[Bioperl-l] Getting values from a GenBank File

Barry Moore barry.moore at genetics.utah.edu
Fri Mar 5 09:26:47 EST 2004


Sure,  but I've got to figure out DocBook first - never used it.  I've  
got the web site, and downloaded the book.  I'll get to that as soon as 
I can.


Heikki Lehvaslaiho wrote:

>I like your RichSeq breakdown! It would make a great addition into BioPerl 
>howtos. Would you be interested in converting it into DocBook yourself? 
>	-Heikki
>On Thursday 04 Mar 2004 20:30, Barry Moore wrote:
>>While learning BioPerl, I've spent a good bit of time trying to figure
>>out where some bit of information in a GenBank file might be tucked away
>>in that RichSeq object, and how the hell to get at it.  I finally
>>decided it was time to sift through that object and find out what's in
>>there and where it is.  Along the way I wrote down  what I found, and
>>then added a bit to it to try and turn it into something that I would
>>like to have found when I first started learning Bioperl.  The result is
>>a "GeneBank-file-centric" crib sheet for Bioperl.  The document is
>>centered around a "standard" GenBank file where each seperate item of
>>information is marked-up with  numbers and codes that refer to
>>information later in the document about how to get at that particular
>>value in using BioPerl.  It also includes a script at the end that can
>>be modified easily to get at all the major stuff in the GenBank file.
>>This document is aimed at beginners to BioPerl, but assumes a working
>>knowledge of Perl.  The file is, of course, free to be used by anyone in
>>anyway that they wish.  I'd appreciate any corrections or improvements
>>if you find errors or shortcomings.

Barry Moore
Dept. of Human Genetics
University of Utah
Salt Lake City, UT

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