Example1:
perl -e 'while(<>) {if($_=~/^>/) {print $_;} else {$_=~tr/ATCG/TAGC/; print $_;}}'  FILE

##</code><code>##

perl -nle 'if($_=~/^>/) {print $_;} else {$_=~tr/ATCG/TAGC/; print $_;}' FILE

##</code><code>##

perl -nle 'if(/^>/) {print;} else { tr/ATCG/TAGC/; print; }' FILE

##</code><code>##

perl -ple 'if(/^>/) { ; } else { tr/ATCG/TAGC/; }' FILE

##</code><code>##

perl -ple 'tr/ATCG/TAGC/ unless( /^>/ );' FILE

##</code><code>##

perl -ple '/^>/ or tr/ATCG/TAGC/' FILE