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#!/bin/bash
cmd="";
for i in "$@"
do
case $i in
-o=*|--outname=*)
OUTNAME="${i#*=}"
shift # past argument=value
;;
*)
cmd="$cmd $i"
;;
esac
done
bl_asn=${OUTNAME}.asn
bl0_out="$OUTNAME.html"
blm_out="$OUTNAME.msa"
blt_out="$OUTNAME.bl_tab"
# echo "OUTFILE = ${OUTNAME}"
#export BLAST_PATH="/ebi/extserv/bin/ncbi-blast+/bin"
export BLAST_PATH="/usr/bin"
$BLAST_PATH/blastp -outfmt 11 $cmd > $bl_asn
$BLAST_PATH/blast_formatter -archive $bl_asn -outfmt 0 -html > $bl0_out
$BLAST_PATH/blast_formatter -archive $bl_asn -outfmt '7 qseqid qlen sseqid slen pident length mismatch gapopen qstart qend sstart send evalue bitscore score btop' > $blt_out
$BLAST_PATH/blast_formatter -archive $bl_asn -outfmt 2 > $blm_out
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