From 24f5cba3bcd52ad183123b9f024411780766cc9e Mon Sep 17 00:00:00 2001
From: mcariou <115-mcariou@users.noreply.gitbio.ens-lyon.fr>
Date: Tue, 12 Oct 2021 18:01:42 +0200
Subject: [PATCH] create sub database
---
script/2_make_db.sh | 65 +++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 65 insertions(+)
create mode 100755 script/2_make_db.sh
diff --git a/script/2_make_db.sh b/script/2_make_db.sh
new file mode 100755
index 0000000..dc85914
--- /dev/null
+++ b/script/2_make_db.sh
@@ -0,0 +1,65 @@
+#!/bin/bash
+#$ -S /bin/bash
+## name of the job to follow them
+#$ -N dblegio
+## name of the queue to be used
+#$ -q E5-2670deb*,E5-2667v2*,E5-2667v4*
+#$ -cwd
+#$ -V
+## where to put the log files (output and error) automatically generated by the cluster (different from the .log generated by DGINN)
+## the dirs must exist before job is launched
+#$ -o /home/mcariou/2021_legio/log/
+#$ -e /home/mcariou/2021_legio/log/
+
+### configurer l'environnement
+module purge
+
+
+##################################################################################
+#./2_make_db.sh /home/mcariou/2021_legio/doc/tabAss.txt /home/mcariou/2020_Attaiech/prot_db/Transdecoder/ /home/mcariou/2021_legio/blastdb/phyloref
+
+
+HOME="/home/mcariou/2021_legio/"
+OUT=$HOME"blastdb/phyloref/"
+CAT=$OUT"/cat_phyloref_cds.fasta"
+Trans="/home/mcariou/2020_Attaiech/prot_db/Transdecoder/"
+TAB=$HOME"/phylolegio/doc/tabAss.txt"
+
+mkdir -p $OUT
+
+##################################################################################################################UT
+
+
+### Read tab genomes and cat cds files.
+
+if [[ -s $CAT ]] ; then
+ echo "cat already exists"
+else
+ for genome in `cat $TAB | sed '1d'| awk '{print $1}'`
+ do
+ file=${Trans}/${genome}*/longest_orfs.cds
+ file2=`echo $file`
+ if [[ -s $file2 ]] ; then
+ cat $file2 >> $CAT
+ else
+ echo "doesn't: $file2"
+ fi
+ done
+fi
+
+
+# Re-split concatenate
+#sed '1 s/^/\n/; 2,$ s/>/~\n>/' $CAT | split -t '~' -l 100000 -d --filter="tail -n+2 | grep -v '^~$' > \$OUT\$FILE"
+
+
+### Make Blast db
+
+makeblastdb -dbtype nucl -in $CAT -hash_index -out $OUT/phyloref -parse_seqids
+
+
+
+
+
+
+
+# fin
--
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