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working new_aa.sh

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Tanushree Tunstall 2022-06-13 22:05:41 +01:00
parent c4ae6d2412
commit 03321c261e
1 changed files with 5 additions and 4 deletions
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scripts/aa_index_scripts/new-aa.sh
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@ -1,15 +1,16 @@
#!/bin/sh #!/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" aa_python="/home/tanu/git/LSHTM_analysis/scripts/aa_index_scripts/aaindex/get_scores.py"
snp_dir="/home/tanu/git/Data/${drug}" snp_dir="/home/tanu/git/Data/${drug}"
aa_outfile="/home/tanu/git/Data/${drug}/output/aa_index/${gene}_aa" 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 do
echo -n "${i}," >> $aa_outfile echo -n "${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 done
# How I want it to run # How I want it to run
#gene = "pncA" # force it to be lowercase #gene = "pncA" # force it to be lowercase