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filterMajor.sh
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filterMajor.sh
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#!/bin/bash
# (https://hivdb.stanford.edu/dr-summary/resistance-notes/PI/)
# 31-10-2018
# XXXr highest level of resistance to PI
# XXXp potential contraindication in the use of PI
# (https://hivdb.stanford.edu/pages/3DStructures/pr.html)
# 11-09-2019
# Binding site || Cleft residues: 8,23,25-27,29,30,32,47,48,50,82,84
# D30N NFVr
# V32I ATV DRVp FPVr IDVp LPVp TPV
# L33F ATV DRV FPVp LPV NFV TPV
# M46I ATV FPVp IDVp LPV NFVp TPV
# M46L ATV FPVp IDVp LPV NFVp TPV
# I47V ATV DRVp FPVp IDV LPV NFV TPVp
# I47A DRVp FPVr LPVr TPVp
# G48V ATVp LPV NFVr SQVr
# G48M ATVp LPV NFVr SQVr
# I50L ATVr
# I50V DRVp FPVr LPVp
# I54V ATV FPV IDVr LPVp NFVr SQVp TPVp
# I54T ATV FPV IDVr LPVp NFVr SQVp
# I54A ATV FPV IDVr LPVp NFVr SQVp TPVp
# I54L ATV DRVp FPVr IDV LPVp NFVr SQV
# I54M ATV DRVp FPVr IDV LPVp NFVr SQV TPVp
# L76V DRVp FPVr IDVr LPVr
# V82A ATV FPV IDVr LPVr NFVr SQV
# V82F ATV DRV FPVr IDVr LPVr NFVr
# V82S ATV FPV IDVr LPVr NFVr
# V82T ATV FPV IDVr LPVr NFVr SQV TPVr
# V82L TPVr
# I84V ATVr DRV FPVr IDVr LPVp NFVr SQVr TPVp
# N88S ATVr IDV NFVr SQV
# N88D NFVr
# L90M ATVp FPVp IDVp LPV NFVr SQVr
# Files to filter
ls *_pattern > pattern.tmp
#### Major Mutations ####
while read patfile
do
while read patmut
do
if [[ $patmut == D30N ]]; then echo $patmut >> ${patfile%%_pattern}_majorMut
elif [[ $patmut == V32I ]]; then echo $patmut >> ${patfile%%_pattern}_majorMut
elif [[ $patmut == L33F ]]; then echo $patmut >> ${patfile%%_pattern}_majorMut
elif [[ $patmut == M46[IL] ]]; then echo $patmut >> ${patfile%%_pattern}_majorMut
elif [[ $patmut == I47[VA] ]]; then echo $patmut >> ${patfile%%_pattern}_majorMut
elif [[ $patmut == G48[VM] ]]; then echo $patmut >> ${patfile%%_pattern}_majorMut
elif [[ $patmut == I50[LV] ]]; then echo $patmut >> ${patfile%%_pattern}_majorMut
elif [[ $patmut == I54[VTALM] ]]; then echo $patmut >> ${patfile%%_pattern}_majorMut
elif [[ $patmut == L76V ]]; then echo $patmut >> ${patfile%%_pattern}_majorMut
elif [[ $patmut == V82[AFSTL] ]]; then echo $patmut >> ${patfile%%_pattern}_majorMut
elif [[ $patmut == I84V ]]; then echo $patmut >> ${patfile%%_pattern}_majorMut
elif [[ $patmut == N88[SD] ]]; then echo $patmut >> ${patfile%%_pattern}_majorMut
elif [[ $patmut == L90M ]]; then echo $patmut >> ${patfile%%_pattern}_majorMut
fi
done < $patfile
done < pattern.tmp
#### Major Mutations in the Binding Site ####
while read patfile
do
while read patmut
do
if [[ $patmut == D30N ]]; then echo $patmut >> ${patfile%%_pattern}_majorMutBS
elif [[ $patmut == V32I ]]; then echo $patmut >> ${patfile%%_pattern}_majorMutBS
elif [[ $patmut == I47[VA] ]]; then echo $patmut >> ${patfile%%_pattern}_majorMutBS
elif [[ $patmut == G48[VM] ]]; then echo $patmut >> ${patfile%%_pattern}_majorMutBS
elif [[ $patmut == I50[LV] ]]; then echo $patmut >> ${patfile%%_pattern}_majorMutBS
elif [[ $patmut == V82[AFSTL] ]]; then echo $patmut >> ${patfile%%_pattern}_majorMutBS
elif [[ $patmut == I84V ]]; then echo $patmut >> ${patfile%%_pattern}_majorMutBS
fi
done < $patfile
done < pattern.tmp
rm pattern.tmp