#!/bin/csh

mkdir -p SYN
mkdir -p TSYN

set NNLIN = nnalign_gaps_pan_add_ligands_two_outputs_context_allelelist_exp
set PSEUDO = "./data/MHC_pseudo.dat"
set ALLELELIST = "./data/final_allelelist"
set MPAT = "./data/BLOSUM50"
set BLF = ".data//blosum62.freq_rownorm"
set RANPEP = "./data/ran9mer"

foreach n ( 0 1 2 3 4 )

	set TESF=./data/c00$n"_ba"
	set TEST_EL=./data/c00$n"_el"
	set LEAF=./data/f00$n"_ba"
	set LEAS_EL=./data/f00$n"_el"

	foreach nhid ( 56 66 )
		foreach s ( 1 2 3 4 5 )
			
			set SYN=./SYN/$n.$nhid.$s.syn.bl
			set TSYN=./TSYN/$n.$nhid.$s.syn.bl

			if ( ! -e $SYN ) then 

				touch $SYN

				$NNLIN -ishort -s $s -nt 2 -syn $SYN -nh $nhid -teststop -i 200 -mhc $PSEUDO -allelelist $ALLELELIST -bl -l 9 -eplen 0 -elpfr 0 -fl 0 -gl 10 -il 1 -encgl -encil -classI 8,9,10,11,12,13,14 -mpat $MPAT -blf $BLF -ft $TESF -test_EL $TEST_EL -train_EL $LEAS_EL $LEAF -burnin_HLA 20 -tsyn $TSYN -alternate 0.5 -rpepfile $RANPEP -iresc 1 -ns 300000 -exp > out.$n.$nhid.$s

			endif
		end

	end

end