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|
#!/bin/bash
cmd="";
for i in "$@"
do
case $i in
--outname=*)
OUTNAME="${i#*=}"
shift # past argument=value
;;
--query=*)
QUERY="${i#*=}"
shift # past argument=value
;;
--db=*)
DATABASE="${i#*=}"
shift # past argument=value
;;
--cmd=*)
SRCH_CMD="${i#*=}"
shift
;;
--ktup=*)
KTUP="${i#*=}"
shift
;;
*)
cmd="$cmd $i"
;;
esac
done
# echo "OUTNAME: " $OUTNAME
echo "# CMD: " $cmd
if [[ $OUTNAME == '' ]]; then
OUTNAME=${QUERY}_out
fi
if [[ $SRCH_CMD == '' ]]; then
SRCH_CMD=fasta36
fi
#if [[ $ANN_SCRIPT == '' ]]; then
# ANN_SCRIPT="/seqprg/bin/ann_pfam30.pl --db=pfam31_qfo --host=localhost --neg --vdoms --acc_comment"
#fi
# echo "OUTNAME: " $OUTNAME
bl0_out="$OUTNAME.html"
bla_out="${OUTNAME}_an.html"
blt_out="$OUTNAME.fa_tab"
blr_out="$OUTNAME.fa_tab_rn"
export BLAST_PATH="/usr/bin"
# BLAST_PATH="../bin"
cmd="$cmd -mF8CBL=$blt_out $QUERY $DATABASE"
# echo "tmp_files:"
# echo $bl_asn $bl0_out $bla_out $blt_out
# echo "OUTFILE = ${OUTNAME}"
#echo "cmd: $cmd"
#echo "==="
#echo "bl0_out: $bl0_out"
#echo "==="
# echo "$BLAST_PATH/$SRCH_CMD $cmd > $bl0_out"
# run the program
$BLAST_PATH/$SRCH_CMD $cmd > $bl0_out
/usr/share/fasta3/scripts/rename_exons.py --have_qslen --dom_info $blt_out > $blr_out
if [ ! -s $blr_out ]; then
# echo "# " `ls -l $blt_out $blr_out`
blr_out=$blt_out
# echo "# " `ls -l $blt_out $blr_out`
fi
/usr/share/fasta3/scripts/merge_fasta_btab.pl --plot_url="plot_domain6t.cgi" --have_qslen --dom_info --btab $blr_out $bl0_out
|
