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!