#!/bin/sh

HLA_type_choose=$1
netMHC="/home/weitinglin66/tools/netMHC-4.0/netMHC"
declare -A HLA_type
HLA_type[0]="HLA-A0101"
HLA_type[1]="HLA-A0201"
HLA_type[2]="HLA-A0301"
HLA_type[3]="HLA-A2402"
HLA_type[4]="HLA-A2601"
HLA_type[5]="HLA-B0702"
HLA_type[6]="HLA-B0801"
HLA_type[7]="HLA-B2705"
HLA_type[8]="HLA-B3901"
HLA_type[9]="HLA-B4001"
HLA_type[10]="HLA-B5801"
HLA_type[11]="HLA-B1501"
#pbpaste| awk 'BEGIN{RS=",";ORS="\n";i=-1}{i ++}{print "HLA_type["i"]="$0}'

declare -A Peptides
Peptides[0]=14
Peptides[1]=13
Peptides[2]=12
Peptides[3]=11
Peptides[4]=10
Peptides[5]=9
Peptides[6]=8

declare -A PeptidesFasta
PeptidesFasta[0]="cosmic_neoantigen_27.fasta"
PeptidesFasta[1]="cosmic_neoantigen_25_length_from_27.fasta"
PeptidesFasta[2]="cosmic_neoantigen_23_length_from_27.fasta"
PeptidesFasta[3]="cosmic_neoantigen_21_length_from_27.fasta"
PeptidesFasta[4]="cosmic_neoantigen_19_length_from_27.fasta"
PeptidesFasta[5]="cosmic_neoantigen_17_length_from_27.fasta"
PeptidesFasta[6]="cosmic_neoantigen_15_length_from_27.fasta"

for i in {0,1,2,3,4,5,6}
do

(/home/weitinglin66/tools/netMHC-4.0/netMHC -a ${HLA_type[$HLA_type_choose]} -l ${Peptides[$i]}  -xls -xlsfile ${HLA_type[$HLA_type_choose]}_${Peptides[$i]}  ${PeptidesFasta[$i]}  & )
done


#!/bin/sh

declare -A HLA_type
HLA_type[0]="HLA_A0101"
HLA_type[1]="HLA_A0201"
HLA_type[2]="HLA_A0301"
HLA_type[3]="HLA_A2402"
HLA_type[4]="HLA_A2601"
HLA_type[5]="HLA_B0702"
HLA_type[6]="HLA_B0801"
HLA_type[7]="HLA_B2705"
HLA_type[8]="HLA_B3901"
HLA_type[9]="HLA_B4001"
HLA_type[10]="HLA_B5801"
HLA_type[11]="HLA_B1501"

declare -A Server
Server[0]=01
Server[1]=02
Server[2]=03
Server[3]=04
Server[4]=05
Server[5]=06
Server[6]=07
Server[7]=08
Server[8]=09
Server[9]=10
Server[10]=11
Server[11]=12


echo $SCRIPT
for i in 0 1 2 3 4 5 6 7 8 9 10 11
do
 MESSAGE=$i
 SCRIPT="cd /home/weitinglin66/Project/MHCprediction/${HLA_type[$MESSAGE]} ; sh netMHC_all_peptide_length.sh ${MESSAGE}"
 ssh -l weitinglin66 MIBngs-${Server[$i]} "${SCRIPT}"
done