#!/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