One improvement that should be straight forward to implement is to group everything by chromosome first.

So far example read only those records from the file that are related to chr1. Build your %reps hash from them. Then search for all those coordinates on chr1 that you find interesting.

Then empty the hash with %reps = () to save memory, and read all chr2 coordinates.

Other possible improvements: instead of using a hash for the coordinates, use two arrays (for begin and end), and then do a binary search in them.

Of course a relational database like sqlite or postgres can do all these things for you if you build appropriate indexes over the coloumns.

Perl 6 - second systems done right

In reply to Re: Reducing memory footprint when doing a lookup of millions of coordinates by moritz
in thread Reducing memory footprint when doing a lookup of millions of coordinates by richardwfrancis

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.