4th script runs on multiple genes

script/4_parse_PSIblast.R

@@ -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")

script/4_parse_PSIblast.sh

@@ -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

script/runscript_78Lp_step34.sh

@@ -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