T.step3

#!
#########################################################
# 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 analyzed"
   echo "D     Path and name of external database"
   echo "M     Path and file of external database metadata file"
   echo "i     Minimum within-group prevalence"
   echo "o     Maximum outside-group prevalence"
}

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

while getopts ":HD:M:i:o:p:" opt; do
   case $opt in
      H) # Help info
         Help
         exit;;
      p) # Plasmid Type
	 PLASMID="$OPTARG";;
      D) # External database
         EXDB="$OPTARG";;
      M) # Metadata file for external database
         EXDBMET="$OPTARG";;
      i) # minimum threshold value
         MINWITHIN="$OPTARG";;
      o) # maximum threshold value
         MAXWITHOUT="$OPTARG";;
      \?) #Invalid option
      echo "Option does not exist"
      exit;;
   esac
done

cat ./$PLASMID/unvalidated/fwd.coding.coords |
while read LINE LOCUS START END STRAND LENGTH SEQLINE
	do 
	echo \>$LOCUS
	awk -v XLINE=$SEQLINE '{if(NR==XLINE) print $0}' ./roary/merged.gff | awk -v SEQSTART=$START -v SEQLEN=$LENGTH '{print substr($0,SEQSTART,SEQLEN + 1)}'
	done > ./$PLASMID/unvalidated/unvalidated_FWDcoding.fasta
cat ./$PLASMID/unvalidated/rev.coding.coords |
while read LINE LOCUS START END STRAND LENGTH SEQLINE
	do 
	echo \>$LOCUS	
	awk -v XLINE=$SEQLINE '{if(NR==XLINE) print $0}' ./roary/merged.gff | awk -v SEQSTART=$START -v SEQLEN=$LENGTH '{print substr($0,SEQSTART,SEQLEN + 1)}'| tr ACGTacgt TGCAtgca | rev
	done > ./$PLASMID/unvalidated/unvalidated_REVcoding.fasta

cat ./$PLASMID/unvalidated/unvalidated_FWDcoding.fasta ./$PLASMID/unvalidated/unvalidated_REVcoding.fasta ./$PLASMID/unvalidated/intergenic.fasta > ./$PLASMID/unvalidated/unvalidated_loci.fasta
rm ./$PLASMID/unvalidated/unvalidated_FWDcoding.fasta
rm ./$PLASMID/unvalidated/unvalidated_REVcoding.fasta

mkdir ./$PLASMID/validated

blastn -db $EXDB -query ./$PLASMID/unvalidated/unvalidated_loci.fasta -perc_identity 80.0 -outfmt 6 > ./$PLASMID/validated/validation.hits

echo validation query complete

./R.step3 $EXDBMET $MINWITHIN $MAXWITHOUT $PLASMID