Re: Keeping track of substituted regions with a while loop

[kschwab]

Based on your sample data, this seems more straightforward, and avoids the issue of substituting something that was already translated. Caveat: I'm guessing based on the sample data, so I may have missed something crucial.

my $protein;
# split $rna into groups of 3 characters
for ( unpack("(A3)*",$rna)) {
   if (exists($gencode{$_}) {
       $protein.=$gencode{$_};
   } else {
       die "No mapping for [$_]\n";
   }
}

[kschwab]

Missed a paren...

for ( unpack("(A3)*",$rna)) {
   if (exists($gencode{$_})) {
       $protein.=$gencode{$_};
   } else {
       die "No mapping for [$_]\n";
   }
}

[enderk]

Hi kschwab, thanks for your reply. You're absolutely right, that is another way of solving this problem (by sequentially appending the one-letter codes to a new string instead of substituting an existing string) and it is similar to the "alternative" method I described in my original post.

However, I was not looking so much into getting the right answer as rather trying to learn more about how to use regexes, combined with a while loop, in this situation. Is there an "easy" way for Perl to keep track of the position it is in, as it moves along a string in a while loop, or would that be an overkill to do, considering there are easier options available?