In that case, I'd suggest using Tie::File:
use Tie::File;
...
tie my @seq_data, 'Tie::File', $sequence_fname
or die "Can't open $sequence_fname: $!";
if(!($permute)){
for (@seq_data) {
my @line = split /\t/;
...
}
...
{
else{
open(OUT,">>$out")||die "Cannot open $out\n";
for (...) {
...
for (@seq_data) {
my @line = split /\t/;
...
}
foreach my $key(keys %ktc){
...
print OUT ...
...
}
}
close OUT;
}
untie @seq_data;
That'll be a little slower because you'll be repeating the split /\t/, but at least you won't have memory issues.
Also, note the change I made to die.
This is not for optimising the efficiency of your code; it's to improve feedback if things go wrong.
When you terminate the die message with a newline, you prevent file and line information from being output.
Also, "$!" provides addition information about why open failed, see "perlvar: Error Variables".
This is a good practice to get into the habit of doing; alternatively, consider using autodie.