echo" -f <string> fasta file with all proteins of all the compared genetic elements."
echo" -i <string> fasta file with all proteins of all the compared genetic elements."
echo" All identifiers must be formatted as:"
echo" All identifiers must be formatted as:"
echo" >element_identifier_XXX"
echo" >element_identifier_XXX"
echo" where XXX is a serie of numbers unique for each protein of each element."
echo" where XXX is a serie of numbers unique for each protein of each element."
...
@@ -44,6 +44,8 @@ display_usage() {
...
@@ -44,6 +44,8 @@ display_usage() {
echo" Only applicable to Maestro, for the wGRR calculation step."
echo" Only applicable to Maestro, for the wGRR calculation step."
echo" default: not set"
echo" default: not set"
echo" -T Test run. Useful to get stats on the input file and correctly set the -a parameter."
echo" -T Test run. Useful to get stats on the input file and correctly set the -a parameter."
echo" -f In sbatch mode, will use the fast QOS (jobs limited to 2 hours)"
echo" Warning: be sure the jobs will run under 2 hours otherwise they will fail."
echo""
echo""
echo"${bold}DESCRIPTION:${normal}"
echo"${bold}DESCRIPTION:${normal}"
echo"This pipeline will do all proteins pairwise comparisons using the MMseqs2 software and then process "
echo"This pipeline will do all proteins pairwise comparisons using the MMseqs2 software and then process "
...
@@ -90,7 +92,7 @@ textifyDuration() {
...
@@ -90,7 +92,7 @@ textifyDuration() {
}
}
## parameters initialization
## parameters initialization
PRT="N.O.P.R.T"## -f
PRT="N.O.P.R.T"## -i
MMPATH="N.O.P.A.T.H"## -p
MMPATH="N.O.P.A.T.H"## -p
OUT="N.O.O.U.T"## -o
OUT="N.O.O.U.T"## -o
THREADS=1 ## -t
THREADS=1 ## -t
...
@@ -102,17 +104,19 @@ MMS_DEF_MAX_SEQS=300
...
@@ -102,17 +104,19 @@ MMS_DEF_MAX_SEQS=300
MIDENT=0
MIDENT=0
MMS_MAX_SEQ_PARAM=""
MMS_MAX_SEQ_PARAM=""
TESTRUN=0 ## -T
TESTRUN=0 ## -T
FAST=0 ## -f
## catch option values
## catch option values
while getopts :Tf:p:o:t:a:m: option ;do
while getopts :fTi:p:o:t:a:m: option ;do
case$optionin
case$optionin
f)PRT="$OPTARG";if[!-f$PRT];then echo"[ERROR] -- fasta file '$PRT' not found (option -f).";exit 1 ;fi;;
i)PRT="$OPTARG";if[!-f$PRT];then echo"[ERROR] -- fasta file '$PRT' not found (option -f).";exit 1 ;fi;;
p)MMPATH="$OPTARG";;
p)MMPATH="$OPTARG";;
o)OUT="$OPTARG";if[-f"$OUT".wgrr.final.txt ];then echo"[ERROR] -- file $OUT.wgrr.final.txt already exists. Change option -o or remove this file and relaunch.";exit 1 ;fi;;
o)OUT="$OPTARG";if[-f"$OUT".wgrr.final.txt ];then echo"[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 echo"[ERROR] -- number of threads $THREADS must be an integer (option -t).";exit 1 ;fi;;
t)THREADS="$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 $ARRAYSIZE must be an integer (option -a).";exit 1 ;fi;;
a)ARRAYSIZE="$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 $MAXJOBS must be an integer (option -m).";exit 1 ;fi;;
m)MAXJOBS="$OPTARG";if[[!$MAXJOBS=~ ^[0-9]+$ ]];then echo"[ERROR] -- max number of simulteaneous jobs $MAXJOBS must be an integer (option -m).";exit 1 ;fi;;