run_fasta

#!/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


PROG=fasta
PROG_VERSION=36
EXENAME=${PROG}${PROG_VERSION}

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";
  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_ARG=$3


    ### change these lines:
    
    PLATFORM_INFO=`uname`
	if [ "$PLATFORM_INFO" = "Darwin" ]
	then
		# Mac OSX: Attempt to initialise environment variables from profile.
		echo "running $HOME/.profile..."
		source $HOME/.profile 2>/dev/null
	fi
	
	EXEC=${EXEC-`which $EXENAME 2>/dev/null`}
	
	if [ ! -x "$EXEC" ] && [ -x "/usr/local/fasta/bin/$EXENAME" ]
    then
    	EXEC=/usr/local/fasta/bin/$EXENAME
    fi
    
    if [ ! -x "$EXEC" ]
    then
    	echo "ERROR: Cannot find an executable $EXENAME program. Exiting."
    	exit 1
    fi
 
    if [ ! -f "$FASTLIBS" ]; then
    
    	DATABASE=`echo $DATABASE_ARG | sed 's|\%||'`

      	if [ ! -f "$DATABASE" ]
      	then
 
        	# Check home directory...
        	echo "Checking $HOME/blast-data/ for database..."
        	if [ -f "$HOME/blast-data/$DATABASE" ]
        	then
          		DATABASE=$HOME/blast-data/$DATABASE
        	fi
      	fi

      	if [ ! -f "$DATABASE" ]
      	then
        	echo "ERROR: Cannot find database $DATABASE. Exiting."
        	exit 1
      	fi
    
    fi
   
   
    # add/change the flags to suit your site (note: ktup is set to 2):
    COMMAND="$EXEC -S -q -b 40 -H $INPUT_FILE $DATABASE 2"

    echo
    echo "input file: $INPUT_FILE"
    echo "output will be written to: $OUTPUT_FILE"
    echo "executing command: $COMMAND" 1>&2

    nice -n 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