create sub database

script/2_make_db.sh

+#!/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