
| 9 |
set excmd="$excmd --geneseed 60 -x 50 --proteinwordlen 4 --saturatethreshold 80 $1 $2" |
| 10 |
|
| 11 |
if ( $3'x' == 'x' ) then |
| 12 |
$excmd |
| 13 |
else |
| 14 |
$excmd | fltexonerate -c70 -p70 > $3 |
| 15 |
endif |
