echo ## snapmake.script =================================

# set dp=dvir
# set species=virilis
# set dpid=${dp}_caf051209
# set scd=$sc/${dp}3
# set dp3=${dp}3
# set scaffoldgff=$scd/$dp-scaffolds.gff
# set chrfasta=$scd/$dpid.fa.gz

# (source snapmake.script )> log.snapmake.$dpid

echo ## ===== snaptrain =================================
setenv ZOE /bio/bio-grid/mb/SNAP
# ZOE=/bio/bio-grid/mb/SNAP; export ZOE
set hmm=fly

echo "snaptrain $dpid-$hmm .."

/bin/rm -rf snaptrain
mkdir snaptrain
cd snaptrain

if ( -e "$trainfasta.gz" ) then
 gunzip -c $trainfasta > $dpid-train.fa
else if ( -e "$trainfasta" ) then
 cp -p $trainfasta $dpid-train.fa
else
 $bg/blast/fa2multizfa.pl -minlen=5000000 -qdb=$dpid -chrin=$scaffoldgff \
 -in=$chrfasta -out=$dpid-train.fa
endif

## getting segfaults here when chr fasta record is big.. out of mem
## need shredded chrs instead
echo "bootstrap snap $hmm $dpid-train.fa .."
$ZOE/snap -quiet $hmm $dpid-train.fa > $dpid-$hmm.zff
echo "fathom $dpid-$hmm.zff $dpid-train.fa -categorize .."
$ZOE/fathom $dpid-$hmm.zff $dpid-train.fa -categorize 1000
echo "fathom uni.ann .."
$ZOE/fathom uni.ann uni.dna -export 1000 -plus
echo "forge export.ann .."
$ZOE/forge export.ann export.dna

cd ..

echo "hmm-assembler snap-$dpid.hmm"
$ZOE/hmm-assembler.pl $dpid snaptrain > snap-$dpid.hmm

/bin/cp -p snap-$dpid.hmm $scd/
/bin/cp -p snaptrain/$dpid-$hmm.zff $scd/snaptrain-$dpid-$hmm.zff
gzip $scd/snaptrain-$dpid-$hmm.zff

#?? save snaptrain/$dpid-$hmm.zff
echo "/bin/rm -rf snaptrain"


echo ## ===== snaprun =================================

## problem with running snap on full scaffolds.fa is that when it chokes on one,
## it dies; need to skip on to next scaffold instead

## need to run Kent soft on linux
##/bin/rm -rf $scd/perchr
if (! -d $scd/perchr) then
 echo "faSplit $chrfasta $scd/perchr/ .."
 mkdir $scd/perchr
 chmod g+w $scd/perchr
 ssh pumapr /usr/local/bio/ucsc/bin/faSplit byname $chrfasta $scd/perchr/
endif

pushd $scd/perchr/ 
set chrs=`ls -1 | sed -e"s/.fa//"`
popd

set hmm=snap-$dpid.hmm

/bin/rm -rf snapout
mkdir snapout
echo "snaprun snap-$dpid.hmm .."

foreach chr ($chrs)
$ZOE/snap -quiet -name 'SNAP.eugenes' -gff3 -aa snapout/$chr.aa -tx snapout/$chr.tr $hmm $scd/perchr/$chr.fa > snapout/$chr.gff
end
echo "done snaprun snap-$dpid.hmm .."

## sed snap names ?
cat snapout/*.gff > snap-$dpid.gff
cat snapout/*.aa > snap-$dpid.aa
cat snapout/*.tr > snap-$dpid.tr
gzip snap-$dpid.gff snap-$dpid.aa snap-$dpid.tr 
/bin/mv snap-$dpid.gff.gz snap-$dpid.aa.gz snap-$dpid.tr.gz $scd/

echo "/bin/rm -rf snapout"
echo "/bin/rm -rf $scd/perchr/"

echo ## ======================================