To profile the INDEL patterns in amplicon sequncing reads

INDEL profiler

printf "\nINDEL.profiler\n\n   usage: ./INDEL.profiler.sh READs.fasta Amplicon.seq.fasta\n\n"

cat $1 | \
while read l; do
	printf " \n"
      read L
	echo $l $L | sed 's/ /\n/g' | cat - $2 | muscle -quiet | fasta_formatter | \
	while read c; do
		printf "\n"$c"\nDEL:\n"
	      read d;
		echo $d | grep -bo "-" | cut -d: -f1 | \
		awk 'NR==1 {a=$1;b=$1;next} ($1 != b+1){print a+1"-"b+1; a=$1} {b=$1} END{print a+1"-"b+1}'
	     read e
		printf $e"\nINS:\n"
	     read f
		echo $f | grep -bo "-" | cut -d: -f1 | \
		awk 'NR==1 {a=$1;b=$1;next} ($1 != b+1){print a+1"+"b+1; a=$1} {b=$1} END{print a+1"+"b+1}'
	done | grep -v ">" | paste -s -d" "
done | sort | uniq -c | sort -rh > $1.INDEL.profile