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filterMinor.sh
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filterMinor.sh
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#!/bin/bash
# (https://hivdb.stanford.edu/dr-summary/resistance-notes/PI/)
# 03-09-2019
# XXXc common nonpolymorphic accessory resistance mutations to PI
# XXXa accessory resistance mutations associated with reduced PI susceptibility
# XXXr rare nonpolymorphic PI-selected variants (not well-studied)
# L10F DRVc FPVc IDVc LPVc NFVc
# L10I ATVa DRVa FPVa IDVa LPVa NFVa SQVa TPVa
# L10V ATVa DRVa FPVa IDVa LPVa NFVa SQVa TPVa
# L10R ATVr DRVr FPVr IDVr LPVr NFVr SQVr TPVr
# L10Y ATVr DRVr FPVr IDVr LPVr NFVr SQVr TPVr
# V11I DRVa FPVa
# V11L DRVr FPVr
# K20R ATVc DRVc FPVc IDVc LPVc NFVc SQVc TPVc
# K20I NFVa # consensus amino acid in subtype G and CRF02_AG viruses
# K20M ATVr DRVr FPVr IDVr LPVr NFVr SQVr TPVr
# K20T ATVa FPVa IDVa LPVa NFVa SQVa
# K20V ATVr DRVr FPVr IDVr LPVr NFVr SQVr TPVr
# L23I NFVr
# L24I ATVc FPVc IDVc LPVc SQVc # increases susceptibility to TPV
# L24F ATVa FPVa IDVa LPVa SQVa
# L24M ATVr DRVr FPVr IDVr LPVr NFVr SQVr TPVr
# M36I ATVa DRVa FPVa IDVa LPVa NFVa SQVa TPVa # increases replication fitness of viruses with PI-resistance mutations # consensus amino acid in most of the non-B subtypes
# K43T ATVr DRVr FPVr IDVr LPVr NFVr SQVr TPVa
# M46V ATVr DRVr FPVr IDVr LPVr NFVr SQVr TPVr
# G48A ATVr LPVr NFVr SQVr
# G48S ATVr LPVr NFVr SQVr
# G48T ATVr LPVr NFVr SQVr
# G48Q ATVr LPVr NFVr SQVr
# G48L ATVr LPVr NFVr SQVr
# F53L ATVc IDVc LPVc NFVa SQVc
# F53Y ATVr DRVr FPVr IDVr LPVr NFVr SQVr TPVr
# I54S ATVa FPVa IDVa LPVa NFVa SQVa TPVa
# I54T ATVa FPVa IDVa LPVa NFVa SQVa TPVa
# Q58E ATVc DRVc FPVc IDVc LPVc NFVc SQVc TPVc
# A71V ATVc DRVc FPVc IDVc LPVc NFVc SQVc TPVc
# A71T ATVc DRVc FPVc IDVc LPVc NFVc SQVc TPVc
# A71I ATVa DRVa FPVa IDVa LPVa NFVa SQVa TPVa
# A71L ATVa DRVa FPVa IDVa LPVa NFVa SQVa TPVa
# G73S ATVc DRVa FPVa IDVc LPVa NFVc SQVc TPVa
# G73T ATVc DRVa FPVa IDVc LPVa NFVc SQVc TPVa
# G73C ATVc DRVa FPVa IDVc LPVa NFVc SQVc TPVa
# G73A ATVc DRVa FPVa IDVc LPVa NFVc SQVc TPVa
# G73D ATVr DRVr FPVr IDVr LPVr NFVr SQVr TPVr
# G73V ATVr DRVr FPVr IDVr LPVr NFVr SQVr TPVr
# T74P ATVa DRVa FPVa IDVa LPVa NFVa SQVa TPVa
# T74S ATVa DRVa FPVa IDVa LPVa NFVa SQVa TPVa # consensus amino acid in most non-B subtypes
# V82M ATVr DRVr FPVr IDVa LPVa NFVr SQVr TPVr # in most subtypes, it requires a 2-bp mutation # in subtype G, it usually requires a single bp mutation (IDV!)
# V82C ATVr DRVr FPVr IDVr LPVr NFVr SQVr TPVr
# N83D ATVc IDVc NFVc SQVc TPVc
# N83S ATVr DRVr FPVr IDVr LPVr NFVr SQVr TPVr
# I84A ATVr DRVr FPVr IDVr LPVr NFVr SQVr TPVr # high-level resistance to PI
# I84C ATVr DRVr FPVr IDVr LPVr NFVr SQVr TPVr # less marked effect on PI susceptibility
# I85V ATVc DRVc FPVc IDVc LPVc NFVc SQVc TPVc # minimal, if any, effect on PI susceptibility
# N88T ATVa DRVr FPVr IDVr LPVr NFVa SQVr TPVr
# N88G ATVa DRVr FPVr IDVr LPVr NFVa SQVr TPVr
# L89V DRVc FPVc IDVc LPVc NFVc
# L89T ATVr DRVr FPVr IDVr LPVr NFVr SQVr TPVr # uncertain phenotypic and clinical significance
# Files to filter
ls *_pattern > pattern.tmp
#### Minor Mutations ####
while read patfile
do
while read patmut
do
if [[ $patmut == L10[FIVRY] ]]; then echo $patmut >> ${patfile%%_pattern}_minorMut
elif [[ $patmut == V11[IL] ]]; then echo $patmut >> ${patfile%%_pattern}_minorMut
elif [[ $patmut == K20[RIMTV] ]]; then echo $patmut >> ${patfile%%_pattern}_minorMut
elif [[ $patmut == L23I ]]; then echo $patmut >> ${patfile%%_pattern}_minorMut
elif [[ $patmut == L24[IFM] ]]; then echo $patmut >> ${patfile%%_pattern}_minorMut
elif [[ $patmut == M36I ]]; then echo $patmut >> ${patfile%%_pattern}_minorMut
elif [[ $patmut == K43T ]]; then echo $patmut >> ${patfile%%_pattern}_minorMut
elif [[ $patmut == M46V ]]; then echo $patmut >> ${patfile%%_pattern}_minorMut
elif [[ $patmut == G48[ASTQL] ]]; then echo $patmut >> ${patfile%%_pattern}_minorMut
elif [[ $patmut == F53[LY] ]]; then echo $patmut >> ${patfile%%_pattern}_minorMut
elif [[ $patmut == I54[ST] ]]; then echo $patmut >> ${patfile%%_pattern}_minorMut
elif [[ $patmut == Q58E ]]; then echo $patmut >> ${patfile%%_pattern}_minorMut
elif [[ $patmut == A71[VTIL] ]]; then echo $patmut >> ${patfile%%_pattern}_minorMut
elif [[ $patmut == G73[STCADV] ]]; then echo $patmut >> ${patfile%%_pattern}_minorMut
elif [[ $patmut == T74[PS] ]]; then echo $patmut >> ${patfile%%_pattern}_minorMut
elif [[ $patmut == V82[MC] ]]; then echo $patmut >> ${patfile%%_pattern}_minorMut
elif [[ $patmut == N83[DS] ]]; then echo $patmut >> ${patfile%%_pattern}_minorMut
elif [[ $patmut == I84[AC] ]]; then echo $patmut >> ${patfile%%_pattern}_minorMut
elif [[ $patmut == I85V ]]; then echo $patmut >> ${patfile%%_pattern}_minorMut
elif [[ $patmut == N88[TG] ]]; then echo $patmut >> ${patfile%%_pattern}_minorMut
elif [[ $patmut == L89[VT] ]]; then echo $patmut >> ${patfile%%_pattern}_minorMut
fi
done < $patfile
done < pattern.tmp
# L23I NFVr
# G48A ATVr LPVr NFVr SQVr
# G48S ATVr LPVr NFVr SQVr
# G48T ATVr LPVr NFVr SQVr
# G48Q ATVr LPVr NFVr SQVr
# G48L ATVr LPVr NFVr SQVr
# V82M ATVr DRVr FPVr IDVa LPVa NFVr SQVr TPVr # in most subtypes, it requires a 2-bp mutation # in subtype G, it usually requires a single bp mutation (IDV!)
# V82C ATVr DRVr FPVr IDVr LPVr NFVr SQVr TPVr
# I84A ATVr DRVr FPVr IDVr LPVr NFVr SQVr TPVr # high-level resistance to PI
# I84C ATVr DRVr FPVr IDVr LPVr NFVr SQVr TPVr # less marked effect on PI susceptibility
#### Minor Mutations in the Binding Site ####
while read patfile
do
while read patmut
do
if [[ $patmut == L23I ]]; then echo $patmut >> ${patfile%%_pattern}_minorMutBS
elif [[ $patmut == G48[ASTQL] ]]; then echo $patmut >> ${patfile%%_pattern}_minorMutBS
elif [[ $patmut == V82[MC] ]]; then echo $patmut >> ${patfile%%_pattern}_minorMutBS
elif [[ $patmut == I84[AC] ]]; then echo $patmut >> ${patfile%%_pattern}_minorMutBS
fi
done < $patfile
done < pattern.tmp
rm pattern.tmp