From 3597c451fb49d56f9522dc612fb492aab0cdb4f0 Mon Sep 17 00:00:00 2001
From: Julien Guglielmini <julien.guglielmini@pasteur.fr>
Date: Sun, 2 Apr 2023 22:12:45 +0200
Subject: [PATCH] Bold font for colored messages.
---
wGRR | 72 ++++++++++++++++++++++++++++++------------------------------
1 file changed, 36 insertions(+), 36 deletions(-)
diff --git a/wGRR b/wGRR
index b4b12fe..b0d91cb 100755
--- a/wGRR
+++ b/wGRR
@@ -128,19 +128,19 @@ JACCARD=0 ## -j
## catch option values
while getopts :fTsji:p:o:t:a:m:l: option ; do
case $option in
- i) PRT="$OPTARG"; if [[ ! -s $PRT ]]; then printf "${red}%-17s -- %s\n${normal}" "[ERROR]" "Fasta file '$PRT' not found or empty (option -i)." ; exit 1 ; fi ;;
+ i) PRT="$OPTARG"; if [[ ! -s $PRT ]]; then printf "${bold}${red}%-17s -- %s\n${normal}" "[ERROR]" "Fasta file '$PRT' not found or empty (option -i)." ; exit 1 ; fi ;;
p) MMPATH="$OPTARG" ;;
- o) OUT="$OPTARG"; if [[ -f "$OUT".wgrr.final.txt ]]; then printf "${red}%-17s -- %s\n${normal}" "[ERROR]" "File $OUT.wgrr.final.txt already exists. Change option -o or remove this file and relaunch." ; exit 1 ; fi ;;
- t) THREADS="$OPTARG"; if [[ ! $THREADS =~ ^[0-9]+$ ]]; then printf "${red}%-17s -- %s\n${normal}" "[ERROR]" "Number of threads $THREADS must be an integer (option -t)." ; exit 1 ; fi ;;
- a) ARRAYSIZE="$OPTARG"; if [[ ! $ARRAYSIZE =~ ^[0-9]+$ ]]; then if [[ $ARRAYSIZE != "AUTO" ]] ; then printf "${red}%-17s -- %s\n${normal}" "[ERROR]" "Number of genomes comparisons $ARRAYSIZE must be an integer (option -a)." ; exit 1 ; fi ; fi ;;
- l) IDLIST="$OPTARG"; if [[ ! -s ${IDLIST} ]] ; then printf "${red}%-17s -- %s\n${normal}" "[ERROR]" "File ${IDLIST} not found or empty (option -l)." ; exit 1 ; fi ;;
- m) MAXJOBS="$OPTARG"; if [[ ! $MAXJOBS =~ ^[0-9]+$ ]]; then printf "${red}%-17s -- %s\n${normal}" "[ERROR]" "Max number of simulteaneous jobs $MAXJOBS must be an integer (option -m)." ; exit 1 ; fi ;;
+ o) OUT="$OPTARG"; if [[ -f "$OUT".wgrr.final.txt ]]; then printf "${bold}${red}%-17s -- %s\n${normal}" "[ERROR]" "File $OUT.wgrr.final.txt already exists. Change option -o or remove this file and relaunch." ; exit 1 ; fi ;;
+ t) THREADS="$OPTARG"; if [[ ! $THREADS =~ ^[0-9]+$ ]]; then printf "${bold}${red}%-17s -- %s\n${normal}" "[ERROR]" "Number of threads $THREADS must be an integer (option -t)." ; exit 1 ; fi ;;
+ a) ARRAYSIZE="$OPTARG"; if [[ ! $ARRAYSIZE =~ ^[0-9]+$ ]]; then if [[ $ARRAYSIZE != "AUTO" ]] ; then printf "${bold}${red}%-17s -- %s\n${normal}" "[ERROR]" "Number of genomes comparisons $ARRAYSIZE must be an integer (option -a)." ; exit 1 ; fi ; fi ;;
+ l) IDLIST="$OPTARG"; if [[ ! -s ${IDLIST} ]] ; then printf "${bold}${red}%-17s -- %s\n${normal}" "[ERROR]" "File ${IDLIST} not found or empty (option -l)." ; exit 1 ; fi ;;
+ m) MAXJOBS="$OPTARG"; if [[ ! $MAXJOBS =~ ^[0-9]+$ ]]; then printf "${bold}${red}%-17s -- %s\n${normal}" "[ERROR]" "Max number of simulteaneous jobs $MAXJOBS must be an integer (option -m)." ; exit 1 ; fi ;;
T) TESTRUN=1 ;;
f) FAST=1 ;;
s) SKIP=1 ;;
j) JACCARD=1 ;;
- :) printf "${red}%-17s -- %s\n${normal}" "[ERROR]" "option $OPTARG : missing argument" ; exit 1 ;;
- \?) printf "${red}%-17s -- %s\n${normal}" "[ERROR]" "$OPTARG : invalid option" ; exit 1 ;;
+ :) printf "${bold}${red}%-17s -- %s\n${normal}" "[ERROR]" "option $OPTARG : missing argument" ; exit 1 ;;
+ \?) printf "${bold}${red}%-17s -- %s\n${normal}" "[ERROR]" "$OPTARG : invalid option" ; exit 1 ;;
esac
done
shift "$((OPTIND - 1))"
@@ -152,7 +152,7 @@ unalias -a
STIME=$(date +%s)
if [[ -e ${OUT}.wgrr.log ]] ; then
- printf "${yellow}%-17s -- %s\n${normal}" "[WARNING]" "Appending to existing log"
+ printf "${bold}${yellow}%-17s -- %s\n${normal}" "[WARNING]" "Appending to existing log"
printf "\n####################################\n" >> ${OUT}.wgrr.log
fi
@@ -210,10 +210,10 @@ printf "%-17s -- %s\n" "["$(textifyDuration $SECONDS)"]" "wGRR version ${VERSI
if [[ $BATCHFLAG == 0 ]] ; then
if [[ $FAST == 1 ]] ; then
- printf "${yellow}%-17s -- %s\n${normal}" "[WARNING]" "The fast flag (-f) is useless when not using sbatch" | tee -a ${OUT}.wgrr.log
+ printf "${bold}${yellow}%-17s -- %s\n${normal}" "[WARNING]" "The fast flag (-f) is useless when not using sbatch" | tee -a ${OUT}.wgrr.log
fi
if [[ $THREADS -gt $(nproc) ]] ; then
- printf "${red}%-17s -- %s\n${normal}" "[ERROR]" "You requested $THREADS threads but your machine has $(nproc) cores." | tee -a ${OUT}.wgrr.log
+ printf "${bold}${red}%-17s -- %s\n${normal}" "[ERROR]" "You requested $THREADS threads but your machine has $(nproc) cores." | tee -a ${OUT}.wgrr.log
exit 1
fi
printf "%-17s -- %s\n" "["$(textifyDuration $SECONDS)"]" "The command is:" >> ${OUT}.wgrr.log
@@ -224,25 +224,25 @@ else
fi
if [[ ! -f wGRR.awk ]] ; then
- printf "${red}%-17s -- %s\n${normal}" "[ERROR]" "awk script wGRR.awk not found." | tee -a ${OUT}.wgrr.log
+ printf "${bold}${red}%-17s -- %s\n${normal}" "[ERROR]" "awk script wGRR.awk not found." | tee -a ${OUT}.wgrr.log
exit 1
fi
if [[ ! -f wGRR_worker.zsh ]] ; then
- printf "${red}%-17s -- %s\n${normal}" "[ERROR]" "awk script wGRR_worker.zsh not found." | tee -a ${OUT}.wgrr.log
+ printf "${bold}${red}%-17s -- %s\n${normal}" "[ERROR]" "awk script wGRR_worker.zsh not found." | tee -a ${OUT}.wgrr.log
exit 1
fi
## Check awk
if ! AWKEXE=$(command -v gawk) ; then
if ! AWKEXE=$(command -v awk) ; then
- printf "${red}%-17s -- %s\n${normal}" "[ERROR]" "Could not find awk or gawk executable." | tee -a ${OUT}.wgrr.log
+ printf "${bold}${red}%-17s -- %s\n${normal}" "[ERROR]" "Could not find awk or gawk executable." | tee -a ${OUT}.wgrr.log
exit 1
fi
fi
if ! echo "" | $AWKEXE '{a[1][2]=3}' &> /dev/null ; then
- printf "${red}%-17s -- %s\n${normal}" "[ERROR]" "Your awk version is too old. Please install a more recent version (gawk is recommended)." | tee -a ${OUT}.wgrr.log
+ printf "${bold}${red}%-17s -- %s\n${normal}" "[ERROR]" "Your awk version is too old. Please install a more recent version (gawk is recommended)." | tee -a ${OUT}.wgrr.log
exit 1
fi
@@ -251,16 +251,16 @@ alias awk=$AWKEXE
## Check MMseqs
if [[ $MMPATH == "N.O.P.A.T.H" ]] ; then
if ! MMSEQS=$(command -v mmseqs) ; then
- printf "${red}%-17s -- %s\n${normal}" "[ERROR]" "MMseqs binary not found." | tee -a ${OUT}.wgrr.log
+ printf "${bold}${red}%-17s -- %s\n${normal}" "[ERROR]" "MMseqs binary not found." | tee -a ${OUT}.wgrr.log
exit 1
fi
else
if ! MMSEQS=$(command -v $MMPATH/mmseqs) ; then
if ! MMSEQS=$(command -v mmseqs) ; then
- printf "${red}%-17s -- %s\n${normal}" "[ERROR]" "MMseqs binary not found in your PATH." | tee -a ${OUT}.wgrr.log
+ printf "${bold}${red}%-17s -- %s\n${normal}" "[ERROR]" "MMseqs binary not found in your PATH." | tee -a ${OUT}.wgrr.log
exit 1
else
- printf "${red}%-17s -- %s\n${normal}" "[ERROR]" "MMseqs binary not found in ${MMPATH}." | tee -a ${OUT}.wgrr.log
+ printf "${bold}${red}%-17s -- %s\n${normal}" "[ERROR]" "MMseqs binary not found in ${MMPATH}." | tee -a ${OUT}.wgrr.log
fi
fi
fi
@@ -313,22 +313,22 @@ fi
NPAIRS=$(wc -l $OUT.allpairs.txt | awk '{print $1}')
if [[ ! -f $OUT.allpairs.txt ]] || [[ $NPAIRS < 1 ]] ; then
- printf "${red}%-17s -- %s\n${normal}" "[ERROR]" "An error occurred when writing the $OUT.allpairs.txt file." | tee -a ${OUT}.wgrr.log
+ printf "${bold}${red}%-17s -- %s\n${normal}" "[ERROR]" "An error occurred when writing the $OUT.allpairs.txt file." | tee -a ${OUT}.wgrr.log
exit 1
fi
NJOBS=$(( (NPAIRS+ARRAYSIZE-1)/ARRAYSIZE))
if [[ $BATCHFLAG == 1 && $SKIP == 1 ]] ; then
- printf "${yellow}%-17s -- %s\n${normal}" "[WARNING]" "Skipping estimation of required memory (option -s) is not available with sbatch runs" | tee -a ${OUT}.wgrr.log
- printf "${yellow}%-17s -- %s\n${normal}" "[WARNING]" "The run will continue ignoring the -s option" | tee -a ${OUT}.wgrr.log
+ printf "${bold}${yellow}%-17s -- %s\n${normal}" "[WARNING]" "Skipping estimation of required memory (option -s) is not available with sbatch runs" | tee -a ${OUT}.wgrr.log
+ printf "${bold}${yellow}%-17s -- %s\n${normal}" "[WARNING]" "The run will continue ignoring the -s option" | tee -a ${OUT}.wgrr.log
elif [[ $SKIP == 1 ]] ; then
- printf "${yellow}%-17s -- %s\n${normal}" "[WARNING]" "Skipping estimation of required memory (option -s) can lead to exhaustion of system resources!"${normal} | tee -a ${OUT}.wgrr.log
+ printf "${bold}${yellow}%-17s -- %s\n${normal}" "[WARNING]" "Skipping estimation of required memory (option -s) can lead to exhaustion of system resources!"${normal} | tee -a ${OUT}.wgrr.log
fi
if [[ $BATCHFLAG == 1 && $TESTRUN == 1 ]] ; then
- printf "${yellow}%-17s -- %s\n${normal}" "[WARNING]" "Test run (option -T) is not available with sbatch runs" | tee -a ${OUT}.wgrr.log
- printf "${yellow}%-17s -- %s\n${normal}" "[WARNING]" "The run will continue ignoring the -T option" | tee -a ${OUT}.wgrr.log
+ printf "${bold}${yellow}%-17s -- %s\n${normal}" "[WARNING]" "Test run (option -T) is not available with sbatch runs" | tee -a ${OUT}.wgrr.log
+ printf "${bold}${yellow}%-17s -- %s\n${normal}" "[WARNING]" "The run will continue ignoring the -T option" | tee -a ${OUT}.wgrr.log
printf "%-17s -- %s\n" "["$(textifyDuration $SECONDS)"]" "Estimating required memory" | tee -a ${OUT}.wgrr.log
elif [[ $TESTRUN == 1 ]] ; then
printf "%-17s -- %s\n" "["$(textifyDuration $SECONDS)"]" "This is a test run (option -T)" | tee -a ${OUT}.wgrr.log
@@ -358,7 +358,7 @@ if [[ $SKIP == 0 || $BATCHFLAG == 1 ]] ; then
printf "%-17s -- %s\n" "["$(textifyDuration $SECONDS)"]" "Each worker will require approximately $REQMEM" | tee -a ${OUT}.wgrr.log
printf "%-17s -- %s\n" "["$(textifyDuration $SECONDS)"]" "With the number of threads you specified (-t $THREADS) you will need a total of $REQMEMT" | tee -a ${OUT}.wgrr.log
if [[ $TOTALMEM == 0 ]] ; then
- printf "${yellow}%-17s -- %s\n${normal}" "[WARNING]" "Total memory of your system could not be determined" | tee -a ${OUT}.wgrr.log
+ printf "${bold}${yellow}%-17s -- %s\n${normal}" "[WARNING]" "Total memory of your system could not be determined" | tee -a ${OUT}.wgrr.log
else
printf "%-17s -- %s\n" "["$(textifyDuration $SECONDS)"]" "Total memory of your system: $(numfmt --to=iec $TOTALMEM)" | tee -a ${OUT}.wgrr.log
fi
@@ -371,14 +371,14 @@ if [[ $SKIP == 0 || $BATCHFLAG == 1 ]] ; then
if [[ $TESTRUN == 0 && $BATCHFLAG == 0 ]] ; then
if [[ $TOTALMEM -lt $(bc -l <<< $(numfmt --from=iec $REQMEM)*$THREADS) ]] ; then
- printf "${red}%-17s -- %s\n${normal}" "[ERROR]" "Your system does not have enough memory (${REQMEMT} required). Try decreasing the -a parameter and/or the number of threads." | tee -a ${OUT}.wgrr.log
+ printf "${bold}${red}%-17s -- %s\n${normal}" "[ERROR]" "Your system does not have enough memory (${REQMEMT} required). Try decreasing the -a parameter and/or the number of threads." | tee -a ${OUT}.wgrr.log
exit 1
fi
fi
fi
if [[ $TESTRUN == 1 && $BATCHFLAG == 0 ]] ; then
- printf "${green}%-17s -- %s\n${normal}" "["$(textifyDuration $SECONDS)"]" "Done." | tee -a ${OUT}.wgrr.log
+ printf "${bold}${green}%-17s -- %s\n${normal}" "["$(textifyDuration $SECONDS)"]" "Done." | tee -a ${OUT}.wgrr.log
exit 0
fi
@@ -426,7 +426,7 @@ else
fi
if [[ ! -f $OUT.m8 ]] ; then
- printf "${red}%-17s -- %s\n${normal}" "Something went wrong during the MMseqs step." | tee -a ${OUT}.wgrr.log
+ printf "${bold}${red}%-17s -- %s\n${normal}" "Something went wrong during the MMseqs step." | tee -a ${OUT}.wgrr.log
exit 1
fi
@@ -473,8 +473,8 @@ else
fi
JID=$(sbatch --parsable --wait -p ${PARTITION} --array="$JOBARRAY" -c 1 -J "wGRR_worker" --mem=$REQMEM --wrap="./wGRR_worker.zsh $AWKEXE $ARRAYSIZE $OUT $NJOBS 1 $PRT $tmp")
if [[ `sacct -j $JID | grep "TIMEOUT"` ]] ; then
- printf "${red}%-17s -- %s\n${normal}" "[ERROR]" "Some workers encountered a TIMEOUT." | tee -a ${OUT}.wgrr.log
- printf "${red}%-17s -- %s\n${normal}" "[ERROR]" "Saving the partial files in ${OUT}.wgrr_part directory." | tee -a ${OUT}.wgrr.log
+ printf "${bold}${red}%-17s -- %s\n${normal}" "[ERROR]" "Some workers encountered a TIMEOUT." | tee -a ${OUT}.wgrr.log
+ printf "${bold}${red}%-17s -- %s\n${normal}" "[ERROR]" "Saving the partial files in ${OUT}.wgrr_part directory." | tee -a ${OUT}.wgrr.log
rm -rf "$OUT".wgrr_part
mkdir "$OUT".wgrr_part
mv $tmp/"$OUT".wgrr_part.* "$OUT".wgrr_part/
@@ -491,8 +491,8 @@ printf "%-17s -- %s\n" "["$(textifyDuration $SECONDS)"]" "Sorting results" | t
sort -m "$tmp"/$OUT.wgrr_part.* | sort -u -k1,1V -k2,2V | awk 'BEGIN{print "GenomeA\tGenomeB\twGRR\tSørensen-Dice\tCommon\tNprotA\tNprotB"}1' > $OUT.wgrr.txt
if [[ ! -f "$OUT".wgrr.txt ]] ; then
- printf "${red}%-17s -- %s\n${normal}" "[ERROR]" "Failed to sort the wGRR table." | tee -a ${OUT}.wgrr.log
- printf "${red}%-17s -- %s\n${normal}" "[ERROR]" "Saving the partial files in ${OUT}.wgrr_part directory." | tee -a ${OUT}.wgrr.log
+ printf "${bold}${red}%-17s -- %s\n${normal}" "[ERROR]" "Failed to sort the wGRR table." | tee -a ${OUT}.wgrr.log
+ printf "${bold}${red}%-17s -- %s\n${normal}" "[ERROR]" "Saving the partial files in ${OUT}.wgrr_part directory." | tee -a ${OUT}.wgrr.log
rm -rf "$OUT".wgrr_part
mkdir "$OUT".wgrr_part
mv $tmp/"$OUT".wgrr_part.* "$OUT".wgrr_part/
@@ -508,9 +508,9 @@ fi
NLINES=$(wc -l "$OUT".wgrr.txt | awk '{print $1}')
NWGRR=$((STATS[1]*STATS[1]+1))
if [[ $NLINES -lt $NWGRR ]] ; then
- printf "${red}%-17s -- %s\n${normal}" "[ERROR]" "An error occurred during wGRR calculation:" | tee -a ${OUT}.wgrr.log
- printf "${red}%-17s -- %s\n${normal}" "[ERROR]" "less lines than expected in the final file." | tee -a ${OUT}.wgrr.log
- printf "${red}%-17s -- %s\n${normal}" "[ERROR]" "Saving the partial files in ${OUT}.wgrr_part directory." | tee -a ${OUT}.wgrr.log
+ printf "${bold}${red}%-17s -- %s\n${normal}" "[ERROR]" "An error occurred during wGRR calculation:" | tee -a ${OUT}.wgrr.log
+ printf "${bold}${red}%-17s -- %s\n${normal}" "[ERROR]" "less lines than expected in the final file." | tee -a ${OUT}.wgrr.log
+ printf "${bold}${red}%-17s -- %s\n${normal}" "[ERROR]" "Saving the partial files in ${OUT}.wgrr_part directory." | tee -a ${OUT}.wgrr.log
rm -rf "$OUT".wgrr_part
mkdir "$OUT".wgrr_part
mv $tmp/"$OUT".wgrr_part.* "$OUT".wgrr_part/
@@ -526,7 +526,7 @@ fi
rm -rf "$OUT".logs
-printf "${green}%-17s -- %s\n${normal}" "["$(textifyDuration $SECONDS)"]" "Done." | tee -a ${OUT}.wgrr.log
+printf "${bold}${green}%-17s -- %s\n${normal}" "["$(textifyDuration $SECONDS)"]" "Done." | tee -a ${OUT}.wgrr.log
if [[ $QT != 0 ]] ; then
printf "%-17s -- %s\n" "["$(textifyDuration $SECONDS)"]" "Total time in queue: $(textifyDuration $QT)" | tee -a ${OUT}.wgrr.log
fi
--
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