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added scripts and files to make AA index work for all drug targets, add header to the aa index output and fetch the aa index headers

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Tanushree Tunstall 2022-06-15 11:24:07 +01:00
parent 03321c261e
commit 1204f1faba
14 changed files with 1746 additions and 1969 deletions
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31
scripts/aa_index_scripts/run_aaindex.sh Executable file
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#!/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