Fields, Christopher J | 9 Mar 23:06 2013

Re: is Bio::DB::Biblio::eutils duplicate of Bio::DB::EUtilities ?

On Mar 9, 2013, at 3:20 PM, Carnë Draug <carandraug+dev <at>>

> On 9 March 2013 15:07, Fields, Christopher J <cjfields <at>> wrote:
>> On Mar 9, 2013, at 8:47 AM, Carnë Draug <carandraug+dev <at>> wrote:
>>> Hi
>>> I was looking at EUtilities and found Bio::DB::Biblio::eutils. This
>>> module, part of bioperl-live, seems to be re-implementing pieces of
>>> Bio::DB::EUtilities, part of Bio-EUtilities. Is this correct?
>> Sort of; it predates Bio::DB::EUtilities but is very specific for bibliographic data.
>>> According to Bio::DB::Biblio::eutils documentation, it should not be
>>> used directly, instead should be used through Bio::DB::Biblio. This
>>> means that it could be replaced by Bio::DB::EUtilities without any
>>> disturbance (other than adding a dependency and as long as users have
>>> been respecting the recommendations).
>>> Carnë
>> Right; the intent is at some point to also do something similar with other eutils-related tools
(Bio::DB::GenBank, etc).
> So I was looking at this but seems that would cause an issue with
> circular dependency. Not at module level, but at distribution level
> (Bio-Eutilities is dependent on bioperl-live and bioperl-live
> dependent on Bio-EUtilities because of Bio::DB::Biblio).
> This could be fixed by excising Bio::DB::Biblio out of bioperl-live.
> Could this be done and a separate distribution created for it? None of
> the empty repositories seems fitting for it.
> Carnë

Yes, that could be done.  I don't think it is a well-fleshed out part of bioperl, but I'm not a big user myself. 
Not sure how much it is actually used, tell the truth.