# snaprun3.sh
# source me ; dspp snap predict version 2 using prot-hsps; hmm built
# all scaffolds/chrs, preserve hmm-build subset

# set dp=dvir
# set dpid=...
# dir /bio/bio-grid/dspp/caf1snap/dvir

set hmm=snapho-$dpid.hmm

## screen small scaffs 1st pass ? find .. -size 1 .. -size 9 (all < 5kb)
# set chrs=`chdir $scd/perchr; /bin/ls -1 [cs]*.fa | sed -e's/.fa//'`

# do small junk as one input file, no -xdef
## chdir $scd/perchr; /bin/ls -l
set chrsmall=`chdir $scd/perchr; /bin/ls -l | egrep -v '^l|total' | sed -e's/.*gilbertd.[a-z]* *//' |\
  sort -k1,1nr | perl -ne'($n)=/(\d+)/;print if($n<40000);' | sed -e's,.* ,,' -e's,.fa,,' | grep -v ^p`

set chrsbig=`chdir $scd/perchr; /bin/ls -l | egrep -v '^l|total' | sed -e's/.*gilbertd.[a-z]* *//' | \
 sort -k1,1nr | perl -ne'($n)=/(\d+)/;print if($n>=40000);' | sed -e's,.* ,,' -e's,.fa,,' | grep -v ^p`

foreach chr ( $chrsbig )
 
 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

 if ( ! -f "snapout/$dp-snapho-$chr.gff" ) then
  if ( -z "snapout/$dp-hsp-$chr.zff" ) then
    echo $chr : no hsp data
    $ZOE/snap -quiet -name 'snapho' -gff3 \
    -aa snapout/$dp-snapho-$chr.aa -tx snapout/$dp-snapho-$chr.tr \
    $hmm $scd/perchr/$chr.fa > snapout/$dp-snapho-$chr.gff

  else
    $ZOE/snap -quiet -name 'snapho' -gff3 -xdef snapout/$dp-hsp-$chr.zff \
    -aa snapout/$dp-snapho-$chr.aa -tx snapout/$dp-snapho-$chr.tr \
    $hmm $scd/perchr/$chr.fa > snapout/$dp-snapho-$chr.gff

  endif

 endif
 
end

cp /dev/null snapout/chrsmall.fa
foreach chr ( $chrsmall )
  cat $scd/perchr/$chr.fa >> snapout/chrsmall.fa
end

if ( ! -z snapout/chrsmall.fa ) then
set chr=chrsmall
$ZOE/snap -quiet -name 'snapho' -gff3 \
  -aa snapout/$dp-snapho-$chr.aa -tx snapout/$dp-snapho-$chr.tr \
  $hmm snapout/chrsmall.fa > snapout/$dp-snapho-$chr.gff
endif

cat snapout/$dp-snapho-*.gff > snapho-$dpid.gff
cat snapout/$dp-snapho-*.tr > snapho-$dpid.tr
cat snapout/$dp-snapho-*.aa > snapho-$dpid.aa