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;

[download]

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.

-- Ken

In reply to Re^3: Code Optimization by kcott
in thread Code Optimization by azheid

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.