Commit b67e2fbc authored by mcariou's avatar mcariou
Browse files

4th script runs on multiple genes

parent 7e4d8611
......@@ -2,8 +2,8 @@
args = commandArgs(trailingOnly=TRUE)
# test if there is at least one argument: if not, return an error
if (length(args)!=6) {
stop("5 arguments must be supplied.\n", call.=FALSE)
if (length(args)!=8) {
stop("7 arguments must be supplied.\n", call.=FALSE)
}
#args<-c("/home/mcariou/2021_legio/fasta/78Lp/Q5ZXP3_lpg0688/Q5ZXP3_lpg0688.psiblast.mod", "0.0001", "0.3", "0.5", "1", "/home/mcariou/2021_legio/fasta/78Lp/Q5ZXP3_lpg0688/Q5ZXP3_lpg0688.fasta")
......
......@@ -52,6 +52,8 @@ echo $rscript
for Gene in $GENES
do
mkdir -p $FASTA_REP/$Gene
echo "in the loop"
echo $Gene
subblast=$FASTA_REP"/"$Gene"/"$Gene".psiblast"
grep $Gene $OUT_BLAST > $subblast
......
......@@ -16,7 +16,7 @@
## IN TRIAL
/home/mcariou/2021_legio/phylolegio/script/4_parse_PSIblast.sh ~/2021_legio/out_blastn/78Lp_uniprot.psiblast ~/2021_legio/phylolegio/doc/tabAss.txt ~/2021_legio/fasta/lpg2300_50_50 ~/2021_legio/genes/78Lp_uniprot.fasta 0.0001 0.5 0.5 1
/home/mcariou/2021_legio/phylolegio/script/4_parse_PSIblast.sh ~/2021_legio/out_blastn/78Lp_uniprot.psiblast ~/2021_legio/phylolegio/doc/tabAss.txt ~/2021_legio/fasta/78Lp ~/2021_legio/genes/78Lp_uniprot.fasta 0.0001 0.5 0.5 1
# fin
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