# chdir $scd/perchr;
set chrtr=`chdir $scd/perchr; /bin/ls -l | egrep -v '^l|total' | sed -e's/.*gilbertd.[a-z]* *//' |\
   sort -k1,1nr | head -10 | sed -e's,.* ,,' -e's,.fa,,' | egrep -v '^(U|p)'`

mkdir snaptrain
mkdir snapout

set dptrain=$dpid-train
set hmmtrain=fly 

/bin/cp /dev/null  snaptrain/$dptrain.fa

foreach chr ($chrtr)
 
 if (! -f snapout/$dp-hsp-$chr.zff ) then
   gzcat $sc/caf1a/dgil/${dp}prot9-hsp.gff.gz | egrep '#|modDM' | perl -ne \
    "print if(/^#/ || /^$chr\b/);" | perl ../gff2zff2.pl > ! snapout/$dp-hsp-$chr.zff
 endif

 cat $scd/perchr/$chr.fa >> snaptrain/$dptrain.fa

 $ZOE/snap -quiet -xdef snapout/$dp-hsp-$chr.zff \
 -ACoding -0.001 -AStart -2 -AStop -2 \
 $hmmtrain $scd/perchr/$chr.fa > snaptrain/$dpid-$chr-$hmmtrain.zff

end

cd snaptrain
/bin/cp /dev/null $dptrain.zff
foreach chr ($chrtr)
 cat $dpid-$chr-$hmmtrain.zff >> $dptrain.zff
end

$ZOE/fathom $dptrain.zff $dptrain.fa -categorize 1000
$ZOE/fathom uni.ann uni.dna -export 1000 -plus
$ZOE/forge export.ann export.dna

cd ../
$ZOE/hmm-assembler.pl -o ${dpid}-snapho snaptrain > snapho-$dpid.hmm
set hmm=snapho-$dpid.hmm