
## redo w/ updated evigene soft, input oid aablast=evg4corn.aa.btall changed params for bad utr,gaps
pt=evg4corn
idp=Zeamay4EVm 
idpg=Zeamay4gEVm 
spp=Zea_mays
refaa=twoplants

env trset=$pt.tr  aablast=$pt.aa.btall datad=`pwd` prog=./runtr2cds.sh sbatch srun_comet.sh
env idprefix=$idp trclass=$pt.trclass  names=$pt.names species=$spp datad=`pwd` prog=./run_evgmrna2tsa.sh sbatch srun_comet.sh

mkdir geno1f
cd geno1f
ln -s ../publicset/$pt.cds_pub.fa $pt.cds
ln -s ../publicset/$pt.aa_pub.fa $pt.aa
ln -s ../genoasm.fa genoasm.fa

env oid=1 off=1 $evigene/scripts/prot/aaqual.sh $pt.aa

## add to runtr2genome: -aablast=evgpubaa_bugref.blastp 
env protin=$pt.aa prodb=../refset/$refaa datad=`pwd` prog=../blastpc.sh sbatch ../srun_comet.sh

## do this instead:
aablast=sdc-$refaa-$pt.aa.blastp.gz
mbaopts="-tall -aasize $pt.aa.qual,../refset/$refaa.aa.qual"
aabltab=sdc-refaa-$pt.aa.btall

$evigene/scripts/makeblastscore3.pl $mbaopts $aablast > $aabltab 

## runtr2genome2b.sh to runtr2genome3.sh : is it ready?
env idpre=$idpg cdsseq=$pt.cds aablast=$aabltab chrseq=genoasm.fa gtag=chra datad=`pwd` prog=../runtr2genome3.sh sbatch ../srun_comet.sh

