From 03321c261e313d3208e9565bc6d1d7f6f01e24d3 Mon Sep 17 00:00:00 2001 From: Tanushree Tunstall Date: Mon, 13 Jun 2022 22:05:41 +0100 Subject: [PATCH] working new_aa.sh --- scripts/aa_index_scripts/new-aa.sh | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/scripts/aa_index_scripts/new-aa.sh b/scripts/aa_index_scripts/new-aa.sh index 14e6701..6bbd144 100755 --- a/scripts/aa_index_scripts/new-aa.sh +++ b/scripts/aa_index_scripts/new-aa.sh @@ -1,15 +1,16 @@ #!/bin/sh +drug=${1:-pyrazinamide} +gene=${2:-pnca} -drug="pyrazinamide" -gene="pnca" 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" -for i in $(cat ${snp_dir}/output/*mcsm_snps*) +echo "Running for drug: ${drug} and gene ${gene}. Output to: ${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/pnca_complex.pdb A $i >> $aa_outfile + python $aa_python $snp_dir/input/${gene}_complex.pdb A $i >> $aa_outfile done # How I want it to run #gene = "pncA" # force it to be lowercase