ls -ltr synNoContext/*bl | args 9 > synlist_noContext.txt
ls -ltr synContext/*bl | args 9 > synlist_Context.txt

synlist2bin -o synlist_nocontext.bin synlist_noContext.txt
synlist2bin -o synlist_context.bin synlist_Context.txt


cat allele.list | gawk '{print substr($1,1,4)"*" substr($1,5,2)":" substr($1,7,2) "-" substr($1,10,4) "*" substr($1,14,2) ":" substr($1,16,4), $1}' > convert_pseudo.dat 

for a in DQA1 DQB1 DPA1 DPB1; do cat allelelist_ps|awk -v a=$a 'substr($1,1,4) == a'|awk '{print $1,$5}'|sort|uniq > pseudo/$a; done

# Update pseudosequence file
#cat pseudosequence.2022.all.X.dat pseudo/all_dqdp |awk '{print $1,$2}'|sort|uniq > pseudosequence.2022.all.X.dat.new
#mv pseudosequence.2022.all.X.dat pseudosequence.2022.all.X.dat_
#mv pseudosequence.2022.all.X.dat.new pseudosequence.2022.all.X.dat

# Update convert_pseudo.dat
#python make_convert_pseudo.py  > convert_pseudo.dat.new
#mv convert_pseudo.dat convert_pseudo.dat_
#mv convert_pseudo.dat.new convert_pseudo.dat

cat pseudosequence.2022.all.X.dat|awk '{print $1,$1}' > allelelist.txt.new

cat /net/sund-nas.win.dtu.dk/storage/services/www/html/services/NetMHCIIpan-4.2/allelelist|awk '{print $1}' > webserver_alleles


# Add missing pseudoseqs
cat /net/sund-nas.win.dtu.dk/storage/services/www/html/services/NetMHCIIpan-4.2/allelelist|awk '{print $1}' > webserver_alleles

cat pseudosequence.2022.all.X.dat pseudo/extra_pseudo |sort -nk1 > pseudosequence.2022.all.X.dat_
mv pseudosequence.2022.all.X.dat pseudosequence.2022.all.X.dat.old
mv pseudosequence.2022.all.X.dat_ pseudosequence.2022.all.X.dat

# Add missing alleles
pepgrep -v webserver_alleles allelelist.txt|grep -v DP|grep -v DQ |sort|uniq|awk '{print $1,$1}' > missing_alleles

cat allelelist.txt missing_alleles |sort -nk1 > allelelist.txt_
mv allelelist.txt allelelist.txt.old
mv allelelist.txt_ allelelist.txt

