Hello Everyone,
I have question regarding efficiency of suffix arrays in Perl.

If string = abaaba
suffix_array = (6, 3, 4, 1, 5, 2)
corresponding to ('a', 'aaba', 'aba', 'abaaba', 'ba', 'baaba')

A brutal approach is to create the list of suffixes
('abaaba', 'baaba', 'aaba', 'aba', 'ba', 'a')
then order it
('a', 'aaba', 'aba', 'abaaba', 'ba', 'baaba')
then extract the positions
(6, 3, 4, 1, 5, 2)

Easily done in perl with:
@ordered_list = sort map { substr($string, $_) } 0 .. $length - 1;

foreach my $elt (@ordered_list) {
print $length - length($elt) . "\n";
}

If string is very long (working with 200.000bp here), the sort does not cope

Any suggestions?

In reply to suffix array efficiency by RobertCraven

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.