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QTLPlotter.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 "$1" # additional error message
echoerror ""
echoerror "========================================================================================================="
echoerror " OPTION LIST"
echoerror ""
echoerror " * Argument #1 configurationfile: qtl.config."
echoerror " * Argument #2 summary directory to put all summarized files in."
echoerror " * Argument #3 directory where clump data can be found."
echoerror " * Argument #4 whether the data was clumped or not [Y/N]."
echoerror ""
echoerror " An example command would be: "
echoerror ""
echoerror "./QTLSummarizer.sh [arg1] [arg2] [arg3] [arg4]"
echoerror ""
echoerror "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
# The wrong arguments are passed, so we'll exit the script now!
script_copyright_message
exit 1
}
echobold "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echobold "+ QUANTITATIVE TRAIT LOCUS PLOTTER +"
echobold "+ +"
echobold "+ +"
echobold "+ * Written by : Sander W. van der Laan; Jacco Schaap +"
echobold "+ * E-mail : s.w.vanderlaan-2@umcutrecht.nl; jacco_schaap@hotmail.com +"
echobold "+ * Last update : 2018-07-29 +"
echobold "+ * Version : 1.3.2 +"
echobold "+ +"
echobold "+ * Description : This script will produce regional association plots of QTL results, using +"
echobold "+ LocusZoom v1.3. +"
echobold "+ +"
echobold "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echo "Today's date and time: "$(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="$1" # Depends on arg1 -- but also on where it resides!!!
### MAIL SETTINGS
EMAIL=${YOUREMAIL}
MAILTYPE=${MAILSETTINGS}
### QSUB SETTINGS
QUEUE_QCTOOL=${QUEUE_QCTOOL_CONFIG}
VMEM_QCTOOL=${VMEM_QCTOOL_CONFIG}
QUEUE_NOM=${QUEUE_NOM_CONFIG}
VMEM_NOM=${VMEM_NOM_CONFIG}
QUEUE_PERM=${QUEUE_PERM_CONFIG}
VMEM_PERM=${VMEM_PERM_CONFIG}
### QTL SETTINGS
SEEDNO=${SEEDNO_CONFIG}
PERMSTART=${PERMSTART_CONFIG}
PERMEND=${PERMEND_CONFIG}
NOMINAL_P=${NOMINAL_P}
### QCTOOL SETTINGS
MAF=${MAF_CONFIG}
INFO=${INFO_CONFIG}
HWE=${HWE_CONFIG}
### SET STUDY AND SAMPLE TYPE
### Note: All analyses with AE data are presumed to be constrained to CEA-patients only.
### You can set the exclusion criteria 'NONAEGS/FEMALES/MALES' if you want to analyse
### all AE data!
### Set the analysis type.
STUDY_TYPE=${STUDY_TYPE} # AEMS450K1/AEMS450K2/CTMM
### Set the analysis type.
SAMPLE_TYPE=${SAMPLE_TYPE} # AE: PLAQUES/BLOOD; CTMM: MONOCYTES
### GENERIC SETTINGS
SOFTWARE=${SOFTWARE}
QTLTOOLKIT=${QTLTOOLKIT}
QCTOOL=${QCTOOL}
SNPTEST252=${SNPTEST252}
QTLTOOLS=${QTLTOOLS}
LOCUSZOOM=${LOCUSZOOM}
BGZIP=${BGZIP}
TABIX=${TABIX}
PLINK=${PLINK}
PYTHON=${PYTHON}
STUDYNAME=${STUDYNAME} # What is the study name to be used in files -- refer to 'qtl.config' for information
PROJECTDIR=${ROOTDIR}/${PROJECTNAME} # What is the project directory? -- refer to 'qtl.config' for for information
PROJECTNAME=${PROJECTNAME} # What is the projectname? E.g. 'CAD' -- refer to f'qtl.config' for for information
SUMMARY=${2} # The summary directory to put all summarized files in -- refer to 'qtl.config' for for information
REGIONS=${REGIONS_FILE} # The file containing the regions of interest -- refer to 'qtl.config' for for information
EXCLUSION_TYPE=${EXCLUSION_TYPE} # The exclusion type -- refer to 'qtl.config' for for information
CLUMPDIR=${3} # Directory with clump information
QTL_TYPE=${QTL_TYPE} # CIS or TRANS
CLUMP=${4} # Clumped or nominal data. Y for Clumped, N for Nominal
### START of if-else statement for the number of command-line arguments passed ###
if [[ $# -lt 4 ]]; then
echo " *** Oh no! Computer says no! ***"
echo ""
script_arguments_error "You must supply at least [4] arguments when plotting QTL SUMMARYs!"
else
###FOR DEBUGGING
echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echo "The following is set:"
echo ""
echo "Software directory ${SOFTWARE}"
echo "Where \"qctool\" resides ${QCTOOL}"
echo "Where \"QTLTools\" resides. ${QTLTOOLS}"
echo "Where \"bgzip\" resides ${BGZIP}"
echo "Where \"tabix\" resides ${TABIX}"
echo "Where \"snptest \" resides ${SNPTEST252}"
echo "Where \"LocusZoom 1.3\" resides ${LOCUSZOOM}"
echo "Where \"PLINK\" resides ${PLINK}"
echo "Where \"Python\" resides ${PYTHON}"
echo ""
echo "Project directory ${PROJECTDIR}"
echo "Summary directory ${SUMMARY}"
echo "Clump directory ${CLUMPDIR}"
echo "Regions of interest file ${REGIONS}"
echo "Exclusion type ${EXCLUSION_TYPE}"
echo "QTL-type ${QTL_TYPE}"
echo "Did we apply clumping? ${CLUMP}"
echo ""
echo "We will run this script on ${TODAY}"
echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
### OVERVIEW OF REGIONS
echo ""
echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echo "The list of regions to investigate:"
echo "* Variant Locus Chr BP StartRange EndRange WindowSize Type Phenotype"
while IFS='' read -r REGION || [[ -n "$REGION" ]]; do
LINE=${REGION}
echo "* ${LINE}"
done < ${REGIONS}
echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echo "Parse nominal SUMMARYs to get Hits per Locus and (mapped) Gene, and input files for LocusZoom v1.2+."
echo ""
### Jacco 17-6-17, standardize to find both nominal and permuted data instead of only nominal
### Select the right dataset for python script
### Nominal set
NOM_DATA=''
if [ ${CLUMP} = 'N' ]; then
NOM_DATA=${SUMMARY}/${STUDYNAME}_QC_qtlnom_summary.txt.gz
echo "We are not using clumped nominal data."
fi
### Clumped set
if [ ${CLUMP} = 'Y' ]; then
NOM_DATA=${SUMMARY}/${STUDYNAME}_QC_qtlnom_clumped_summary.txt.gz
echo "We are using clumped nominal data."
fi
### First we will collect all the nominal association SUMMARYs.
echo ""
echo "Parsing nominal SUMMARYs..."
cd ${SUMMARY}
echo ""
# Normal set, old
### FOR DEBUG
### echo "${PYTHON} ${QTLTOOLKIT}/NominalResultsParser.py ${NOM_DATA}"
${PYTHON} ${QTLTOOLKIT}/NominalResultsParser.py ${NOM_DATA}
#### Now we will start plotting per locus each gene-probe-pair.
echo ""
# When not clumping
if [ ${CLUMP} = 'N' ]; then
while IFS='' read -r REGIONOFINTEREST || [[ -n "$REGIONOFINTEREST" ]]; do
### 1 2 3 4 5 6 7 8 9
### Variant Locus Chr BP BP-1Mb BP+1Mb 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 " INITIALISING LOCUSZOOM PLOTTING FOR ${VARIANT} LOCUS"
echo "============================================================================="
echo ""
### Getting only the top part of the variant-gene-probeid list
cat ${SUMMARY}/_loci/${VARIANT}.txt | tail -n +2 > ${SUMMARY}/_loci/${VARIANT}.LZ.txt
LOCUSHITS=${SUMMARY}/_loci/${VARIANT}.LZ.txt
echo "These are the hits we're interested in for ${VARIANT}..."
echo ""
cat ${LOCUSHITS}
echo ""
while IFS='' read -r VARIANTGENEPROBE || [[ -n "$VARIANTGENEPROBE" ]]; do
### 1 2 3 4 5
### Locus GeneName ProbeID N_Variants N_Significant
LINE=${VARIANTGENEPROBE}
LOCUSVARIANT=$(echo "${LINE}" | awk '{print $1}')
GENENAME=$(echo "${LINE}" | awk '{print $2}')
PROBEID=$(echo "${LINE}" | awk '{print $3}')
N_VARIANTS=$(echo "${LINE}" | awk '{print $4}')
N_SIGNIFICANT=$(echo "${LINE}" | awk '{print $5}')
echo "============================================================================="
echo "Plotting SUMMARYs for the ${LOCUSVARIANT} locus on ${CHR}:${START}-${END}."
echo " * Plotting association SUMMARYs for ${GENENAME} and ${PROBEID}."
echo " * Total number of variants analysed: [ ${N_VARIANTS} ]."
echo " * Total number of significant variants: [ ${N_SIGNIFICANT} ]."
echo ""
### FOR DEBUGGING
### echo "Checking existence of proper input file..."
### ls -lh ${SUMMARY}/_probes/${LOCUSVARIANT}_${GENENAME}_${PROBEID}.lz
### echo ""
### echo "Head:"
### head ${SUMMARY}/_probes/${LOCUSVARIANT}_${GENENAME}_${PROBEID}.lz
### echo ""
### echo "Tail:"
### tail ${SUMMARY}/_probes/${LOCUSVARIANT}_${GENENAME}_${PROBEID}.lz
### echo ""
### echo "Row count:"
### cat ${SUMMARY}/_probes/${LOCUSVARIANT}_${GENENAME}_${PROBEID}.lz | wc -l
### Setting up LocusZoom v1.2+ plotting
### Some general settings
### LOCUSZOOM_SETTINGS="refsnpTextColor='black' legendColor='black' legendBoxColor='white' legendInnerBoxColor='black' legend='auto' drawMarkerNames=TRUE ldColors=\"#595A5C,#4C81BF,#1396D8,#C5D220,#F59D10,red,#9A3480\" showRecomb=TRUE ldCol='r^2' drawMarkerNames=FALSE refsnpTextSize=0.8 geneFontSize=0.6 showRug=FALSE showAnnot=FALSE showRefsnpAnnot=TRUE showGenes=TRUE clean=TRUE bigDiamond=TRUE ymax=12 rfrows=10 refsnpLineWidth=2 condLdColors=\"gray60,#E41A1C,#377EB8,#4DAF4A,#984EA3,#FF7F00,#A65628,#F781BF\" "
### Setting up LocusZoom v1.3+ plotting
### Some general settings
LOCUSZOOM_SETTINGS=${LOCUSZOOM_SETTINGS}
# LOCUSZOOM_SETTINGS="ldColors=\"#595A5C,#4C81BF,#1396D8,#C5D220,#F59D10,red,#9A3480\" showRecomb=TRUE drawMarkerNames=FALSE showRug=FALSE showAnnot=TRUE showRefsnpAnnot=TRUE showGenes=TRUE clean=TRUE bigDiamond=TRUE rfrows=10 refsnpLineWidth=2 refsnpTextSize=1.0 axisSize=1.25 axisTextSize=1.25 geneFontSize=1.25"
echo "*** DEBUGGING ***"
echo $LOCUSZOOM_SETTINGS
### The proper genome-build
LDMAP="--pop ${LDPOP} --build ${LDBUILD} --source ${LDSOURCE}"
echo "*** DEBUGGING ***"
echo $LDMAP
### Directory prefix
PREFIX="${LOCUSVARIANT}_${GENENAME}_${PROBEID}_excl_${EXCLUSION_TYPE}"
# find ranges to highlight with locuszoom
HISTART=$(grep ${LOCUSVARIANT} ${CLUMPDIR}/highlight_ranges_${LOCUSVARIANT}.list | cut -d ',' -f 2)
HIEND=$(grep ${LOCUSVARIANT} ${CLUMPDIR}/highlight_ranges_${LOCUSVARIANT}.list | cut -d ',' -f 3)
### Actual plotting
${LOCUSZOOM} --metal ${SUMMARY}/_probes/${LOCUSVARIANT}_${GENENAME}_${PROBEID}.lz --refsnp ${LOCUSVARIANT} --markercol ${LZMARKERNAME} --pvalcol ${LZPVALUE} --delim ${LZDELIMITER} --chr ${CHR} --start ${START} --end ${END} ${LDMAP} ${LOCUSZOOM_SETTINGS} --prefix=${PREFIX} hiStart=${HISTART} hiEnd=${HIEND} theme=${LZTHEME} title="${LOCUSVARIANT} - ${GENENAME} (${PROBEID})"
done < ${LOCUSHITS}
### Should we gzip this shizzle?
gzip -fv ${SUMMARY}/_loci/${VARIANT}.LZ.txt
done < ${REGIONS}
fi
# When clumping
if [ ${CLUMP} = 'Y' ]; then
PERMUTEDHITS=${SUMMARY}/${STUDYNAME}_qtl_perm_tophits.csv
### head of perm_tophits.csv
### 1 lead_SNP, 2 e_SNP, 3 chr_tag_snp, 4 pos_tag_snp, 5 e_Gene, 6 probe,
### 7 nom_p_value, 8 perm_p_value, 9 approx_perm_p_value, 10 rsquared, 11 FDR
### rs9970807,rs56170783,1,57016131,C8B,ILMN_1731293,0.00304069,0.004995,0.00191528,0.977,0.01340696
### rs7528419,rs7528419,1,109817192,PSRC1,ILMN_2315964,3.6016e-17,0.000999001,1.48056e-20,1,1.1252256e-18
### rs7528419,rs7528419,1,109817192,PSRC1,ILMN_1671843,6.73537e-14,0.000999001,6.65731e-17,1,2.5297778e-15
cat ${PERMUTEDHITS} | awk -F "," '{ print $1, $2, $3, $4, $5, $6, $7, $8, $9, $10, $11 }' | tail -n +2 > ${SUMMARY}/${STUDYNAME}_qtl_perm_tophits.parsed.txt
PERMUTEDHITSPARSED=${SUMMARY}/${STUDYNAME}_qtl_perm_tophits.parsed.txt
echo ""
while IFS='' read -r VARIANTGENEPROBE || [[ -n "$VARIANTGENEPROBE" ]]; do
### 1 2 3 4 5
### Locus GeneName ProbeID N_Variants N_Significant
LINE=${VARIANTGENEPROBE}
LOCUSVARIANT=$(echo "${LINE}" | awk '{print $1}')
TAGVARIANT=$(echo "${LINE}" | awk '{print $1}')
GENENAME=$(echo "${LINE}" | awk '{print $5}')
PROBEID=$(echo "${LINE}" | awk '{print $6}')
PERMPVALUE=$(echo "${LINE}" | awk '{print $9}')
RSQUARED=$(echo "${LINE}" | awk '{print $10}')
FDR=$(echo "${LINE}" | awk '{print $11}')
VARIANT=$(cat ${REGIONS} | awk ' $1 == "'$LOCUSVARIANT'" ' | awk ' { print $1 } ')
CHR=$(cat ${REGIONS} | awk ' $1 == "'$LOCUSVARIANT'" ' | awk ' { print $3 } ')
BP=$(cat ${REGIONS} | awk ' $1 == "'$LOCUSVARIANT'" ' | awk ' { print $4 } ')
START=$(cat ${REGIONS} | awk ' $1 == "'$LOCUSVARIANT'" ' | awk ' { print $5 } ')
END=$(cat ${REGIONS} | awk ' $1 == "'$LOCUSVARIANT'" ' | awk ' { print $6 } ')
echo "============================================================================="
echo " INITIALISING LOCUSZOOM PLOTTING FOR ${VARIANT} LOCUS -- AFTER CLUMPING"
echo "============================================================================="
echo "Plotting SUMMARYs for the ${LOCUSVARIANT} locus on ${CHR}:${START}-${END}."
echo " * Plotting association SUMMARYs for ${GENENAME} and ${PROBEID}."
echo " * The ${TAGVARIANT} tags ${LOCUSVARIANT} with r^2 = ${RSQUARED}, and permuted p-value = ${PERMPVALUE} (FDR: ${FDR})."
echo " Note: the tagging variant can be the same as the index-variant!"
echo ""
### Setting up LocusZoom v1.2+ plotting
### Some general settings
### LOCUSZOOM_SETTINGS="refsnpTextColor='black' legendColor='black' legendBoxColor='white' legendInnerBoxColor='black' legend='auto' drawMarkerNames=TRUE ldColors=\"#595A5C,#4C81BF,#1396D8,#C5D220,#F59D10,red,#9A3480\" showRecomb=TRUE ldCol='r^2' drawMarkerNames=FALSE refsnpTextSize=0.8 geneFontSize=0.6 showRug=FALSE showAnnot=FALSE showRefsnpAnnot=TRUE showGenes=TRUE clean=TRUE bigDiamond=TRUE ymax=12 rfrows=10 refsnpLineWidth=2 condLdColors=\"gray60,#E41A1C,#377EB8,#4DAF4A,#984EA3,#FF7F00,#A65628,#F781BF\" "
### Setting up LocusZoom v1.3+ plotting
### Some general settings
LOCUSZOOM_SETTINGS=${LOCUSZOOM_SETTINGS}
# LOCUSZOOM_SETTINGS="ldColors=\"#595A5C,#4C81BF,#1396D8,#C5D220,#F59D10,red,#9A3480\" showRecomb=TRUE drawMarkerNames=FALSE showRug=FALSE showAnnot=TRUE showRefsnpAnnot=TRUE showGenes=TRUE clean=TRUE bigDiamond=TRUE rfrows=10 refsnpLineWidth=2 refsnpTextSize=1.0 axisSize=1.25 axisTextSize=1.25 geneFontSize=1.25"
echo "*** DEBUGGING ***"
echo $LOCUSZOOM_SETTINGS
### The proper genome-build
LDMAP="--pop ${LDPOP} --build ${LDBUILD} --source ${LDSOURCE}"
echo "*** DEBUGGING ***"
echo $LDMAP
### Directory prefix
PREFIX="${LOCUSVARIANT}_${GENENAME}_${PROBEID}_excl_${EXCLUSION_TYPE}"
# find ranges to highlight with locuszoom
HISTART=$(grep ${LOCUSVARIANT} ${CLUMPDIR}/highlight_ranges_${LOCUSVARIANT}.list | cut -d ',' -f 2)
HIEND=$(grep ${LOCUSVARIANT} ${CLUMPDIR}/highlight_ranges_${LOCUSVARIANT}.list | cut -d ',' -f 3)
### Actual plotting
${LOCUSZOOM} --metal ${SUMMARY}/_probes/${LOCUSVARIANT}_${GENENAME}_${PROBEID}.lz --add-refsnp ${TAGVARIANT} --markercol ${LZMARKERNAME} --pvalcol ${LZPVALUE} --delim ${LZDELIMITER} --chr ${CHR} --start ${START} --end ${END} ${LDMAP} ${LOCUSZOOM_SETTINGS} --prefix=${PREFIX} hiStart=${HISTART} hiEnd=${HIEND} theme=${LZTHEME} title="${LOCUSVARIANT} tagged by ${TAGVARIANT} - ${GENENAME} (${PROBEID})"
done < ${PERMUTEDHITSPARSED}
### Should we gzip this shizzle?
gzip -fv ${SUMMARY}/_loci/${VARIANT}.LZ.txt
fi
### END of if-else statement for the number of command-line arguments passed ###
fi
script_copyright_message