#this pulls header lines into a new file
grep -F ">" $1 > headers.txt
#this adds quotes around st
sed 's/^/="/' headers.txt > headers_mod.txt
sed 's/$/"/' headers_mod.txt > headers_mod2.txt
#this adds line number
cat -n headers_mod2.txt > headers_numbers.txt
#this adds brackets around the line number
awk '{$1="%%>"$1"%%"}8' headers_numbers.txt > hn2.txt
#replace spaces with underscores
#for string in hn2.txt

#awk -F '"' -v OFS='"' '{
#	for (i=2; i<=NF; i+=2)
#		gsub(/[[:blank:]]/, "_",
#}'<<END

sed -e 's/\ /_/2g' hn2.txt > hn3.txt
#awk 'sub(/\(\s*$/,"]"){printf "%s",$0;next}7' hn2.txt > hn3.txt

#awk '{$1="["$1"]"}8' headers_numbers.txt > headers_numbers2.txt
#sed ':a;/($/{N;s/\n//;ba}' headers_numbers2.txt > headers_numbers3.txt
#for lines in {1..4..1}
#do
	#sed 's/^/'[$lines]'/' headers_mod2.txt
#done > headers_num.txt

#awk '/^>/{print ">" ++i; next}{print}' <$1 >replaced_headers.fasta
#for item in $(grep -F "^>" $1)
#do
#	echo $item
#done

#sed 's/$item/$number/g'
#done

#declare -A ary
#readarray -t lines < headers_numbers.txt
#for line in "${lines[@]}"
#do
#	key=${line%%=*}
#	value=${line#*=}
#	array[$key]=$value
#done