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|
#!/bin/bash
################
## blastp_annot_cmd.sh --query=seq/gstm1_human.aa --ann_script=scripts/ann_pfam_sql.pl --q_ann_script=scripts/ann_pfam_sql.pl -db /slib2/bl_dbs/pfam34_qfo78
##
## blastp reseults and intermediate files are saved in the same location as the query file
## annotation scripts must fully qualified
## --html=0 produces domain annotations but no domain graphics
## --html=1 provides exon mapping (if available) and domain graphics
##
cmd="";
DO_HTML=1
PGM='blastp'
for i in "$@"
do
case $i in
-p=*|--pgm=*)
PGM="${i#*=}"
shift # past argument=value
;;
-o=*|--outname=*)
OUTNAME="${i#*=}"
shift # past argument=value
;;
-q=*|--query=*)
QUERY="${i#*=}"
cmd="$cmd -query $QUERY"
shift # past argument=value
;;
--ann_script=*)
ANN_SCRIPT="${i#*=}"
shift
;;
--q_ann_script=*)
Q_ANN_SCRIPT="${i#*=}"
shift
;;
--html=*)
DO_HTML="${i#*=}"
shift
;;
*)
cmd="$cmd $i"
;;
esac
done
# echo "OUTNAME: " $OUTNAME
# echo "CMD: " $cmd
if [[ $OUTNAME == '' ]]; then
OUTNAME=${QUERY}_out
fi
#if [[ $ANN_SCRIPT == '' ]]; then
# ANN_SCRIPT="/seqprg/bin/ann_pfam30.pl --db=pfam31_qfo --host=localhost --neg --vdoms --acc_comment"
#fi
# echo "OUTNAME2: " $OUTNAME
bl_asn="$OUTNAME.asn"
bl0_out="$OUTNAME.html"
bla_out="${OUTNAME}_ann.html"
blm_out="$OUTNAME.msa"
blt_out="$OUTNAME.bl_tab"
blt_ann="$OUTNAME.bl_tab_ann"
blr_out="$OUTNAME.bl_tab_rn"
# echo "tmp_files:"
# echo $bl_asn $bl0_out $blt_out
# echo "OUTFILE = ${OUTNAME}"
#export BLAST_PATH="/ebi/extserv/bin/ncbi-blast+/bin"
export BLAST_PATH="/seqprg/bin"
$BLAST_PATH/$PGM -num_threads=8 -outfmt 11 $cmd > $bl_asn
$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
# annot_cmd="annot_blast_btop2.pl --query $QUERY --raw --have_qslen --dom_info --ann_script "$ANN_SCRIPT" --q_ann_script "$Q_ANN_SCRIPT" $blt_out > $blt_ann"
# echo "# $annot_cmd"
/usr/share/fasta3/scripts/annot_blast_btop2.pl --query $QUERY --raw --have_qslen --dom_info --ann_script "$ANN_SCRIPT" --q_ann_script "$Q_ANN_SCRIPT" $blt_out > $blt_ann
if [[ $DO_HTML == 1 ]]; then
## rename_exons.py --have_qslen --dom_info $blt_ann > $blr_out
$BLAST_PATH/blast_formatter -archive $bl_asn -outfmt 0 -html > $bl0_out
## echo "# merge_blast_btab.pl --plot_url=plot_domain6t.cgi --have_qslen --dom_info --btab $blt_out $bl0_out"
/usr/share/fasta3/scripts/merge_blast_btab.pl --plot_url="plot_domain6t.cgi" --have_qslen --dom_info --btab $blt_ann $bl0_out
else
$BLAST_PATH/blast_formatter -archive $bl_asn -outfmt 0 > $bl0_out
merge_cmd="merge_blast_btab.pl --have_qslen --dom_info --btab $blt_ann $bl0_out"
# echo "# $merge_cmd"
/usr/share/fasta3/scripts/merge_blast_btab.pl --have_qslen --dom_info --btab $blt_ann $bl0_out
fi
# $BLAST_PATH/blast_formatter -archive $bl_asn -outfmt 2 > $blm_out
|
