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gwastoolkit.plotter.qc.sh
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gwastoolkit.plotter.qc.sh
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#!/bin/bash
### Creating display functions
### Setting colouring
NONE='\033[00m'
OPAQUE='\033[2m'
FLASHING='\033[5m'
BOLD='\033[1m'
ITALIC='\033[3m'
UNDERLINE='\033[4m'
STRIKETHROUGH='\033[9m'
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 ${1} is the text for echo
}
function echoitalic {
echo -e "${ITALIC}${1}${NONE}"
}
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 ""
echoerror "An example command would be: gwastoolkit.plotter.qc.sh [arg1: path_to_configuration_file] [arg2: phenotype]"
echoerror ""
echoerror "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
# The wrong arguments are passed, so we'll exit the script now!
exit 1
}
echobold "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echobold " GWASTOOLKIT PLOTTER -- AFTER QC"
echobold " plotting of SNPTEST analysis results after quality control"
echobold ""
echobold " Version : v1.1.6"
echobold ""
echobold " Last update: 2023-11-29"
echobold " Written by : Sander W. van der Laan (s.w.vanderlaan-2@umcutrecht.nl)."
echobold ""
echobold " Testers : - Saskia Haitjema (s.haitjema@umcutrecht.nl)"
echobold " - Aisha Gohar (a.gohar@umcutrecht.nl)"
echobold " - Jessica van Setten (j.vansetten@umcutrecht.nl)"
echobold ""
echobold " Description: Plotting of a SNPTEST analysis: making Manhattan, and QQ plots of"
echobold " the filtered data."
echobold ""
echobold "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
### 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 [[ $# -lt 2 ]]; then
echo "Oh, computer says no! Number of arguments found "$#"."
script_arguments_error "You must supply at least [2] arguments when plotting *** GWASToolKit *** results!"
echo ""
script_copyright_message
else
echo "All arguments are passed. These are the settings:"
### SET INPUT-DATA
OUTPUT_DIR=${PROJECTDIR}/${PROJECTNAME}/snptest_results/${PHENOTYPE} # depends on arg1
echo "The output directory is...................: ${OUTPUT_DIR}"
echo "The phenotypes is.........................: ${PHENOTYPE}"
echo ""
# PLOT GWAS RESULTS
echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echo " PLOTTING SNPTEST ANALYSIS RESULTS"
echo ""
echo "Please be patient...this can take a long time depending on the number of files."
echo "We started at: "$(date)
echo ""
SCRIPTS=${GWASTOOLKITDIR}/SCRIPTS
echo ""
echo "Plotting reformatted FILTERED data."
# what is the basename of the file?
RESULTS=${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.summary_results.QC.txt.gz
FILENAME=$(basename ${RESULTS} .txt.gz)
echo "The basename is: "${FILENAME}
echo ""
### COLUMN NAMES & NUMBERS
### 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
### ALTID RSID CHR BP OtherAlleleA CodedAlleleB AvgMaxPostCall Info all_AA all_AB all_BB TotalN MAC MAF CAF HWE P BETA SE
#### QQ-plot including 95%CI and compute lambda [P]
echo "Making QQ-plot including 95%CI and compute lambda..."
zcat ${OUTPUT_DIR}/${FILENAME}.txt.gz | ${GWASTOOLKITDIR}/SCRIPTS/parseTable.pl --col P | tail -n +2 | grep -v NA > ${OUTPUT_DIR}/${FILENAME}.QQplot.txt
# Rscript ${SCRIPTS}/plotter.qq.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${FILENAME}.QQplot.txt -o ${OUTPUT_DIR} -s PVAL -f PDF
Rscript ${SCRIPTS}/plotter.qq.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${FILENAME}.QQplot.txt -o ${OUTPUT_DIR} -s PVAL -f PNG
echo ""
### Manhattan plot for publications [CHR, BP, P]
echo "Manhattan plot for publications ..."
zcat ${OUTPUT_DIR}/${FILENAME}.txt.gz | ${GWASTOOLKITDIR}/SCRIPTS/parseTable.pl --col CHR,BP,P | tail -n +2 | grep -v NA > ${OUTPUT_DIR}/${FILENAME}.Manhattan.txt
# Rscript ${SCRIPTS}/plotter.manhattan.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${FILENAME}.Manhattan.txt -o ${OUTPUT_DIR} -c FULL -f PDF -t ${FILENAME}
Rscript ${SCRIPTS}/plotter.manhattan.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${FILENAME}.Manhattan.txt -o ${OUTPUT_DIR} -c FULL -f PNG -t ${FILENAME}
# Rscript ${SCRIPTS}/plotter.manhattan.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${FILENAME}.Manhattan.txt -o ${OUTPUT_DIR} -c TWOCOLOR -f PDF -t ${FILENAME}
Rscript ${SCRIPTS}/plotter.manhattan.R -p ${OUTPUT_DIR} -r ${OUTPUT_DIR}/${FILENAME}.Manhattan.txt -o ${OUTPUT_DIR} -c TWOCOLOR -f PNG -t ${FILENAME}
echo "Finished plotting, zipping up and re-organising intermediate files!"
rm -v ${OUTPUT_DIR}/${FILENAME}.QQplot.txt
rm -v ${OUTPUT_DIR}/${FILENAME}.Manhattan.txt
echo ""
echo ""
### END of if-else statement for the number of command-line arguments passed ###
fi
# script_copyright_message