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#!/bin/sh -
# this script will run a search program on a sequence input file or on each
# file in a file of filenames
# to customise this script see the function called run_one_prog below
RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_fasta,v 1.18 2008-05-16 10:15:49 tjc Exp $"
PROG=`echo $RCS_HEADER | sed 's/.*run_\(.*\),v.*/\1/'`
if [ $# = 4 -a x$1 = x-onefile ]
then
shift
ONEFILE=t
DATABASE=$3 export DATABASE
else
if [ $# = 2 ]
then
DATABASE=$2 export DATABASE
else
echo usage: $0 -onefile input_file output_file database 1>&2
echo or: $0 file_of_filenames database 1>&2
exit 1
fi
fi
#
# Exchange DB name for fasta reference
#
if [ -f "$FASTLIBS" ]; then
if [ "$DATABASE" = "%uniprot" ]; then
DATABASE="%U";
elif [ "$DATABASE" = "%uniprot_archaea" ]; then
DATABASE="%A";
elif [ "$DATABASE" = "%uniprot_bacteria" ]; then
DATABASE="%B";
elif [ "$DATABASE" = "%uniprot_eukaryota" ]; then
DATABASE="%E";
elif [ "$DATABASE" = "%uniprot_viruses" ]; then
DATABASE="%V";
elif [ "$DATABASE" = "%uniprot_rest" ]; then
DATABASE="%R";
elif [ "$DATABASE" = "%malaria" ]; then
DATABASE="%M";
elif [ "$DATABASE" = "%kineto_aa" ]; then
DATABASE="%K";
fi
fi
# expand any ~ or environment variables
#EXPANDED_DATABASE=`echo "echo $DATABASE" | /bin/csh -f`
eval EXPANDED_DATABASE="$DATABASE"
### change this function to suit your site:
run_one_prog () {
INPUT_FILE=$1
OUTPUT_FILE=$2
DATABASE=$3
### change these lines:
EXEC=${EXEC-`which fasta34 2>/dev/null`}
if [ ! -x "$EXEC" ]; then
EXEC=`find Artemis* -name fasta34 2>/dev/null`
fi
if [ ! -f "$FASTLIBS" ]; then
DATABASE_TMP=`echo $DATABASE | sed 's|\%||'`
DATABASE_TMP="$PWD/"`find Artemis* -name blast-data 2>/dev/null`"/$DATABASE_TMP"
if [ -f "$DATABASE_TMP" ]; then
DATABASE="$DATABASE_TMP"
fi
fi
echo "about to start $EXEC with input from $INPUT_FILE and output to" 1>&2
echo "$OUTPUT_FILE using database $DATABASE" 1>&2
# add/change the flags to suit your site:
COMMAND="$EXEC -B -S -q -b 40 -H $INPUT_FILE $DATABASE ktup 2"
echo "command line: $COMMAND" 1>&2
nice -19 $COMMAND 2>&1 > $OUTPUT_FILE |
tee ${PROG}_errors.new 1>&2
#### end of changes
# Artemis can read compressed files
gzip -9 $OUTPUT_FILE &
if [ -s ${PROG}_errors.new ]
then
( echo ERROR running $PROG: ; echo;
echo ===================================================
cat ${PROG}_errors.new ) >> $OUTPUT_FILE
cat ${PROG}_errors.new >> ${PROG}_errors
fi
}
(echo "#!/bin/sh -"; echo "kill $$") > $PROG.kill
chmod a+x $PROG.kill
if [ x$ONEFILE = x ]
then
for i in `cat $1`
do
run_one_prog $i $i.out $EXPANDED_DATABASE
done
else
run_one_prog $1 $2 $EXPANDED_DATABASE
fi
exit 0
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