[Bioperl-l] HIV db post with linebreaks.

Chris Fields cjfields at illinois.edu
Wed Oct 29 12:32:44 EDT 2008


Looks very interesting and useful!  We would need to know what prereqs  
are needed for the modules; we are trying to refrain from adding any  
more than we already have.  Also, recent updates to Bio::AnnotationI  
which disallow operator overloading (read: maintenance nightmare)  
require a display_text() method for data comparison.

Feel free to attach the modules to a bug report in Bugzilla (as an  
enhancement request) so we can test them out.


On Oct 28, 2008, at 1:33 PM, Mark A. Jensen wrote:

> [once more, with linebreaks]
> Hello all,
> I've been working on a set of Bioperl modules that access the
> (difficult to navigate) Los Alamos HIV sequence database. The modules
> have a couple of features that I think could boost the usage of that
> resource. What makes LANL really useful is the richness of the
> annotations, with information on geography, virology, patient health,
> and other epidemiologically useful stuff. However, the db interface is
> cgi-based and difficult to use in batch or to create complex queries
> without cramping your right index finger. The modules take care of
> this, slurp the desired annotations and attach them correctly (I
> think) to Bio::Seq objects delivered by a SeqIO stream. The interface
> understands NCBI-like query strings (with ANDs, ORs, and parens).
> I've put the APIs up on my site so as not to cram your inbox: please
> see
> http://fortinbras.us/HIVQueryAPI
> All the modules exist, work, and have their own .t files. I'd
> appreciate your comments.
> cheers,
> Mark Jensen
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign

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