#!/bin/tcsh
# run per genome dir
# add formatdb call here? predict exon split?
set nb=/bio/bio-grid/ncbi-20060507/ncbi/bin

foreach dir (scaffold_*)
 set faz="$dir/*_caf060210.fa.gz"
 set fna=`echo $faz | sed -e's/.gz//'`
 gzcat $faz | $nb/formatdb -pF -n $fna  -i stdin

 #set nsq="$dir/*_caf060210.fa.nsq"
 #set fna=`echo $nsq | sed -e's/.nsq//'`
 echo "# megablast start" $fna , `date`
 foreach predict ($dir/*-exons.fa)
  echo "# megablast query=$predict"
  $nb/megablast -W11 -t16 -N0 -gT -e0.05 -D3 -i $predict -d $fna -o $predict.mbout
 end
 echo "# megablast done" $fna , `date`
end

exit
# ---- formatdb ------
foreach faz (scaffold_*/*_caf060210.fa.gz)
 echo "# formatdb $faz"
 set fna=`echo $faz | sed -e's/.gz//'`
 gzcat $faz | $nb/formatdb -pF -n $fna  -i stdin
end

#--- exon split ----
foreach faz (scaffold*/*_caf060210_exons.fa.gz)
echo "# split $faz by predictors"
gzcat $faz | env fin=$faz  perl -ne 'use FileHandle;\
if(/^>(\D+)/){ $gr=$1; $gr=~s/_$//; $fh=undef; $skip=0;
$skip= ($gr=~m/DGIL_SNO|BATZ_CNA|RGUI_GID|^TRd\w+/); next if($skip)\
$fn=$ENV{fin}; $fn=~s,/[^/]*$,/$gr-exons.fa, or die;  \
$fh=$fhs{$fn}; unless($fh){ $fhs{$fn}= $fh= new FileHandle "> $fn"; } }\
print $fh $_ unless($skip);'
end