EUtilities help

[Warren Gallin]

Hi,

        Is there a cogent document on using Bio::DB::EUtilities with Bioperl  
1.5.2 around somewhere?

        We upgraded and now my scripts are broken when invoking it.

        Any pointers appreciated.

Thanks,

Warren Gallin
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[Dave Messina-3]

Hi Warren,

Are you upgrading to 1.5.2 or downgrading from bioperl-live?

If the former, you might consider going all the way to bioperl-live, whose
EUtilities support is improved significantly and documented extensively
here:

http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook

If the latter, I don't believe there is, but Chris Fields will know for sure
and will probably chime in.


Dave

To get bioperl-live
as a tarball: http://www.bioperl.org/DIST/nightly_builds/
or via Subversion: http://www.bioperl.org/wiki/Using_Subversion
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[Chris Fields-5]

As mentioned in previous posts and in the original POD, the original  
Bio::DB::EUtilities was experimental (unstable API).  It is deprecated  
in favor of the bioperl-live interface, which splits the user agent  
and parameter handling (Bio::DB::EUtilities, EUtilParameters) from the  
parsers (Bio::Tools::EUtilities).  Unfortunately, the original design  
was too rushed so any XML changes broke the tools; I basically had to  
start from the ground up again.  Any changes to eutil output should  
now be easier to deal with (famous last words).

I am still planning on adding a few things to it (including tests for  
the parser and user agent) but it shouldn't change substantially from  
what is in the cookbook.

chris

On Aug 19, 2008, at 2:30 AM, Dave Messina wrote:

> Hi Warren,
>
> Are you upgrading to 1.5.2 or downgrading from bioperl-live?
>
> If the former, you might consider going all the way to bioperl-live,  
> whose
> EUtilities support is improved significantly and documented  
> extensively
> here:
>
> http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook
>
> If the latter, I don't believe there is, but Chris Fields will know  
> for sure
> and will probably chime in.
>
>
> Dave
>
> To get bioperl-live
> as a tarball: http://www.bioperl.org/DIST/nightly_builds/
> or via Subversion: http://www.bioperl.org/wiki/Using_Subversion
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@...
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign




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