From what I can see, the problem is, that if you go straight and substitute all 'A's wit 'T's you can't tell for sure which 'T's to substitute with 'A's afterwards. This can be for instance solved by simply replacing all 'A's by another character (for instance '_' or whatever you like), then replacing all 'T's by 'A's, and then replacing all '_'s (or whatever character you chose) by 'A's:
<?php
$dna = "AGTCTGCCCTAG";
echo str_replace(array("A","G","C","T","_","-"), array("_","-","G","A","T","C"), $dna); ?>
Although I don't know how transliteration in perl works (though I remember that is kind of similar to the UNIX command "tr") I would suggest following function for "switching" single chars:
<?php
function switch_chars($subject,$switch_table,$unused_char="_") {
foreach ( $switch_table as $_1 => $_2 ) {
$subject = str_replace($_1,$unused_char,$subject);
$subject = str_replace($_2,$_1,$subject);
$subject = str_replace($unused_char,$_2,$subject);
}
return $subject;
}
echo switch_chars("AGTCTGCCCTAG", array("A"=>"T","G"=>"C")); ?>
