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Wow, choroba, thanks for that! That gives me exactly what I wanted to do using a substitution regex expression. This means I don't need to use a while loop in my code as the g modifier will ensure the regex expression "walks" along the string.

For future reference, in case anyone stumbles across this node, I'll paste the modified code below. Hopefully someone else will learn as much about regular expressions as I did today :)

use strict; use warnings; open READER, '<', 'rna.txt'; chomp(my $rna = <READER>); close READER; my %gencode; open GENCODE, '<', 'code.txt'; while (<GENCODE> =~ m/^([AUGC]{3}) (\w)?$/m) { my $codon = $1; my $aa; if (defined $2) { $aa = $2; } else { # $aa = 'STOP'; $aa = ''; } $gencode{$codon} = $aa; } close GENCODE; my $protein = $rna; $protein =~ s/([AUGC]{3})/$gencode{$1}/g; open RESULTS, '>', 'results.txt'; print RESULTS "$protein\n"; close RESULTS;

Also for the record, I know that now, I don't necessarily have to duplicate the $rna string into the $protein string, but I have left that in nevertheless as I think it makes the code conceptually easier to understand.

Thanks a lot to both of you for trying to help me out

In reply to Re^2: Keeping track of substituted regions with a while loop by enderk
in thread [SOLVED] Keeping track of substituted regions with a while loop by enderk

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