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gwastoolkit.locuszoomer.sh
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gwastoolkit.locuszoomer.sh
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#!/bin/bash
### 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'
function echobold { #'echobold' is the function name
echo -e "${BOLD}${1}${NONE}" # this is whatever the function needs to execute, note ${1} is the text for echo
}
function echonooption {
echo -e "${OPAQUE}${RED}${1}${NONE}"
}
function echoerrorflash {
echo -e "${RED}${BOLD}${FLASHING}${1}${NONE}"
}
function echoerror {
echo -e "${RED}${1}${NONE}"
}
# errors no option
function echoerrornooption {
echo -e "${YELLOW}${1}${NONE}"
}
function echoerrorflashnooption {
echo -e "${YELLOW}${BOLD}${FLASHING}${1}${NONE}"
}
### MESSAGE FUNCTIONS
script_copyright_message() {
echo ""
THISYEAR=$(date +'%Y')
echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echo "+ The MIT License (MIT) +"
echo "+ Copyright (c) 2015-${THISYEAR} Sander W. van der Laan +"
echo "+ +"
echo "+ Permission is hereby granted, free of charge, to any person obtaining a copy of this software and +"
echo "+ associated documentation files (the \"Software\"), to deal in the Software without restriction, +"
echo "+ including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, +"
echo "+ and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, +"
echo "+ subject to the following conditions: +"
echo "+ +"
echo "+ The above copyright notice and this permission notice shall be included in all copies or substantial +"
echo "+ portions of the Software. +"
echo "+ +"
echo "+ THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT +"
echo "+ NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND +"
echo "+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES +"
echo "+ OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN +"
echo "+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. +"
echo "+ +"
echo "+ Reference: http://opensource.org. +"
echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
}
script_arguments_error() {
echoerror "$1" # ERROR MESSAGE
echoerror ""
echoerror "- Argument #1 is path_to the configuration file."
echoerror "- Argument #2 is the phenotype analysed."
echoerror "- Argument #3 is the gene analysed -- gene-based analysis only."
echoerror ""
echoerror "An example command would be: gwastoolkit.locuszoomer.sh [arg1: path_to_configuration_file] [arg2: phenotype] [arg3: gene]"
echoerror ""
echoerror "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
# The wrong arguments are passed, so we'll exit the script now!
exit 1
}
script_arguments_error_analysis_type() {
echoerror "$1"
echoerror ""
echoerror " *** ERROR *** ERROR --- $(basename "${0}") --- ERROR *** ERROR ***"
echoerror ""
echoerror " You must supply the correct argument:"
echoerror " * [GWAS] -- genome-wide association study of traits in ${PHENOTYPE_FILE}."
echoerror " * [VARIANT] -- genetic analysis of variants in ${VARIANTLIST} for traits in ${PHENOTYPE_FILE}."
echoerror " * [REGION] -- genetic analysis of a specific region [chr${CHR}:${REGION_START}-${REGION_END}] for traits in ${PHENOTYPE_FILE}."
echoerror " * [GENE] -- genetic analysis of specific genes in ${GENES_FILE} for traits in ${PHENOTYPE_FILE}."
echoerror ""
echoerror " Please refer to instruction above."
echoerror ""
echoerror "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
# The wrong arguments are passed, so we'll exit the script now!
exit 1
}
echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echo " GWASTOOLKIT LOCUSZOOMER"
echo " regional association plotting of clumped results"
echo ""
echo " Version : v1.5.1"
echo ""
echo " Last update: 2018-01-24"
echo " Written by : Sander W. van der Laan ([email protected])."
echo ""
echo " Description: Plot a LocusZoom for (imputed) (meta-)ExomeChip or (meta-)GWAS hits "
echo " (determined after clumping!). "
echo ""
echo ""
echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
### LOADING CONFIGURATION FILE
source "$1" # Depends on arg1.
### REQUIRED | GENERALS
CONFIGURATIONFILE="$1" # Depends on arg1 -- but also on where it resides!!!
PHENOTYPE="$2" # Depends on arg2
### START of if-else statement for the number of command-line arguments passed ###
if [[ ${ANALYSIS_TYPE} = "GWAS" && $# -lt 2 ]]; then
echo "Oh, computer says no! Number of arguments found "$#"."
script_arguments_error "You must supply [2] arguments for regional association plotting of *** GENOME-WIDE ANALYSIS *** results!"
script_copyright_message
elif [[ ${ANALYSIS_TYPE} = "REGION" && $# -lt 3 ]]; then
echo "Oh, computer says no! Number of arguments found "$#"."
script_arguments_error "You must supply [3] arguments for regional association plotting of *** REGIONAL ANALYSIS *** results!"
script_copyright_message
elif [[ ${ANALYSIS_TYPE} = "GENES" && $# -lt 3 ]]; then
echo "Oh, computer says no! Number of arguments found "$#"."
script_arguments_error "You must supply [3] arguments for regional association plotting of *** GENE ANALYSIS *** results!"
script_copyright_message
else
echo "All arguments are passed. These are the settings:"
if [[ ${ANALYSIS_TYPE} = "GWAS" ]]; then
### SET INPUT-DATA
INPUTDIR=${PROJECTDIR}/${PROJECTNAME}/snptest_results/${PHENOTYPE} # depends on arg1
RESULTS=${INPUTDIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.summary_results.QC.txt.gz
elif [[ ${ANALYSIS_TYPE} = "REGION" ]]; then
### SET INPUT-DATA
INPUTDIR=${PROJECTDIR}/${PROJECTNAME}/snptest_results/${PHENOTYPE} # depends on arg1
RESULTS=${INPUTDIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.summary_results.QC.txt.gz
elif [[ ${ANALYSIS_TYPE} = "GENES" ]]; then
### SET INPUT-DATA
GENE="$3"
INPUTDIR=${PROJECTDIR}/${PROJECTNAME}/snptest_results/${GENE}/${PHENOTYPE} # depends on arg1
RESULTS=${INPUTDIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.${GENE}_${RANGE}.summary_results.QC.txt.gz
else
echo "Oh, computer says no! Number of arguments found "$#"."
script_arguments_error "You must supply [2-3] arguments for regional association plotting of *** GWASToolKit *** results!"
script_copyright_message
fi
echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echo " MAKE LOCUSZOOM PLOTS"
echo ""
### CHECKING ARGUMENTS ###
### Determine which reference and thereby input data to use, arg1 [1kGp3v5GoNL5/1kGp1v3/GoNL4]
if [[ ${REFERENCE} = "1kGp3v5GoNL5" ]]; then
echo "You're references is [${REFERENCE}]; using pop=EUR, build=hg19, and source=1000G_March2012."
LDMAP="--pop EUR --build hg19 --source 1000G_March2012"
elif [[ ${REFERENCE} = "1kGp1v3" ]]; then
echo "You're references is [${REFERENCE}]; using pop=EUR, build=hg19, and source=1000G_March2012."
LDMAP="--pop EUR --build hg19 --source 1000G_March2012"
elif [[ ${REFERENCE} = "GoNL4" ]]; then
echo "You're references is [${REFERENCE}]; using pop=EUR, build=hg19, and source=1000G_March2012."
LDMAP="--pop EUR --build hg19 --source 1000G_March2012"
else
### If arguments are not met than the
echoerror ""
echoerror " *** ERROR *** ERROR --- $(basename "${0}") --- ERROR *** ERROR ***"
echoerror ""
echoerror " You must supply the correct argument:"
echoerror " * [1kGp3v5GoNL5] -- for use of data imputed using 1000G (phase 3, version 5, \"Final release\") plus GoNL5."
echoerror " * [1kGp1v3] -- for use of data imputed using 1000G (phase 1, version 3)."
echoerror " * [GoNL4] -- for use of data imputed using GoNL4, note that this data *does not* include chromosome X."
echoerror ""
echoerror "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
# The wrong arguments are passed, so we'll exit the script now!
exit 1
fi
### SETTING VARIABLES BASED ON ARGUMENTS PASSED
# Plus make a new directory which will serve as the output directory!
if [ ! -d ${INPUTDIR}/locuszoom ]; then
echo ""
mkdir -v ${INPUTDIR}/locuszoom
OUTPUTDIR=${INPUTDIR}/locuszoom
echo "The output directory is set...: ${OUTPUTDIR}"
else
OUTPUTDIR=${INPUTDIR}/locuszoom
echo "Output directory already exists...: ${OUTPUTDIR}"
fi
echo ""
LOCUSZOOM_SETTINGS="ldColors=\"#595A5C,#4C81BF,#1396D8,#C5D220,#F59D10,red,#9A3480\" showRecomb=TRUE dCol='r^2' drawMarkerNames=FALSE refsnpTextSize=0.8 showRug=TRUE showAnnot=TRUE showRefsnpAnnot=TRUE showGenes=TRUE clean=FALSE bigDiamond=TRUE ymax=8 rfrows=10 refsnpLineWidth=2"
if [[ ${ANALYSIS_TYPE} = "GWAS" ]]; then
### Which variant to look at.
echo "We will lookup the following variants:"
VARIANTLIST="${INPUTDIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.summary_results.QC.${CLUMP_R2}.indexvariants.txt"
while read VARIANTS; do
for VARIANT in ${VARIANTS}; do
echo "* ${VARIANT}"
done
done < ${VARIANTLIST}
echo ""
N_VARIANTS=$(cat ${VARIANTLIST} | wc -l)
echo "Number of variants to plot...: ${N_VARIANTS} variants"
echo "Investigating range..........: ± ${RANGE}kb around each of these variants."
echo ""
echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echo "Initiating lookup..."
echo ""
### Making the input file for LocusZoom for the phenotype.
### Example header of input file
### MarkerName P-value
### rs7098888 0.000686966
### rs9733444 0.00149974
echo "Making the LocusZoom input-file for the phenotype..."
echo "MarkerName P-value" > ${OUTPUTDIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.${GENE}_${RANGE}.summary_results.QC.locuszoom
zcat ${RESULTS} | ${GWASTOOLKITDIR}/SCRIPTS/parseTable.pl --col RSID,P | tail -n +2 >> ${OUTPUTDIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.${GENE}_${RANGE}.summary_results.QC.locuszoom
while read VARIANTS; do
for VARIANT in ${VARIANTS}; do
echo "Plotting variant: ${VARIANT} ± ${RANGE}kb..."
cd ${OUTPUTDIR}
${LOCUSZOOM13} --metal ${OUTPUTDIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.${GENE}_${RANGE}.summary_results.QC.locuszoom --markercol MarkerName --delim space --refsnp ${VARIANT} --flank ${RANGE}kb ${LDMAP} theme=publication title="${VARIANT} in ${PHENOTYPE} (${EXCLUSION})" ${LOCUSZOOM_SETTINGS}
done
done < ${VARIANTLIST}
# gzipping locuszoom input
gzip -v ${OUTPUTDIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.summary_results.QC.locuszoom
echo ""
echo "All finished. Done making regional association plots for ${PHENOTYPE} data."
echo ""
echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
elif [[ ${ANALYSIS_TYPE} = "REGION" ]]; then
# Loading the lookup list file (should be a space-delimited list of variants with range, 1 PER line as they
# appear in the results output-files, e.g. 'rs12345 chr1 12345 98713'). Can also be a file
# with just one line - of course.
REGIONS_FILE="$3" # depends on arg3
echo ""
echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echo "Initiating lookup..."
echo ""
### Making the input file for LocusZoom for the phenotype.
### Example header of input file
### MarkerName P-value
### rs7098888 0.000686966
### rs9733444 0.00149974
echo "Making the LocusZoom input-file for the phenotype..."
echo "MarkerName P-value" > ${OUTPUTDIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.summary_results.QC.locuszoom
zcat ${RESULTS} | ${GWASTOOLKITDIR}/SCRIPTS/parseTable.pl --col RSID,P | tail -n +2 >> ${OUTPUTDIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.summary_results.QC.locuszoom
while IFS='' read -r REGIONOFINTEREST || [[ -n "$REGIONOFINTEREST" ]]; do
LINE=${REGIONOFINTEREST}
VARIANT=$(echo "${LINE}" | awk '{print $1}')
CHR=$(echo "${LINE}" | awk '{print $2}')
START=$(echo "${LINE}" | awk '{print $3}')
END=$(echo "${LINE}" | awk '{print $4}')
echo "Processing ${VARIANT} locus on ${CHR} between ${START} and ${END}..."
cd ${OUTPUTDIR}
${LOCUSZOOM13} --metal ${OUTPUTDIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.summary_results.QC.locuszoom --markercol MarkerName --delim space --refsnp ${VARIANT} --chr ${CHR} --start ${START} --end ${END} ${LDMAP} theme=publication title="${VARIANT} in ${PHENOTYPE} (${EXCLUSION})" ${LOCUSZOOM_SETTINGS}
done < ${REGIONS_FILE}
# gzipping locuszoom input
gzip -v ${OUTPUTDIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.summary_results.QC.locuszoom
echo ""
echo "All finished. Done making regional association plots for ${PHENOTYPE} data."
echo ""
echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
elif [[ ${ANALYSIS_TYPE} = "GENES" ]]; then
### Determine the gene to look at
echo "We will plot regional association ± ${RANGE}kb around the following [ ${GENE} ]."
echo ""
echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echo "Initiating lookup..."
echo ""
### Making the input file for LocusZoom for the phenotype.
### Example header of input file
### MarkerName P-value
### rs7098888 0.000686966
### rs9733444 0.00149974
echo "Making the LocusZoom input-file for the phenotype..."
echo "MarkerName P-value" > ${OUTPUTDIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.summary_results.QC.locuszoom
zcat ${RESULTS} | ${GWASTOOLKITDIR}/SCRIPTS/parseTable.pl --col RSID,P | tail -n +2 >> ${OUTPUTDIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.summary_results.QC.locuszoom
echo "Plotting variant: ${GENE}"
cd ${OUTPUTDIR}
${LOCUSZOOM13} --metal ${OUTPUTDIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.summary_results.QC.locuszoom --markercol MarkerName --delim space --refgene ${GENE} --flank ${RANGELZ}kb ${LDMAP} theme=publication title="${GENE} in ${PHENOTYPE} (${EXCLUSION})" ${LOCUSZOOM_SETTINGS}
# gzipping locuszoom input
gzip -v ${OUTPUTDIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.summary_results.QC.locuszoom
echo ""
echo "All finished. Done making regional association plots for ${PHENOTYPE} data."
echo ""
echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
else
### If arguments are not met then this error message will be displayed
script_arguments_error_analysis_type
fi
### END of if-else statement for the number of command-line arguments passed ###
fi
# script_copyright_message