Rotate_circular_reference.sh

##No warranty expressed or implied.  Hackish code to use Seqkit to "rotate" circular genomes.  
##Intended for use with Quiver, or other polishing tools like Pilon, to ensure that
##there isn't a coverage drop at the end of the circular sequence which prevents calling of the true consensus bases
##Graphmap is the only aligner that I'm aware of that properly deals with circular references!

FASTA=$1
NAME=$(basename $FASTA)

LENGTH=$(seqkit stat $FASTA | grep "FASTA" | tr -s " "| cut -f 5 -d " " | tr -d ",")
HALF=$(expr $LENGTH / 2 )
echo $LENGTH $HALF




##If length == even, will get 2 contigs and want to pick the 2nd one
if [(expr $LENGTH % 2) -eq 0]
then
FILTERME=$(seqkit sliding -C $FASTA -s $HALF -W $LENGTH | grep ">" | tail -n 1)
echo $FILTERME
seqkit sliding -C $FASTA -s $HALF -W $LENGTH | seqkit grep -v -p "$FILTERME" > rotated_$NAME

##If length == odd, will get three contigs and want to pick the middle one
elif
FILTERME1=$(seqkit sliding -C $FASTA -s $HALF -W $LENGTH | grep ">" | tail -n 1)
FILTERME1=${FILTERME#">"}
FILTERME2=$(seqkit sliding -C $FASTA -s $HALF -W $LENGTH | grep ">" | head -n 1)
FILTERME2=${FILTERME#">"}
FILTERME="$FILTERME1 $FILTERME2"
seqkit sliding -C $FASTA -s $HALF -W $LENGTH | seqkit grep -v -p "$FILTERME" > rotated_$NAME

fi