3_make_blast.sh

#!/bin/bash

echo "USAGE: ./3_make_blast.sh \$1=blast_db \$2=gene_query \$3=out_path"
echo "--------------------------------------------------"

##################################################################################################################
### En local 
#./make_blast.sh /home/adminmarie/Documents/CIRI_BIBS_projects/2021_04_Doublet/pipeline/blastdb/cdslegio /home/adminmarie/Documents/CIRI_BIBS_projects/2021_04_Doublet/pipeline/genes/lp0952.fasta /home/adminmarie/Documents/CIRI_BIBS_projects/2021_04_Doublet/pipeline/out_blastn

### PSMN
#./make_blast.sh /Xnfs/ciridb/shared_data/Databases/legio_cds/blastdb_ncbi/cdslegio ~/2021_legio/genes/lp0952.fasta ~/2021_legio/out_blastn
##################################################################################################################

# variable
REP_DB=$1
gene=`echo $2 | sed 's/.fasta//g'`
REP_OUT=$3
gene_name=`echo $gene | awk -F "/" '{print $NF}'`

# Check argument
if [[ -s $gene.fasta ]] ; then
echo "Gene exists:$gene" 
else
echo "Missing or wrong gene argument: $2" 
exit 1
fi ;

mkdir -p $REP_OUT

if [[ -s $REP_OUT ]] ; then
echo "Out repertory exists: $REP_OUT" 
else
echo "Missing or wrong out repertory argument: $3"
exit 1 
fi ;

echo "--------------------------------------------------"

echo "make db if not available:"

if [[ -s $REP_DB.nal ]] ; then 
echo "$REP_DB.nal exists" 
else 
echo "$REP_DB.nal doesn't exist" 
origdb=`echo x{00..31}`
echo $origdb
blastdb_aliastool -dbtype nucl -dblist "$origdb" -out $REP_DB -title "blastdb with ncbi legionella cds"
fi ;

echo "--------------------------------------------------"


blastn -db $REP_DB -query ${gene}.fasta -evalue 10 \
-outfmt "7 qseqid qlen sseqid slen length pident evalue nident mismatch gapopen qstart qend qseq bitscrore score sstart send sseq sstrand" \
-out $REP_OUT/${gene_name}.blastn -max_target_seqs 5000 

echo "program done!"