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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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scripts/aa_index_scripts/run_aa_eg.sh Executable file
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#!/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/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
#----------------------
# How I want it to run
#---------------------
#drug = "pyrazinamide"
#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
#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