02_pvactools.sh

#!/bin/bash
###
 # @Author: Shuai Yi
 # @Date: 2023-01-07 23:34:27
 # @LastEditTime: 2023-06-18 01:14:18
 # @LastEditors: Shuai Yi
 # @Description: 
### 

#SBATCH -J pvactools #job name
#SBATCH -p normal
#SBATCH -o pvactools.log # log name
#SBATCH -e pvactools.log # err log name
#SBATCH --nodes=1
#SBATCH --nodelist=cpu3
#SBATCH --ntasks-per-node=1  
#SBATCH --cpus-per-task=32


#install pvactools 
#pip install pvactools #need python=3.6


#calculate the binding affinity of MHC-I and neoantigens
#all 70 tumor hla 
binding_affinity(){
local input_file="$1"
local output_directory="$2"
local hla_alleles="$3"
local prefix="$4"
source /master/shuai_yi/anaconda3/bin/activate pvactools_2
mkdir -p ${output_directory}

pvacbind run \
--blastp-path /usr/bin/blastp \
--iedb-install-directory /master/shuai_yi/Projects/neoantigen/pvactools \
${input_file} \
${prefix} \
${hla_alleles} \
NetMHCpan \
${output_directory} \
-e1 8,9,10,11 \
-t 128 > ${output_directory}/pvactools.log 2>&1 
}

#binding_affinity ${input_file} ${output_directory} ${hla_alleles} ${prefix}