Guys
I enjoyed the node. Here is a suggested topic that would be worth pursuing for the biological crowd
Data Structures. So BioPerl gives you some pretty cool data structures that are easy to handle. Its when you run into custom structures that you get problems. For instance if I'm working with E.coli, I have ~5e6 bp of DNA - 1e7bp if I'm working on each nucleotide on both strands. How do I manage working with an analysis that needs to annotate every base, eg working with coverage from next gen analysis. Using arrays or hashes gets ugly because you will typically run out of memory. I'm not aware of an out of the box BioPerl solution, though I could stand to be corrected. You could use pack and unpack. You could use DB::File. You might even go to Berkeley DB. But the problem is general enough that it would be useful to see one or more tutorials on what to do for these larger analysis problems that are beyond simple scripts and not necessarily part of the BioPerl toolbox.
MadraghRua
yet another biologist hacking perl....
-
Are you posting in the right place? Check out Where do I post X? to know for sure.
-
Posts may use any of the Perl Monks Approved HTML tags. Currently these include the following:
<code> <a> <b> <big>
<blockquote> <br /> <dd>
<dl> <dt> <em> <font>
<h1> <h2> <h3> <h4>
<h5> <h6> <hr /> <i>
<li> <nbsp> <ol> <p>
<small> <strike> <strong>
<sub> <sup> <table>
<td> <th> <tr> <tt>
<u> <ul>
-
Snippets of code should be wrapped in
<code> tags not
<pre> tags. In fact, <pre>
tags should generally be avoided. If they must
be used, extreme care should be
taken to ensure that their contents do not
have long lines (<70 chars), in order to prevent
horizontal scrolling (and possible janitor
intervention).
-
Want more info? How to link
or How to display code and escape characters
are good places to start.
|
