Well, you use the function get_exon to make it more readable, but all you do in that function is manipulate the $begin and $end values. Furthermore, the slowdown comes from the copying of a potential large string: $chromosome. A solution is to make a function that takes just 2 arguments: $begin and $end, and manipulate those. The manipulation doesn't require $chromosome. So: 

sub _ {$_ [0] - 1, $_ [1] - $_ [0] - 1}

while ((my $begin, my $end) =  each %exon_endpoints) {
    print substr ($chromosome => _ $begin, $end), "\n\n";
}

[download]

Of course, that still has the overhead of calling a user defined subroutine for each endpoint.

Abigail

In reply to Re: Large data processing ... by Abigail-II
in thread Large data processing ... by dragonchild

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.