spectmhc.sh

#!/bin/sh
#inputs - netMHC folder, fasta-file, MHC alleles, MHC version, binding Rank cutoff
#-r -> save raw netmhc output
#-f -> final in fasta format
#-s -> split file
#-h -> help

raw_output=0
#fasta_output=1
split_file=0

while getopts ":rfhs:" flag; do
case "$flag" in
    r) raw_output=1
       ;;
	s) split_file=1
	   ;;
	h) echo ""
	   echo "This is a set of scripts that together predict MHC ligands and output a fasta file to be used for downstream mass spectrometry based searches."
	   echo "Please cite this article: MHC-I Ligand Discovery Using Targeted Database Searches of Mass Spectrometry Data: Implications for T-Cell Immunotherapies"
	   echo "Usage: bash ./$0 [-r] [-s] <netMHC folder> <input fasta> <MHC version> <binding Rank cutoff> <allele> <number_of_split_files>"
	   echo ""
     	   echo "    -h -> help"
	   echo "    -r -> save raw netmhc output"
	   #echo "    -f -> final in fasta format"
	   echo "    -s -> split file"
	   echo "    netMHC folder -> path to NetMHC folder, ex: "
     	   echo "    MHC version -> input the version of netMHC 3.4/4.0/pan"
	   echo "    input fasta -> input protein data in fasta format, .fa/.fasta" 
     	   echo "    binding Rank cutoff -> cutoff to be used, ex: 2"
     	   echo "    allele -> allele to predict, ex: H2-Kb"
	   echo "    number_of_split_files -> only works if -s is selected. enter a numeric value,\
	   	                        such that every split file has between 1000-2000 sequences"
	   echo ""
	   exit 1
	    ;;
    \?)
       echo "Invalid option: -$OPTARG" >&2
       ;;
  esac
done

shift $((OPTIND-1))

# parameters
if [ "$#" -ne 5 ]; then
  echo "bash ./$0 [-r] [-s] <netMHC folder> <MHC version> <input fasta> <binding Rank cutoff> <allele> <number_of_split_files>"
  exit 1
fi

path=$1
version=$2
files=$3
cut_off=$4
allele=$5
number=$6

if [ $version == "3.4" ]; then
	echo "Using NetMHC version 3.4"
	
elif [ $version == "4.0" ]; then
	echo "Using NetMHC version 4.0"
	
elif [ $version == "pan" ]; then
	echo "Using NetMHC version pan"
	
else
	echo "Warning: Unrecognized version. NetMHC version must be 3.4/4.0/pan"
	exit 1
fi

length=$(python input_length.py)

#split files

if [ split_file == 1 ]; then
	split_list=$(python split_file.py $files $number)
	
else 
	echo "Skipping split files"
	split_list=$files
fi

#execute netmhc
raw_list=$(python executemhc.py $path $version $split_list $allele $length)

#output as fasta
python tofasta.py $version $raw_list $cut_off
echo "output fasta generated"

#raw netmhc output
if [ raw_output == 0 ]; then
	python remove_raw.py $split_list
	python remove_raw.py $raw_list
	
else 
	python remove_raw.py $split_list
fi


#done
echo "The execution is complete. Your fasta is now available"