31 lines
1.1 KiB
Bash
Executable file
31 lines
1.1 KiB
Bash
Executable file
#!/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
|