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QTLChecker.sh
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#!/bin/bash
#
### REGARDING NOTES ###
### Please note that uncommented notes can be found at the end of this script.
###
### MoSCoW FEATURE LIST ###
###
### 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}"
}
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 "Number of arguments found "$#"."
echoerror ""
echoerror "$1" # additional error message
echoerror ""
echoerror "========================================================================================================="
echoerror " OPTION LIST"
echoerror ""
echoerror " * Argument #1 the study name -- set in QTLAnalyzer.sh (please refer to there)."
echoerror " * Argument #2 exclusion type."
echoerror " * Argument #3 the root directory, e.g. /hpc/dhl_ec/svanderlaan/projects/test_qtl."
echoerror " * Argument #4 where the results are saved -- set in QTLAnalyzer.sh (please refer to there)."
echoerror " * Argument #4 where the summary is saved -- set in QTLAnalyzer.sh (please refer to there)."
echoerror " * Argument #6 project name, e.g. 'CAD'."
echoerror " * Argument #7 file containing the regions of interest."
echoerror " * Argument #8 QTL type [CIS/TRANS]."
echoerror ""
echoerror " An example command would be: "
echoerror "./QTLChecker.sh [arg1] [arg2] [arg3] [arg4] [arg5] [arg6] [arg7]"
echoerror ""
echoerror "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
# The wrong arguments are passed, so we'll exit the script now!
script_copyright_message
exit 1
}
echobold "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echobold "+ QUANTITATIVE TRAIT LOCUS SUMMARIZER +"
echobold "+ +"
echobold "+ +"
echobold "+ * Written by : Sander W. van der Laan +"
echobold "+ * E-mail : [email protected] +"
echobold "+ * Last update : 2018-07-27 +"
echobold "+ * Version : 1.1.6 +"
echobold "+ +"
echobold "+ * Description : This script will check the regular nominal and permuted QTL results for success. +"
echobold "+ +"
echobold "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echo "Today's date and time: "$(date)
TODAY=$(date +"%Y%m%d")
echo ""
### LOADING CONFIGURATION FILE
# Loading the configuration file (please refer to the QTLToolKit-Manual for specifications of this file).
source "$1" # Depends on arg1.
### REQUIRED | GENERALS
CONFIGURATIONFILE="$1" # Depends on arg1 -- but also on where it resides!!!
### Set the study name
STUDYNAME=${STUDYNAME} # What is the study name to be used in files -- refer to QTLAnalyzer.sh for information
EXCLUSION_TYPE=${EXCLUSION_TYPE} # The exclusion type -- refer to QTLAnalyzer.sh for information
### PROJECT SPECIFIC
ROOTDIR=${ROOTDIR} # the root directory, e.g. /hpc/dhl_ec/svanderlaan/projects/test_qtl
RESULTS=${2} # The directory in which the QTLToolKit results are saved -- refer to QTLAnalyzer.sh for information
SUMMARY=${3} # The directory in which the QTLToolKit results are saved -- refer to QTLAnalyzer.sh for information
PROJECTNAME=${PROJECTNAME} # What is the projectname? E.g. 'CAD' -- refer to QTLAnalyzer.sh for information
REGIONS=${REGIONS_FILE} # The file containing the regions of interest -- refer to QTLAnalyzer.sh for information
QTL_TYPE=${QTL_TYPE} # QTL type, cis or trans
### START of if-else statement for the number of command-line arguments passed ###
if [[ $# -lt 1 ]]; then
echo " *** Oh no! Computer says no! ***"
echo ""
script_arguments_error "You must supply at least [1] argument when summarizing QTL results!"
else
### GENERIC SETTINGS
SOFTWARE=${SOFTWARE}
QTLTOOLKIT=${QTLTOOLKIT}
QCTOOL=${QCTOOL}
SNPTEST252=${SNPTEST252}
QTLTOOLS=${QTLTOOLS}
LZ13=${LZ13}
BGZIP=${BGZIP}
TABIX=${TABIX}
PLINK=${PLINK}
PYTHON=${PYTHON}
### OVERVIEW OF REGIONS
echo ""
echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echo "The list of regions to investigate:"
echo "* Variant Locus Chr BP StartRange EndRange WindowSize Type Phenotype"
while IFS='' read -r REGION || [[ -n "$REGION" ]]; do
LINE=${REGION}
echo "* ${LINE}"
done < ${REGIONS}
echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
### CHECKING DATA AND ANALYSIS
echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echo "Checking whether analyses of loci were properly finished."
rm -v ${SUMMARY}/regions_for_qtl.failedQTLs.temp.txt ${ROOTDIR}/analysis.check.txt
rm -v ${SUMMARY}/regions_for_qtl.failedQTLs.txt
rm -v ${SUMMARY}/regions_for_qtl.failedNom.temp.txt
rm -v ${SUMMARY}/regions_for_qtl.failedNom.txt
rm -v ${SUMMARY}/regions_for_qtl.failedPerm.temp.txt
rm -v ${SUMMARY}/regions_for_qtl.failedPerm.txt
touch ${SUMMARY}/regions_for_qtl.failedQTLs.temp.txt # 'touching' a file for the complete rerun
touch ${SUMMARY}/regions_for_qtl.failedNom.temp.txt # 'touching' a file for the nominal rerun
touch ${SUMMARY}/regions_for_qtl.failedPerm.temp.txt # 'touching' a file for the permutation rerun
touch ${SUMMARY}/analysis.check.txt # a file containing some information regarding the check on the analysis
echo ""
while IFS='' read -r REGIONOFINTEREST || [[ -n "$REGIONOFINTEREST" ]]; do
### 1 2 3 4 5 6 7 8 9
###Variant Locus Chr BP StartRange EndRange WindowSize Type Phenotype
LINE=${REGIONOFINTEREST}
VARIANT=$(echo "${LINE}" | awk '{print $1}')
LOCUS=$(echo "${LINE}" | awk '{print $2}')
CHR=$(echo "${LINE}" | awk '{print $3}')
BP=$(echo "${LINE}" | awk '{print $4}')
START=$(echo "${LINE}" | awk '{print $5}')
END=$(echo "${LINE}" | awk '{print $6}')
WINDOWSIZE=$(echo "${LINE}" | awk '{print $7}')
TYPE=$(echo "${LINE}" | awk '{print $8}')
PHENOTYPE=$(echo "${LINE}" | awk '{print $9}')
echo ""
echo ""
echo "========================================================================================================="
echo "Checking whether analyses for ${VARIANT} locus on ${CHR} between ${START} and ${END} went well..."
echo "========================================================================================================="
REGIONALDIR=${RESULTS}/${VARIANT}_${PROJECTNAME} # setting regional directory
echo "Working in directory: ${REGIONALDIR}/[...]"
echo "Checking variant ${VARIANT} locus on ${CHR}:${START}-${END}." >> ${SUMMARY}/analysis.check.txt
echo ""
echo "* Checking data extraction..."
if [[ -n $(grep "Thank you for using qctool." ${REGIONALDIR}/${STUDYNAME}_genex_${VARIANT}_excl_${EXCLUSION_TYPE}.errors) ]]; then
echo "Extraction of data successfully completed for ${VARIANT}."
echo "* data extraction: success" >> ${SUMMARY}/analysis.check.txt
rm -v ${REGIONALDIR}/${STUDYNAME}_genex_${VARIANT}_excl_${EXCLUSION_TYPE}.log
mv -v ${REGIONALDIR}/${STUDYNAME}_genex_${VARIANT}_excl_${EXCLUSION_TYPE}.errors ${REGIONALDIR}/${STUDYNAME}_genex_${VARIANT}_excl_${EXCLUSION_TYPE}.log
gzip -v ${REGIONALDIR}/${STUDYNAME}_genex_${VARIANT}_excl_${EXCLUSION_TYPE}.log
else
echo "*** ERROR *** Extraction of data failed for ${VARIANT}."
echo "* data extraction: failed" >> ${SUMMARY}/analysis.check.txt
#rm -rv ${REGIONALDIR}
echo "${VARIANT} ${LOCUS} ${CHR} ${BP} ${START} ${END} ${WINDOWSIZE} ${TYPE} ${PHENOTYPE}" >> ${SUMMARY}/regions_for_qtl.failedQTLs.temp.txt
fi
echo ""
echo "* Checking data quality control..."
if [[ -n $(grep "Thank you for using qctool." ${REGIONALDIR}/${STUDYNAME}_genqc_${VARIANT}_excl_${EXCLUSION_TYPE}.errors) ]]; then
echo "Quality control of extracted data successfully completed for ${VARIANT}."
echo "* data quality control: success" >> ${SUMMARY}/analysis.check.txt
rm -v ${REGIONALDIR}/${STUDYNAME}_genqc_${VARIANT}_excl_${EXCLUSION_TYPE}.log
mv -v ${REGIONALDIR}/${STUDYNAME}_genqc_${VARIANT}_excl_${EXCLUSION_TYPE}.errors ${REGIONALDIR}/${STUDYNAME}_genqc_${VARIANT}_excl_${EXCLUSION_TYPE}.log
gzip -v ${REGIONALDIR}/${STUDYNAME}_genqc_${VARIANT}_excl_${EXCLUSION_TYPE}.log
else
echo "*** ERROR *** Quality control of extracted data failed for ${VARIANT}."
echo "* data quality control: failed" >> ${SUMMARY}/analysis.check.txt
#rm -rv ${REGIONALDIR}
echo "${VARIANT} ${LOCUS} ${CHR} ${BP} ${START} ${END} ${WINDOWSIZE} ${TYPE} ${PHENOTYPE}" >> ${SUMMARY}/regions_for_qtl.failedQTLs.temp.txt
fi
echo ""
echo "* Checking general statistics..."
if [[ -n $(grep "finito" ${REGIONALDIR}/${STUDYNAME}_genstats_${VARIANT}_excl_${EXCLUSION_TYPE}.log) ]]; then
echo "Calculating general statistics successfully completed for ${VARIANT}."
echo "* calculate summary statistics: success" >> ${SUMMARY}/analysis.check.txt
rm -v ${REGIONALDIR}/${STUDYNAME}_genstats_${VARIANT}_excl_${EXCLUSION_TYPE}.errors
gzip -v ${REGIONALDIR}/${STUDYNAME}_genstats_${VARIANT}_excl_${EXCLUSION_TYPE}.log
else
echo "*** ERROR *** Calculating general statistics failed for ${VARIANT}."
echo "* calculate summary statistics: failed" >> ${SUMMARY}/analysis.check.txt
#rm -rv ${REGIONALDIR}
echo "${VARIANT} ${LOCUS} ${CHR} ${BP} ${START} ${END} ${WINDOWSIZE} ${TYPE} ${PHENOTYPE}" >> ${SUMMARY}/regions_for_qtl.failedQTLs.temp.txt
fi
echo ""
echo "* Checking conversion to VCF..."
if [[ -n $(grep "Thank you for using qctool." ${REGIONALDIR}/${STUDYNAME}_gen2vcf_${VARIANT}_excl_${EXCLUSION_TYPE}.errors) ]]; then
echo "Conversion to VCF successfully completed for ${VARIANT}."
echo "* vcf conversion: success" >> ${SUMMARY}/analysis.check.txt
rm -v ${REGIONALDIR}/${STUDYNAME}_gen2vcf_${VARIANT}_excl_${EXCLUSION_TYPE}.log
mv -v ${REGIONALDIR}/${STUDYNAME}_gen2vcf_${VARIANT}_excl_${EXCLUSION_TYPE}.errors ${REGIONALDIR}/${STUDYNAME}_gen2vcf_${VARIANT}_excl_${EXCLUSION_TYPE}.log
gzip -v ${REGIONALDIR}/${STUDYNAME}_gen2vcf_${VARIANT}_excl_${EXCLUSION_TYPE}.log
else
echo "*** ERROR *** Conversion to VCF failed for ${VARIANT}."
echo "* vcf conversion: failed" >> ${SUMMARY}/analysis.check.txt
#rm -rv ${REGIONALDIR}
echo "${VARIANT} ${LOCUS} ${CHR} ${BP} ${START} ${END} ${WINDOWSIZE} ${TYPE} ${PHENOTYPE}" >> ${SUMMARY}/regions_for_qtl.failedQTLs.temp.txt
fi
echo ""
echo "* Checking gzipping of VCF..."
if [[ ! -s ${REGIONALDIR}/${STUDYNAME}_genvcfgz_${VARIANT}_excl_${EXCLUSION_TYPE}.errors ]]; then
echo "GZipping VCF file was successfully completed for ${VARIANT}."
echo "* gzipping vcf: success" >> ${SUMMARY}/analysis.check.txt
rm -v ${REGIONALDIR}/${STUDYNAME}_vcfgz_${VARIANT}_excl_${EXCLUSION_TYPE}.errors
gzip -v ${REGIONALDIR}/${STUDYNAME}_vcfgz_${VARIANT}_excl_${EXCLUSION_TYPE}.log
else
echo "*** ERROR *** GZipping VCF file failed for ${VARIANT}."
echo "* gzipping vcf: failed" >> ${SUMMARY}/analysis.check.txt
#rm -rv ${REGIONALDIR}
echo "${VARIANT} ${LOCUS} ${CHR} ${BP} ${START} ${END} ${WINDOWSIZE} ${TYPE} ${PHENOTYPE}" >> ${SUMMARY}/regions_for_qtl.failedQTLs.temp.txt
fi
echo ""
echo "* Checking nominal QTLTools analysis..."
if [[ -n $(grep "Running time" ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_${VARIANT}_excl_${EXCLUSION_TYPE}.log) ]]; then
echo "Nominal QTLTools analysis successfully completed for ${VARIANT}."
echo "* nominal analysis: success" >> ${SUMMARY}/analysis.check.txt
rm -v ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_${VARIANT}_excl_${EXCLUSION_TYPE}_NOM.errors
rm -v ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_${VARIANT}_excl_${EXCLUSION_TYPE}_NOM.log
rm -v ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_${VARIANT}_excl_${EXCLUSION_TYPE}_NOM.sh
gzip -v ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_${VARIANT}_excl_${EXCLUSION_TYPE}.log
else
echo "*** ERROR *** Nominal QTLTools analysis failed for ${VARIANT}."
echo "* nominal analysis: failed" >> ${SUMMARY}/analysis.check.txt
echo "* error message: " >> ${SUMMARY}/analysis.check.txt
cat ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_${VARIANT}_excl_${EXCLUSION_TYPE}_NOM.log | grep "ERROR" >> ${SUMMARY}/analysis.check.txt
#rm -v ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_${VARIANT}_excl_${EXCLUSION_TYPE}.*
#rm -v ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_${VARIANT}_excl_${EXCLUSION_TYPE}_NOM.*
echo "${VARIANT} ${LOCUS} ${CHR} ${BP} ${START} ${END} ${WINDOWSIZE} ${TYPE} ${PHENOTYPE}" >> ${SUMMARY}/regions_for_qtl.failedNom.temp.txt
fi
echo ""
echo "* Checking permutation QTLTools analysis..."
if [[ -n $(grep "Running time" ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_${VARIANT}_excl_${EXCLUSION_TYPE}.log) ]]; then
echo "Permutation QTLTools analysis successfully completed for ${VARIANT}."
echo "* permutation analysis: success" >> ${SUMMARY}/analysis.check.txt
rm -v ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_${VARIANT}_excl_${EXCLUSION_TYPE}_PERMUTE.errors
rm -v ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_${VARIANT}_excl_${EXCLUSION_TYPE}_PERMUTE.log
rm -v ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_${VARIANT}_excl_${EXCLUSION_TYPE}_PERMUTE.sh
gzip -v ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_${VARIANT}_excl_${EXCLUSION_TYPE}.log
else
echo "*** ERROR *** Permutation QTLTools analysis failed for ${VARIANT}."
echo "* permutation analysis: failed" >> ${SUMMARY}/analysis.check.txt
echo "* error message: " >> ${SUMMARY}/analysis.check.txt
cat ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_${VARIANT}_excl_${EXCLUSION_TYPE}_PERMUTE.log | grep "ERROR" >> ${SUMMARY}/analysis.check.txt
#rm -v ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_${VARIANT}_excl_${EXCLUSION_TYPE}.*
#rm -v ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_${VARIANT}_excl_${EXCLUSION_TYPE}_PERMUTE.*
echo "${VARIANT} ${LOCUS} ${CHR} ${BP} ${START} ${END} ${WINDOWSIZE} ${TYPE} ${PHENOTYPE}" >> ${SUMMARY}/regions_for_qtl.failedPerm.temp.txt
fi
echo "" >> ${SUMMARY}/analysis.check.txt
done < ${REGIONS}
echo ""
echo "* Removing duplicates from re-run file."
perl ${QTLTOOLKIT}/SCRIPTS/removedupes.pl ${SUMMARY}/regions_for_qtl.failedQTLs.temp.txt NORM ${SUMMARY}/regions_for_qtl.failedQTLs.txt
perl ${QTLTOOLKIT}/SCRIPTS/removedupes.pl ${SUMMARY}/regions_for_qtl.failedNom.temp.txt NORM ${SUMMARY}/regions_for_qtl.failedNom.txt
perl ${QTLTOOLKIT}/SCRIPTS/removedupes.pl ${SUMMARY}/regions_for_qtl.failedPerm.temp.txt NORM ${SUMMARY}/regions_for_qtl.failedPerm.txt
echo " - removing temporary files..."
rm -v ${SUMMARY}/regions_for_qtl.failedQTLs.temp.txt
rm -v ${SUMMARY}/regions_for_qtl.failedNom.temp.txt
rm -v ${SUMMARY}/regions_for_qtl.failedPerm.temp.txt
echo ""
echo "* Counting totals to be re-run."
TOTALQTL=$(cat ${SUMMARY}/regions_for_qtl.failedQTLs.txt | wc -l | awk '{ printf ("%'\''d\n", $0) }')
TOTALNOM=$(cat ${SUMMARY}/regions_for_qtl.failedNom.txt | wc -l | awk '{ printf ("%'\''d\n", $0) }')
TOTALPERM=$(cat ${SUMMARY}/regions_for_qtl.failedPerm.txt | wc -l | awk '{ printf ("%'\''d\n", $0) }')
echo " - failed extractions............: "${TOTALQTL}
echo " - failed nominal analyses.......: "${TOTALNOM}
echo " - failed permutation analyses...: "${TOTALPERM}
echo ""
### END of if-else statement for the number of command-line arguments passed ###
fi
script_copyright_message