[Bioperl-l] EUtilities overhaul started

Siddhartha Basu basu at pharm.stonybrook.edu
Sun Jun 3 10:44:18 EDT 2007


On Sat, 2 Jun 2007 00:16:05 -0500
  Chris Fields <cjfields at uiuc.edu> wrote:
> To anyone using Bio::DB::EUilities,
> 
> I am in the midst of a major overhaul to the various 
>EUtilities tools  
> and to Bio::DB::GenericWebDBI (the latter which I am 
>forming into  
> more or less a test bed for other database interfaces). 
> I'm about  
> 80% done at this point, and will likely start committing 
>changes this  
> coming week.
> 
> The overall interface will change (something I had 
>warned about in  
> the Bio::DB::EUtilities POD) but I am hoping it will be 
>more  
> intuitive and easier to use in the long run.  I'll 
>describe the  
> overall redesign and use in an upcoming HOWTO (as 
>recommended by  
> Brian a while back).

Hi chris,
Being a frequent user of EUtilities, hopefully this api 
facelift and upcoming howto will definitely be more 
helpful.
Anyway, one thing i noticed that for each eutil call such 
as efetch,epost,esearch,esummary a new 
'Bio::DB::Utilities' object has to be
instantiated. And thereafter it cannot be set during 
runtime such as
$eutils->id('ids'), for example....

my $eutils = Bio::DB::Eutilities->new ( -id => $id,
                                        -eutil => 
'esummary',
                                        -db => 'protein',
                                      );
my $ct = $eutils->get_response->content();

## -- now i cannot do this...
$eutils->id($newid);
my $ct = $eutils->get_response->content();

Is the new api going to address something along this line 
or is there currently anyway to reuse
the object.
Thanks again for this nice toolkit.

-siddhartha



> 
> If anyone has any suggestions/ideas/flames, please let 
>me know!
> 
> Cheers!
> 
> chris
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