run_blastn

#!/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_blastn,v 1.4 2005-12-20 13:49:49 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
        echo    or: $0 file_of_filenames database
        exit 1
    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 blastall 2>/dev/null`}

    if [ ! -x "$EXEC" ]; then
      EXEC=`find Artemis* -name blastall 2>/dev/null`
    fi

    if [ ! -d "$BLASTDB" ]; then
      DATABASE_TMP="$PWD/"`find Artemis* -name blast-data 2>/dev/null`"/$DATABASE"
      if [ -f "$DATABASE_TMP" ]; then
        DATABASE="$DATABASE_TMP"
      fi
    fi

    echo "about to start $EXEC with input from $INPUT_FILE and output to"
    echo "$OUTPUT_FILE using database $DATABASE"


    EXTRA_ARGS=

    # add/change the flags to suit your site:
    nice -19 $EXEC -d $DATABASE -i $INPUT_FILE -p blastn \
      $EXTRA_ARGS 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