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gwastoolkit.qc.sh
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gwastoolkit.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 "- Argument #3 is the gene analysed -- gene-based analysis only."
echoerror ""
echoerror "An example command would be: gwastoolkit.qc.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
}
echobold "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echobold " GWASTOOLKIT QUALITY CONTROL"
echobold " quality control of SNPTEST analysis results"
echobold ""
echobold " Version : v1.1.7"
echobold ""
echobold " Last update: 2022-10-30"
echobold " Written by : Sander W. van der Laan ([email protected])."
echobold ""
echobold " Testers: - Saskia Haitjema ([email protected])"
echobold " - Aisha Gohar ([email protected])"
echobold " - Jessica van Setten ([email protected])"
echobold ""
echobold " Description: Quality control of a SNPTEST analysis: filter on INFO, MAC, CAF and BETA/SE."
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 [[ ${ANALYSIS_TYPE} = "GWAS" && $# -lt 2 ]]; then
echo "Oh, computer says no! Number of arguments found "$#"."
script_arguments_error "You must supply [2] arguments for cleaning of *** GENOME-WIDE ANALYSIS *** results!"
script_copyright_message
elif [[ ${ANALYSIS_TYPE} = "REGION" && $# -lt 2 ]]; then
echo "Oh, computer says no! Number of arguments found "$#"."
script_arguments_error "You must supply [2] arguments for cleaning 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 cleaning of *** GENE ANALYSIS *** results!"
script_copyright_message
else
echo "All arguments are passed. These are the settings:"
if [[ ${ANALYSIS_TYPE} = "GWAS" || ${ANALYSIS_TYPE} = "REGION" ]]; then
### SET INPUT-DATA
OUTPUT_DIR=${PROJECTDIR}/${PROJECTNAME}/snptest_results/${PHENOTYPE} # depends on arg1
# what is the basename of the file?
RESULTS="${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.summary_results.txt.gz"
elif [[ ${ANALYSIS_TYPE} = "GENES" ]]; then
### SET INPUT-DATA
GENE="$3"
OUTPUT_DIR=${PROJECTDIR}/${PROJECTNAME}/snptest_results/${GENE}/${PHENOTYPE} # depends on arg1
# what is the basename of the file?
RESULTS="${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.${GENE}_${RANGE}.summary_results.txt.gz"
else
echo "Oh, computer says no! Number of arguments found "$#"."
script_arguments_error "You must supply [2-3] arguments for cleaning of *** GWASToolKit *** results!"
script_copyright_message
fi
echo "The output directory is...................: ${OUTPUT_DIR}"
echo "The phenotypes is.........................: ${PHENOTYPE}"
echo "The minimum info-score filter is..........: ${INFO}"
echo "The minimum minor allele count is.........: ${MAC}"
echo "The minimum coded allele frequency is.....: ${CAF}"
echo "The lower/upper limit of the BETA/SE is...: ${BETA_SE}"
echo ""
# PLOT GWAS RESULTS
echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echo " STARTING QUALITY CONTROL"
echo ""
echo "Please be patient...this can take a long time depending on the number of files."
echo "We started at: "$(date)
echo ""
echo ""
echo "Plotting reformatted FILTERED data."
FILENAME=$(basename ${RESULTS} .txt.gz)
echo "The basename is: "${FILENAME}
echo "Number of pre-QC variants:"
# zcat ${RESULTS} | wc -l
### 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
### --- 1:10177 01 10177 A AC 1 1 223 11 0 234 11 0.0235043 0.0235043 1 0.454287 0.237531 0.31689
### --- 1:10235 01 10235 T TA 1 1 234 0 0 234 0 0 0 1 NA NA NA
### --- 1:10352 01 10352 T TA 1 1 212 21 1 234 23 0.0491453 0.0491453 0.433423 0.869445 0.0353989 0.215128
### 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
### . 1:10177 01 10177 A AC 1 1 1290 49 2 1341 53.0001 0.0197614 0.0197614 0.0914172 0.567409 0.0778573 0.136111
### . 1:10235 01 10235 T TA 1 1 1341 0 0 1341 0 0 0 1 NA NA NA
### . 1:10352 01 10352 T TA 1 1 1266 69 6 1341 80.9999 0.0302013 0.0302013 0.000932758 0.358642 -0.100044 0.108948
### . 1:10539 01 10539 C A 1 1 1341 0 0 1341 0 0 0 1 NA NA NA
echo ""
echo "Filtering data, using the following criteria: "
echo " * ${INFO} <= INFO <= 1 "
echo " * CAF > ${CAF} "
echo " * MAC >= ${MAC} "
echo " * BETA/SE/P != NA "
echo " * -${BETA_SE} <= BETA/SE < ${BETA_SE}. "
zcat ${RESULTS} | head -1 > ${OUTPUT_DIR}/${FILENAME}.QC.txt
### 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
zcat ${OUTPUT_DIR}/${FILENAME}.txt.gz | awk '( $8 >= '${INFO}' && $8 <= 1 && $13 >= '${MAC}' && $15 >= '${CAF}' && $17 != "NA" && $17 <= 1 && $17 >= 0 && $18 != "NA" && $18 < '${BETA_SE}' && $18 > -'${BETA_SE}' && $19 != "NA" && $19 < '${BETA_SE}' && $19 > -'${BETA_SE}' )' >> ${OUTPUT_DIR}/${FILENAME}.QC.txt
### FOR DEBUGS
### zcat ${OUTPUT_DIR}/${FILENAME}.txt.gz | awk '( $8 >= '${INFO}' && $8 <= 1 && $13 >= '${MAC}' && $15 >= '${CAF}' && $17 != "NA" && $17 <= 1 && $17 >= 0 && $18 != "NA" && $18 < '${BETA_SE}' && $18 > -'${BETA_SE}' && $19 != "NA" && $19 < '${BETA_SE}' && $19 > -'${BETA_SE}' )' | head
### echo "zcat ${OUTPUT_DIR}/${FILENAME}.txt.gz | awk '( \${8} >= '${INFO}' && \${8} < 1 && \${13} >= '${MAC}' && \${15} >= '${CAF}' && \${17} != \"NA\" && \${17} <= 1 && \${17} >= 0 && \${18} != \"NA\" && \${18} < '${BETA_SE}' && \${18} > -'${BETA_SE}' && \${19} != \"NA\" && \${19} < '${BETA_SE}' && \${19} > -'${BETA_SE}' )' >> ${OUTPUT_DIR}/${FILENAME}.QC.txt"
echo "Number of QC'd variants:"
cat ${OUTPUT_DIR}/${FILENAME}.QC.txt | wc -l
echo "Head of QC'd file:"
head ${OUTPUT_DIR}/${FILENAME}.QC.txt
echo ""
echo "Tail of QC'd file:"
tail ${OUTPUT_DIR}/${FILENAME}.QC.txt
echo ""
echo ""
echo "Zipping up..."
gzip -fv ${OUTPUT_DIR}/${FILENAME}.QC.txt
echo ""
echo ""
### END of if-else statement for the number of command-line arguments passed ###
fi
# script_copyright_message