option -T added

wGRR

@@ -43,6 +43,7 @@ display_usage() {
 	echo "   -m <integer>      Max number of simulteaneous tasks."
 	echo "                        Only applicable to Maestro, for the wGRR calculation step."
 	echo "                        default: not set"
+	echo "   -T						Test run. Useful to get stats on the input file and correctly set the -a parameter."
 	echo ""
 	echo "${bold}DESCRIPTION:${normal}"
 	echo "This pipeline will do all proteins pairwise comparisons using the MMseqs2 software and then process "
@@ -97,13 +98,13 @@ ARRAYSIZE=10000           ## -a
 BATCHFLAG=0               ## Are we in a sbatch job?
 QT=0                      ## Queing time (for Maestro)
 MAXJOBS=0                 ## -m
-DEFAULT_MAIN_RAM="10G"    ## RAM for the main script (on Maestro)
 MMS_DEF_MAX_SEQS=300
 MIDENT=0
 MMS_MAX_SEQ_PARAM=""
+TESTRUN=0                 ## -T
 
 ## catch option values
-while getopts :f:p:o:t:a:m: option ; do
+while getopts :Tf:p:o:t:a:m: option ; do
    case $option in
    f) PRT="$OPTARG";     if [ ! -f $PRT ]; then echo "[ERROR]     --  fasta file '$PRT' not found (option -f)." ; exit 1 ; fi ;;
    p) MMPATH="$OPTARG"          ;;
@@ -111,6 +112,7 @@ while getopts :f:p:o:t:a:m: option ; do
 	t) THREADS="$OPTARG"; if [[ ! $THREADS =~ ^[0-9]+$ ]]; then echo "[ERROR]     --  number of threads $THREADS must be an integer (option -t)." ; exit 1 ; fi ;;
 	a) ARRAYSIZE="$OPTARG"; if [[ ! $ARRAYSIZE =~ ^[0-9]+$ ]]; then echo "[ERROR]     --  number of genomes comparisons $ARRAYSIZE must be an integer (option -a)." ; exit 1 ; fi ;;
 	m) MAXJOBS="$OPTARG"; if [[ ! $MAXJOBS =~ ^[0-9]+$ ]]; then echo "[ERROR]     --  max number of simulteaneous jobs $MAXJOBS must be an integer (option -m)." ; exit 1 ; fi ;;
+	T) TESTRUN=1 ;;
    :) echo "option $OPTARG : missing argument" ; exit 1  ;;
    \?) echo "$OPTARG : invalid option" ; exit 1  ;;
    esac
@@ -211,8 +213,9 @@ else
 fi
 
 
-STATS=($($AWKEXE '/^>/{p++;g=substr($1,2);gsub(/_[0-9]+$/,"",g);if(!a[g]++){c++};LNR=NR}{if(NR>LNR+1){n=1}}END{if(n!=1){n=0}print c"\t"p"\t"n}' $PRT))
-echo "[INFO]      --  Input file has "$STATS[1]" genomes and a total of "$STATS[2]" proteins"
+STATS=($($AWKEXE '/^>/{p++;g=substr($1,2);gsub(/_[0-9]+$/,"",g);if(!a[g]++){c++};LNR=NR}{if(NR>LNR+1){n=1}}END{if(n!=1){n=0}print c"\t"p"\t"n"\t"p/c}' $PRT))
+echo "[INFO]      --  Input file has "$STATS[1]" genomes and a total of "$STATS[2]" proteins."
+echo "[INFO]      --  Mean number of proteins per genome: $STATS[4]"
 
 if [[ $STATS[3] -eq 1 ]]; then
 	echo "[INFO]      --  Converting fasta file to sequential fasta"
@@ -224,7 +227,7 @@ fi
 duration=$SECONDS
 if [[ -f $OUT.m8 ]] ; then
 	echo "[INFO]      --  Using existing MMseqs output file $OUT.m8"
-else
+elif [[ $TESTRUN == 0 ]] ; then
 	MIDENT=$($AWKEXE '!/^>/{a[$0]++}END{for(i in a){if(a[i]>m){m=a[i]}}print m}' $PRT)
 	printf "%-10s  --  %s\n" "[TIME]" $(textifyDuration $duration)
 	if [[ $((MIDENT*2)) -gt "$MMS_DEF_MAX_SEQS" ]] ; then
@@ -243,7 +246,7 @@ else
 	fi
 fi
 
-if [[ ! -f $OUT.m8 ]] ; then
+if [[ $TESTRUN == 0 ]] && [[ ! -f $OUT.m8 ]] ; then
 	echo "[ERROR]     --  Something went wrong during the MMseqs step."
 	exit 1
 fi
@@ -264,6 +267,14 @@ if [[ ! -f $OUT.allpairs.txt ]] || [[ $NPAIRS < 1 ]] ; then
 	exit 1
 fi
 
+if [[ $TESTRUN == 1 ]] ; then
+	rm -rf "$OUT".logs
+	printf "%-10s  --  %s\n" "[INFO]" "Done"
+	duration=$SECONDS
+	printf "%-10s  --  %s\n" "[TIME]" $(textifyDuration $duration)
+	exit 0
+fi
+
 duration=$SECONDS
 NJOBS=$(( (NPAIRS+ARRAYSIZE-1)/ARRAYSIZE))
 if [[ $BATCHFLAG == 0 ]] ; then