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improved aa script

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Tanushree Tunstall 2022-06-13 21:48:44 +01:00
parent 2307a19d86
commit c4ae6d2412
2 changed files with 29 additions and 2 deletions
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26
scripts/aa_index_scripts/new-aa.sh Executable file
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#!/bin/sh
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 ${snp_dir}/output/*mcsm_snps*)
do
echo -n "${i}," >> $aa_outfile
python $aa_python $snp_dir/input/pnca_complex.pdb A $i >> $aa_outfile
done
# How I want it to run
#gene = "pncA" # force it to be lowercase
#chain = "A"
#mutfile = "/home/tanu/git/Data/output/<gene>_mcsm_snps.csv"
#mut = for i in mutfile
#$1 = "/home/tanu/git/Data/input/<gene>_complex.pdb
#$2 = chain
#$3 = mut
#python /home/tanu/git/LSHTM_analysis/scripts/aa_index_scripts/aaindex/get_scores.py $1 $2 $3

5
scripts/aa_index_scripts/run_aaeg.sh
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@ -1,7 +1,8 @@
#!/bin/sh
#python /home/sportelli/Desktop/Important_Code/structural/aaindex/get_scores.py /home/sportelli/Desktop/Project_2_rpoB/leprae/RMLE_B_RFP.pdb C P28A #python /home/sportelli/Desktop/Important_Code/structural/aaindex/get_scores.py /home/sportelli/Desktop/Project_2_rpoB/leprae/RMLE_B_RFP.pdb C P28A
#python /home/tanu/git/LSHTM_analysis/scripts/aa_index_scripts/aaindex/get_scores.py /home/tanu/git/LSHTM_analysis/scripts/aa_index_scripts/pnca_complex.pdb A L4S #python /home/tanu/git/LSHTM_analysis/scripts/aa_index_scripts/aaindex/get_scores.py /home/tanu/git/LSHTM_analysis/scripts/aa_index_scripts/pnca_complex.pdb A L4S
python /home/tanu/git/LSHTM_analysis/scripts/aa_index_scripts/aaindex/get_scores.py /home/tanu/git/Data/pyrazinamide/input/pnca_complex.pdb A L4S #python /home/tanu/git/LSHTM_analysis/scripts/aa_index_scripts/aaindex/get_scores.py /home/tanu/git/Data/pyrazinamide/input/pnca_complex.pdb A L4S
for i in $(cat /home/tanu/git/Data/pyrazinamide/output/*mcsm_snps*); do echo -n "${i}," >>/home/tanu/git/Data/pyrazinamide/output/aa_index/pnca_aa; python /home/tanu/git/LSHTM_analysis/scripts/aa_index_scripts/aaindex/get_scores.py /home/tanu/git/Data/pyrazinamide/input/pnca_complex.pdb A $i >> /home/tanu/git/Data/pyrazinamide/output/aa_index/pnca_aa; done
# How I want it to run # How I want it to run
#drug = "pyrazinamide" #drug = "pyrazinamide"
#gene = "pncA" # force it to be lowercase #gene = "pncA" # force it to be lowercase