From b67e2fbcfc02e491ad031c0321fd2935bd3aa343 Mon Sep 17 00:00:00 2001
From: mcariou <115-mcariou@users.noreply.gitbio.ens-lyon.fr>
Date: Mon, 22 Nov 2021 18:41:49 +0100
Subject: [PATCH] 4th script runs on multiple genes
---
script/4_parse_PSIblast.R | 4 ++--
script/4_parse_PSIblast.sh | 2 ++
script/runscript_78Lp_step34.sh | 2 +-
3 files changed, 5 insertions(+), 3 deletions(-)
diff --git a/script/4_parse_PSIblast.R b/script/4_parse_PSIblast.R
index a9f47ab..ff2a5ad 100644
--- a/script/4_parse_PSIblast.R
+++ b/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")
diff --git a/script/4_parse_PSIblast.sh b/script/4_parse_PSIblast.sh
index 67d19c6..32b2b2b 100755
--- a/script/4_parse_PSIblast.sh
+++ b/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
diff --git a/script/runscript_78Lp_step34.sh b/script/runscript_78Lp_step34.sh
index 89e7416..0180bd7 100755
--- a/script/runscript_78Lp_step34.sh
+++ b/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
--
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