DDssDD
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In the new/old example, why are the final "s" not replaced? Don't they follow a "D"?

Please, try to be more precise.

Also, you can easily shorten the data, 2 consecutive characters of each type would do.

Ok, let me try again with some examples of how data look now (old) and should look (new):
-case 1: only 's'

old:sssss
new:iiiii
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-case 2: only 's' and 'U'

old:sssUUss
new:iiiMMoo
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-case 3: only 's' and 'D'

old:sssDDss
new:oooMMii
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-case 4: 's', 'D' and 'U' (all possible characters)

old:sssssDDDDDDDssssUUUss
new:oooooMMMMMMMiiiiMMMoo
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OR

old:sssssUUUUUUUssssDDDss
new:iiiiiMMMMMMMooooMMMii
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For some reason, the code I wrote changes many but not all cases... Not that you cannot see s+D+s+D+s+<code> sequence, or <code>s+U+s+U+s+<code>. <code>D and U alternate.

> Not that you cannot see s+D+s+D+s+ sequence, or s+U+s+U+s+. D and U alternate.

If you mean "Note" by "Not", than your sample input is invalid, as both the sequences contain sDsDs.

Also, I think the following works correctly even for the non-alternating sequences in the way you originally showed:

my %before = (U => 'I', D => 'O');
my %after; @after{ keys %before } = reverse values %before;
sub subst {
    local ($_) = @_;
    1 while s/(s+)(?=([DU]))/$before{$2} x length $1/e
          | s/(?<=([DU]))(s+)/$after{$1} x length $2/e;

    tr/DU/MM/ or tr/s/I/;
    return $_
}
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It uses the bitwise or that doesn't short circuit to try both the substitutions every time while there's anything to replace.

Tested against:

Read more... (545 Bytes)

Might need some tweaking if the specification changes.

map{substr$_->[0],$_->[1]||0,1}[\*||{},3],[[]],[ref qr-1,-,-1],[{}],[sub{}^*ARGV,3]

Fixed it after all:


while(<>)
{
    if($_=~/^>/)
    {
        $id=$_;
        $seq=<>;

        print $id.$seq;
        if($seq=~/^s+$/)
        {
            $seq=~s/s/I/g;
            print $seq;
        }

        else
        {
            while($seq=~/(s+)([U|D]+)(s+)/g)
            {
                $part_before=$1;
                    $len_bef=length($part_before);
                $part_TM=$2;
                $part_after=$3;
                    $len_after=length($part_after);

                if($part_TM=~/U/)
                {
                    $part_bef_new='I' x $len_bef;
                    $part_after_new = 'O' x $len_after;
                }
                elsif($part_TM=~/D/)
                {
                    $part_bef_new='O' x $len_bef;
                    $part_after_new = 'I' x $len_after;
                }
                $seq=~s/$part_before/$part_bef_new/;
                $seq=~s/$part_after/$part_after_new/;
            }

            $seq=~s/U/M/g;
            $seq=~s/D/M/g;
            print $seq;
        }
    }
}
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Thank you for your time!