#!/bin/tcsh
# tandxmiss.sh

set td=/bio/bio-grid/dpulex/prots/

set pred=EISE_CGW
# set pred=GLEANR
# set pred=NCBI_GNO

#set dspp=(dsec dsim dyak dere dana dpse dmoj dvir dgri)
set dspp=(dpse)
foreach dp ($dspp)

 echo "# pred:$pred species:$dp :: tandem exons missed inside gene models"

 if( ! -f ${dp}1/${dp}_tandy6jmd_hspnear.gff ) then
 gzcat ${dp}1/${dp}_exons_tandy6jmd.gff.gz | grep HSP | egrep -v 'tandyweak|terepeat' | grep '=-2' \
         > ${dp}1/${dp}_tandy6jmd_hspnear.gff
 endif
         
 gzcat ${dp}1/${dp}*_predict.gff.gz | grep "$pred.CDS" | \
  $td/overlapfilter.perl -act drop -overlaps stdin -typeover overlap -pctover 50 \
  -in ${dp}1/${dp}_tandy6jmd_hspnear.gff > ${dp}1/${dp}_tandy6jmd_hspnear-x$pred.gff

 gzcat ${dp}1/${dp}*_predict.gff.gz | grep "$pred.mRNA" | \
  $td/overlapfilter.perl -act keep -overlaps stdin -typeover overlap -pctover 80 \
  -in ${dp}1/${dp}_tandy6jmd_hspnear-x$pred.gff > ${dp}1/${dp}_tandy6jmd_hspnear-gx$pred.gff

 /bin/rm ${dp}1/${dp}_tandy6jmd_hspnear-x$pred.gff
 
 wc -l ${dp}1/${dp}_tandy6jmd_hspnear-gx$pred.gff
 echo -n "$pred in hsp: "
 grep -c $pred ${dp}1/${dp}_tandy6jmd_hspnear-gx$pred.gff
 echo "# ---------------------------------------------------"

end