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prsice.fhx.metagrs.sh
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prsice.fhx.metagrs.sh
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#!/bin/bash
# Created by Sander W. van der Laan | UMC Utrecht | s.w.vanderlaan[at]gmail[dot]com
# Last edit 2018-10-09
# Version 1.3.0
### Creating display functions
### Setting colouring
NONE='\033[00m'
BOLD='\033[1m'
OPAQUE='\033[2m'
FLASHING='\033[5m'
UNDERLINE='\033[4m'
RED='\033[01;31m'
GREEN='\033[01;32m'
YELLOW='\033[01;33m'
PURPLE='\033[01;35m'
CYAN='\033[01;36m'
WHITE='\033[01;37m'
### Regarding changing the 'type' of the things printed with 'echo'
### Refer to:
### - http://askubuntu.com/questions/528928/how-to-do-underline-bold-italic-strikethrough-color-background-and-size-i
### - http://misc.flogisoft.com/bash/tip_colors_and_formatting
### - http://unix.stackexchange.com/questions/37260/change-font-in-echo-command
### echo -e "\033[1mbold\033[0m"
### echo -e "\033[3mitalic\033[0m" ### THIS DOESN'T WORK ON MAC!
### echo -e "\033[4munderline\033[0m"
### echo -e "\033[9mstrikethrough\033[0m"
### echo -e "\033[31mHello World\033[0m"
### echo -e "\x1B[31mHello World\033[0m"
function echocyan { #'echobold' is the function name
echo -e "${CYAN}${1}${NONE}" # this is whatever the function needs to execute.
}
function echobold { #'echobold' is the function name
echo -e "${BOLD}${1}${NONE}" # this is whatever the function needs to execute, note ${1} is the text for echo
}
function echoitalic { #'echobold' is the function name
echo -e "\033[3m${1}\033[0m" # this is whatever the function needs to execute.
}
script_copyright_message() {
echo ""
THISYEAR=$(date +'%Y')
echoitalic "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echoitalic "+ The MIT License (MIT) +"
echoitalic "+ Copyright (c) 1979-${THISYEAR} Sander W. van der Laan +"
echoitalic "+ +"
echoitalic "+ Permission is hereby granted, free of charge, to any person obtaining a copy of this software and +"
echoitalic "+ associated documentation files (the \"Software\"), to deal in the Software without restriction, +"
echoitalic "+ including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, +"
echoitalic "+ and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, +"
echoitalic "+ subject to the following conditions: +"
echoitalic "+ +"
echoitalic "+ The above copyright notice and this permission notice shall be included in all copies or substantial +"
echoitalic "+ portions of the Software. +"
echoitalic "+ +"
echoitalic "+ THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT +"
echoitalic "+ NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND +"
echoitalic "+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES +"
echoitalic "+ OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN +"
echoitalic "+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. +"
echoitalic "+ +"
echoitalic "+ Reference: http://opensource.org. +"
echoitalic "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
}
echocyan "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echocyan " POLYGENIC SCORE CALCULATIONS"
echocyan ""
echocyan ""
echocyan "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echobold "*Setting the environment."
PROJECTDIR="/hpc/dhl_ec/svanderlaan/projects/polygenicscores"
HERCULESTOOLKIT="/hpc/local/CentOS7/dhl_ec/software/HerculesToolKit"
AEGSDATA="/hpc/dhl_ec/data/_ae_originals"
echobold "* Making some directories."
### Make directories for script if they do not exist yet (!!!PREREQUISITE!!!)
if [ ! -d ${PROJECTDIR}/PRSICEINOUYE/ ]; then
echo "The PRSICE directory does not exist, Mr. Bourne will make it for you!"
mkdir -v ${PROJECTDIR}/PRSICEINOUYE/
fi
chmod -R a+rwx ${PROJECTDIR}
echobold "* Setting some variables specific for PRSice calculations."
echoitalic " > data files ..."
echo " - creating AEGS to GWAS data variantID update list ..."
# SNPID RSID Chr BP A_allele B_allele MinorAllele MajorAllele AA AB BB AA_calls AB_calls BB_calls MAF HWE missing missing_calls Info CAF
# --- 1:10177:A:AC 01 10177 A AC AC A 554.34 731.78 239.87 46 56 8 0.39696 0.018899 6.3195e-06 0.92792 0.35024 0.396962
# --- 1:10235:T:TA 01 10235 T TA TA T 1524.2 1.8055 0 1523 0 0 0.00059159 4.8216e-17 0 0.0019659 0.26078 0.000591577
# --- rs145072688:10352:T:TA 01 10352 T TA TA T 490.88 755.85 279.26 46 55 15 0.43066 0.14578 1.0239e-05 0.92398 0.34431 0.430661
# echo "variantid rsid_aegs" > ${PROJECTDIR}/aegs_combo_1kGp3GoNL5_RAW.matching_variantID.list
# zcat ${AEGSDATA}/AEGS_COMBINED_IMPUTE2_1000Gp3_GoNL5/aegs_combo_1kGp3GoNL5_RAW.stats.gz | \
# awk '{ print $3, $4, $2 }' | \
# awk '{ printf "%2i %s %s\n" , $1, $2 , $3 }' | \
# awk '{ print $1":"$2, $3 }' | \
# tail -n +2 >> ${PROJECTDIR}/aegs_combo_1kGp3GoNL5_RAW.matching_variantID.list
# gzip -fv ${PROJECTDIR}/aegs_combo_1kGp3GoNL5_RAW.matching_variantID.list
echo " - creating 1000G phase 3 update list (for ISGC data)..."
### Header
### #CHROM POS ID REF ALT QUAL FILTER INFO
### 1 10177 rs367896724 A AC 100 PASS AC=2130;AF=0.425319;AN=5008;NS=2504;DP=103152;EAS_AF=0.3363;AMR_AF=0.3602;AFR_AF=0.4909;EUR_AF=0.4056;SAS_AF=0.4949;AA=|||unknown(NO_COVERAGE);VT=INDEL
### 1 10235 rs540431307 T TA 100 PASS AC=6;AF=0.00119808;AN=5008;NS=2504;DP=78015;EAS_AF=0;AMR_AF=0.0014;AFR_AF=0;EUR_AF=0;SAS_AF=0.0051;AA=|||unknown(NO_COVERAGE);VT=INDEL
### 1 10352 rs555500075 T TA 100 PASS AC=2191;AF=0.4375;AN=5008;NS=2504;DP=88915;EAS_AF=0.4306;AMR_AF=0.4107;AFR_AF=0.4788;EUR_AF=0.4264;SAS_AF=0.4192;AA=|||unknown(NO_COVERAGE);VT=INDEL
RAW1000Gdata="/hpc/dhl_ec/data/references/1000G/Phase3/VCF_format/"
# echo "rsid variantid chr position" > ${PROJECTDIR}/1000G.phase3version5b.update_VARIANTIDCHRBP.txt
# zcat ${RAW1000Gdata}/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz | \
# grep -v "##" | awk '$3 ~ '/^rs/' || $3 == "ID" ' | \
# awk '{ print $3, $1":"$2, $1, $2 }' | \
# tail -n +2 >> ${PROJECTDIR}/1000G.phase3version5b.update_VARIANTIDCHRBP.txt
# gzip -fv ${PROJECTDIR}/1000G.phase3version5b.update_VARIANTIDCHRBP.txt
echoitalic "* Inouye M et al. metaGRS ..."
if [ ! -d ${PROJECTDIR}/Inouye_bioRxiv_2018/ ]; then
echo "The INOUYE directory does not exist, Mr. Bourne will make it for you!"
mkdir -v ${PROJECTDIR}/Inouye_bioRxiv_2018/
fi
INOUYEDIR=${PROJECTDIR}/Inouye_bioRxiv_2018
# Head INOUYE
# chr position rsid allele1 allele2 effect_allele beta
# 1 2245570 rs2843152 C G G -2.76009e-02
# 1 22132518 rs35465346 A G G 2.39340e-02
# 1 38386727 rs28470722 A G G -1.74935e-02
# echo "variantid rsid rsid_aegs chr position effect_allele other_allele beta P_ukbb" > ${INOUYEDIR}/metaGRS_hg19_20180205.foo
# zcat ${INOUYEDIR}/metaGRS_hg19_20180205.txt.gz | \
# parseTable --col chr,position,rsid,allele1,allele2,effect_allele,beta | \
# awk '{ if($6 == $5) { print $1":"$2, $3, $3, $1, $2, $6, $4, $7, "NA" } else { print $1":"$2, $3, $3, $1, $2, $6, $5, $7, "NA" } }' >> \
# ${INOUYEDIR}/metaGRS_hg19_20180205.foo
# mergeTablesv2 \
# --file1 ${UKBBDIR}/UKBB.GWAS1KG.EXOME.CAD.SOFT.META.PublicRelease.300517.4pvalupdate.txt \
# --file2 ${INOUYEDIR}/metaGRS_hg19_20180205.foo \
# --index variantid --format NORM --replace > ${INOUYEDIR}/metaGRS_hg19_20180205.4PRSICE.foo
#
# mergeTablesv2 \
# --file1 ${PROJECTDIR}/aegs_combo_1kGp3GoNL5_RAW.matching_variantID.list.gz \
# --file2 ${INOUYEDIR}/metaGRS_hg19_20180205.4PRSICE.foo \
# --index variantid --format GZIP1 --replace > ${INOUYEDIR}/metaGRS_hg19_20180205.4PRSICE.txt
INOUYEBASEDATA="${INOUYEDIR}/metaGRS_hg19_20180205.4PRSICE.txt"
echoitalic " > setting the TARGETDATA (AEGS) ..."
TARGETDATA="/hpc/dhl_ec/data/_ae_originals/AEGS_COMBINED_IMPUTE2_1000Gp3_GoNL5/aegs_combo_1kGp3GoNL5_RAW_chr# "
echoitalic " > getting a phenotype file and exclusion list ..."
echo "FID IID AEGS_type COHORT STUDY_TYPE sex Age AgeSQR OR_year OR_year_C PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8 PC9 PC10 Calcification_bin Collagen_bin Fat10_bin Fat40_bin Macrophages_bin SMC_bin IPH Macrophages_BC Mastcells_BC Neutrophils_BC SMC_BC VesselDensityAvg_BC" > ${PROJECTDIR}/aegscombo_phenocov.pheno
cat ${AEGSDATA}/pheno_cov_exclusions/aegscombo_phenocov.sample | \
parseTable --col ID_1,ID_2,AEGS_type,COHORT,STUDY_TYPE,sex,Age,AgeSQR,OR_year,OR_year_C,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,Calcification_bin,Collagen_bin,Fat10_bin,Fat40_bin,Macrophages_bin,SMC_bin,IPH,Macrophages_BC,Mastcells_BC,Neutrophils_BC,SMC_BC,VesselDensityAvg_BC | tail -n +3 | \
sed 's/FEMALE/2/g' | sed 's/MALE/1/g' >> ${PROJECTDIR}/aegscombo_phenocov.pheno
echoitalic " > PRSice general and plotting settings ..."
# PRSICESETTINGS="--no-clump --print-snp --extract PRSice.valid --score sum --missing center --all-score --perm 10000"
# PRSICESETTINGS="--no-clump --print-snp --extract PRSice.valid --score sum --all-score "
PRSICEVALID="${INOUYEDIR}/PRSice.valid"
#--extract PRSice.valid
PRSICESETTINGS="--print-snp --extract ${PRSICEVALID} --score sum --all-score "
PRSICEPLOTTING="--fastscore --bar-col-high #E55738 --bar-col-low #1290D9 --quantile 100 --quant-break 2.5,5,10,20,40,60,80,90,95,97.5,100 --quant-ref 60"
PRSICETHREADS="8"
PRSICESEED="91149214"
PRSICEBARLEVELS="0.00000005,0.0000005,0.000005,0.00005,0.0005,0.005,0.05,0.1,0.2,0.3,0.4,0.5,1"
# PRSICEBARLEVELS="0.00000005,0.000005,0.0005,0.001,0.01,0.05,0.1,0.2,0.5,1"
SCORETYPE="PRSsum"
DATATYPE="BED"
PERMUTATION="NOPERM_NOCENTER"
PHENOTYPEFILE="${PROJECTDIR}/aegscombo_phenocov.pheno"
COVARIATES="sex,Age,OR_year_C,@PC[1-4],COHORT"
COVARIATESFACTOR="sex,COHORT"
COVARIATESFILE="${PROJECTDIR}/aegscombo_phenocov.pheno"
EXCLUSION="${PROJECTDIR}/aegscombo.exclusion_nonCEA.list"
STATTYPE="--beta"
SNPID="rsid_aegs"
CHRID="chr"
BPID="position"
A1ID="effect_allele"
A2ID="other_allele"
STATID="beta"
# PVALUEID="P_ukbb"
PVALUEID="P"
if [ ! -d ${PROJECTDIR}/PRSICEINOUYE ]; then
echo "The metaGRS directory does not exist, Mr. Bourne will make it for you!"
mkdir -v "${PROJECTDIR}/PRSICEINOUYE"
fi
BASEDATA="${INOUYEBASEDATA}"
PRSICEDIR="${PROJECTDIR}/PRSICEINOUYE"
for PHENO in IPH; do
# for PHENO in Calcification_bin Collagen_bin Fat10_bin Fat40_bin Macrophages_bin SMC_bin IPH; do
echoitalic " > statistics ..."
TARGETTYPE="T"
echoitalic " > phenotypes and covariates ..."
PHENOTYPE="${PHENO}"
PRSICEOUTPUTNAME="--out PRSice.${PHENOTYPE}.${SCORETYPE}.${DATATYPE}.${PERMUTATION}"
cd ${PRSICEDIR}
prsice.R --prsice $(command -v prsice) \
--dir ${PRSICEDIR} \
--seed ${PRSICESEED} \
--bar-levels ${PRSICEBARLEVELS} \
--base ${BASEDATA} \
--target ${TARGETDATA} \
--thread ${PRSICETHREADS} \
${STATTYPE} \
--binary-target ${TARGETTYPE} \
--snp ${SNPID} \
--chr ${CHRID} \
--bp ${BPID} \
--A1 ${A1ID} \
--A2 ${A2ID} \
--stat ${STATID} \
--pvalue ${PVALUEID} \
--cov-file ${COVARIATESFILE} \
--cov-col ${COVARIATES} \
--cov-factor ${COVARIATESFACTOR} \
--pheno-file ${PHENOTYPEFILE} \
--pheno-col ${PHENOTYPE} \
--remove ${EXCLUSION} \
${PRSICEPLOTTING} \
${PRSICESETTINGS} \
${PRSICEOUTPUTNAME}
done
# for PHENO in Macrophages_BC Mastcells_BC Neutrophils_BC SMC_BC VesselDensityAvg_BC; do
# echoitalic " > statistics ..."
# TARGETTYPE="F"
#
# echoitalic " > phenotypes and covariates ..."
# PHENOTYPE="${PHENO}"
# PRSICEOUTPUTNAME="--out PRSice.${PHENOTYPE}.${SCORETYPE}.${DATATYPE}.${PERMUTATION}"
#
# cd ${PRSICEDIR}
#
# prsice.R --prsice $(command -v prsice) \
# --dir ${PRSICEDIR} \
# --seed ${PRSICESEED} \
# --bar-levels ${PRSICEBARLEVELS} \
# --base ${BASEDATA} \
# --target ${TARGETDATA} \
# --thread ${PRSICETHREADS} \
# ${STATTYPE} \
# --binary-target ${TARGETTYPE} \
# --snp ${SNPID} \
# --chr ${CHRID} \
# --bp ${BPID} \
# --A1 ${A1ID} \
# --A2 ${A2ID} \
# --stat ${STATID} \
# --pvalue ${PVALUEID} \
# --cov-file ${COVARIATESFILE} \
# --cov-col ${COVARIATES} \
# --cov-factor ${COVARIATESFACTOR} \
# --pheno-file ${PHENOTYPEFILE} \
# --pheno-col ${PHENOTYPE} \
# --remove ${EXCLUSION} \
# ${PRSICEPLOTTING} \
# ${PRSICESETTINGS} \
# ${PRSICEOUTPUTNAME}
#
# done
echo ""
echocyan "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echobold "Wow. I'm all done buddy. What a job 😱 ! let's have a 🍻🍻 ... 🖖 "
script_copyright_message