## ===== snaprun =================================

setenv ZOE /bio/bio-grid/mb/SNAP

## 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
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/
# ssh pumapr /usr/local/bio/ucsc/bin/faSplit size $scd/perchr/X.fa 10000000 $scd/perchr/pX
endif

# set chrs=`ls -1 $scd/perchr/*.fa | sed -e"s/.fa//" -e"s,$scd/perchr/,,"`
###/usr/bin/ls: Arg list too long.
pushd $scd/perchr/ 
## check for part-chrs: p*.fa ??
set chrs=`ls -1 p*.fa | sed -e"s/.fa//"`
if ("X$chrs" == "X") set chrs=`ls -1 | sed -e"s/.fa//"`
#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/"

## ======================================