use strict; my $final_res=''; open FILE, $infile; while(my $final_line=) { if($final_line=~/^SeqID/) { my $final_line=; 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";