T.step4

#!
#########################################################
# Help                                                  #
#########################################################
Help()
{
   # Display Help
   echo "Add description of the script functions here."
   echo
   echo "Syntax: scriptTemplate [-g|h|v|V]"
   echo "options:"
   echo "H     Print this Help."
   echo "p     Plasmid type to be evaluated"
   echo "d     Directory and name of database"
   echo "f     Path and filename of validated loci"
   echo "i     Maximum allowed distance between loci (bp)"
   echo
}

#########################################################
# PROGRAM						  #
#########################################################

while getopts ":H:d:f:i:p:" opt; do
   case $opt in
      H) # Help info
         Help
         exit;;
      d) # Path and name of external database
         DBPATH="$OPTARG";;
      f) # Path and file of validated loci
         FASTAPATH="$OPTARG";;
      i) # Piggy executable
         INTERDISTANCE="$OPTARG";;
      p) # Plasmid Type
         PLASMID="$OPTARG";;
      \?) #Invalid option
      echo "Option does not exist"
      exit;;
   esac
done


echo Gathering sequence location data from database

mkdir ./$PLASMID/fragments

blastn -db $DBPATH -query $FASTAPATH -perc_identity 80.0 -outfmt 6 > ./$PLASMID/fragments/val_only.hits

echo 

echo Starting R script

./R.step4 $INTERDISTANCE $PLASMID