Shell Programming and Scripting

#!/bin/bash

# get chain as parameter
dna=$1

function rrev() {
	case $1 in
		"T")
		echo -n A
		;;
		"A")
		echo -n T
		;;
		"G")
		echo -n C
		;;
		"C")
		echo -n G
		;;
	esac
}

reversed=`echo $dna | rev`

for i in $(seq 0 $((${#dna}-1))); do
	rrev ${reversed:$i:1};
done
echo

$ ./rev.sh ATCATATCCA
TGGATATGAT

perl -nle'BEGIN {
  @map{ A, C, G, T } = ( T, G, C, A )
  }
  print /^>/ ?
    $_ :
      join //, map $map{ $_ }, split //, scalar reverse
  ' infile

#!/bin/bash

file=$1

function rrev() {
	case $1 in
		"T")
		echo -n A
		;;
		"A")
		echo -n T
		;;
		"G")
		echo -n C
		;;
		"C")
		echo -n G
		;;
	esac
}

while read line; do

	if [ `echo $line | grep -c "^>"` -eq 0 ]; then
		orig_revd=`echo $line | rev`
		for i in $(seq 0 $((${#line}-1))); do
        		rrev ${orig_revd:$i:1};
		done
		echo
	else
		echo $line
	fi

done < $file

awk 'BEGIN {
  j = n = split("A C G T", t)
  for (i = 0; ++i <= n;)
    map[t[i]] = t[j--]
  }
{
  if (/^>/) print
  else {
    for (i = length; i; i--)
	  printf "%s", map[substr($0, i, 1)]
    print x
	}	  
  }'  infile