# ... snip opening the files ...

my %file2data;
while(<$input_file2>)
{ 
 next if /(^\s*$)|(^#)|(^@)/;
 my @columns2 = split;
 $file2data{$columns2[0]} = $columns2[1];
}

while(<$input_file1>)
{ 
 next if /(^\s*$)|(^#)|(^@)/;
 my @columns1 = split;
 print $out_file join("\t", $columns1[0],$columns1[1],
   $file2data{$columns1[0]}), "\n";
}