Carnë Draug | 9 Mar 22:20 2013

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

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.