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";
}