#cp /farm/ftp/pub/incoming/buffalo/noe605.prot ../../xeasy/simnoe/.
#cp /farm/ftp/pub/incoming/buffalo/noe609.peaks ../../xeasy/simnoe/.
cp ../../xeasy/simnoe/sim1014.peaks simnoe.peaks
#cp ../../xeasy/simnoe/Nnoe1101.peaks Nnoe.peaks
#cp ../../xeasy/simnoe/ali1101.peaks ali.peaks
#awk -f spark.awk ../../../analysis/sparky/simnoesy_xeasy.peaks > simnoe.peaks
awk -f ../warn.awk simnoe.peaks > overint.peaks
#cp noe326.peaks simnoe.peaks
cp ../../xeasy/simnoe/noe1014.prot noefold.prot
cp ../../xeasy/hnco/coshift .
#cp ../../../analysis/noesy/noe.seq .
#cp ../../cyana/calc2/talos.aco .
cp ../../xeasy/simnoe/noea1014.peaks aro.peaks
awk -f ../protc2n.awk noefold.prot > noeall.prot
grep -v " C "  noeall.prot > prot1
cat prot1 coshift > prot2
sort -n prot2 > noe.prot
rm -f prot1 prot2
cp simnoe.peaks simnoemod.peaks
cp aro.peaks aromod.peaks
#cp sim2 simnoemod.peaks
awk -f ../peak2c.awk simnoemod.peaks > simc.peaks
awk -f ../peak2a.awk aro.peaks > aronoe.peaks
cat simc.peaks aronoe.peaks > cnoe.peaks
#cp simc.peaks cnoe.peaks
# mv simc.peaks  cnoe.peaks
awk -f ../peak2n.awk simnoemod.peaks > nnoe.peaks
cp ../../xeasy/simnoe/noe.seq .
#sed -f ../seq.sed noe.seq > tr80.seq
sed -f ../c.sed ./cnoe.peaks > cnoe4abs.peaks
sed -f ../c.sed ./nnoe.peaks > nnoe4abs.peaks
#sed -f ../c.sed ./Nnoe.peaks > Nnoe4abs.peaks
#sed -f ../c.sed ./ali.peaks > ali4abs.peaks
awk -f ../unassignc.awk cnoe4abs.peaks > unc.peaks
awk -f ../unassignn.awk nnoe4abs.peaks > unn.peaks
awk -f ../noiseN.awk nnoe4abs.peaks > nnoeabs.peaks
#awk -f ../noiseN.awk Nnoe4abs.peaks > Nnoeabs.peaks
#awk -f ../noiseC.awk ali4abs.peaks > aliabs.peaks
awk -f ../keepN.awk nnoeabs.peaks > nnoe1.peaks
awk -f ../keepNiso.awk nnoeabs.peaks > nnoe2.peaks
awk -f ../noiseC.awk cnoe4abs.peaks > cnoeabs.peaks
awk -f ../keepC.awk cnoeabs.peaks > cnoe1.peaks
awk -f ../keepCiso.awk cnoeabs.peaks > cnoe2.peaks
#awk -f ../shortc.awk cnoe1.peaks > cnoes.peaks
#awk -f ../shortn.awk nnoe1.peaks > nnoes.peaks
#awk -f noiseA.awk anoe2.peaks > anoe1.peaks
#awk -f a.awk anoe4abs.peaks > newa.peaks
#awk -f ../c.awk cnoe4abs.peaks > newc.peaks
#awk -f ../n.awk nnoe4abs.peaks > newn.peaks
#dyana  ./short