#!/bin/sh
drug=${1:-pyrazinamide}
gene=${2:-pnca}
chain=${3:-A}

aa_python="/home/tanu/git/LSHTM_analysis/scripts/aa_index_scripts/aaindex/get_scores.py"
snp_dir="/home/tanu/git/Data/${drug}"
aa_outfile="/home/tanu/git/Data/${drug}/output/aa_index/${gene}_aa.csv"

echo "Running for drug: ${drug} and gene ${gene}
Input from: ${snp_dir}/input/${gene}_complex.pdb
Chain: ${chain}
Output to: ${aa_outfile}"

cat ADD_aa_header.csv > $aa_outfile

for i in $(cat ${snp_dir}/output/${gene}_mcsm_formatted_snps.csv)
do
   echo -n "${i}," >> $aa_outfile
    python $aa_python $snp_dir/input/${gene}_complex.pdb $chain $i >> $aa_outfile
done


# TO RUN
# gene should be in lowercase
# ~/git/LSHTM_analysis/scripts/aa_index_scripts/run_aaindex.sh cycloserine alr A
# ~/git/LSHTM_analysis/scripts/aa_index_scripts/run_aaindex.sh ethambutol embb B
# ~/git/LSHTM_analysis/scripts/aa_index_scripts/run_aaindex.sh streptomycin gid A
# ~/git/LSHTM_analysis/scripts/aa_index_scripts/run_aaindex.sh isoniazid katg A
# ~/git/LSHTM_analysis/scripts/aa_index_scripts/run_aaindex.sh pyrazinamide pnca A
# ~/git/LSHTM_analysis/scripts/aa_index_scripts/run_aaindex.sh rifampicin rpob A