Another idea:

use strict;
my $final_res='';
open FILE, $infile;
while(my $final_line=<FILE>)
{
    if($final_line=~/^SeqID/)
    {
        my $final_line=<FILE>; chomp $final_line;
        
        my @split_final=split(/\t/, $final_line);

        my $final_res = $split_final[7];
        $final_res=~s/D/M/g;
        $final_res=~s/U/M/g;

#print $final_res."\n";
    }
}
close FILE;

print $final_res."\n";

################
# different coding
################

use strict;
my $infile = ''; #some file
open (FILE, "<", $infile) or die "unable to open $infile $!";

while(my $line=<FILE>)
{
    chomp $line;

    my ($token) = (split(/\t/, $line))[7];
    $token=~s/D/M/g;
    print "Token= ", $token, "\n";
}
[download]