Hi all,

I'm trying to write an algorithm that can search a genomic coordinate (chromosome number, position) against a list of other coordinates (from eQTL data) to find the nearest coordinate(s) (eQTL) to the search term.

I was planning on using a hash structure such as $hash{$chr}{$pos}='' for my search terms and another $eQTLhash{$chr}{$pos}='...'. Could anyone recommend to me a good algorithm to accomplish this task?

e.g. (also strange case in which more than 1 site would have to be returned)

search term = 1 50

eqtl hash contains 1=>15, 1=>49, 1=>51, 1=>79

should produce output of 49 AND 51 (this is probably a very rare case and if it's too difficult don't worry about creating both outputs).

In reply to Search a hash for closest match by aquinom

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.