[Bioperl-l] Modern BioPerl vs. Ensembl

[Chris Fields]

Andreas,

Thanks for the response, been waiting for something a bit more  
official for a while now.

We can definitely help you patch these as needed when problems arise,  
just let us know, or file a bug report listing issues.  Scanning  
through there will be a could of future trouble spots:

1) We are very likely deprecating Bio::Species in favor of Bio::Taxon  
(that may be relatively easy to map, as Bio::Species now delegates to  
Bio::Taxon and similar anyway).
2) We will be refactoring Bio::SimpleAlign/LocatableSeq.  There are  
too many corner cases where assumptions are made.  We'll try to stick  
with the current API, but there may be a few delegating methods.

More significantly, we're also planning a significant restructuring of  
bioperl prior to 1.7, basically splitting it into several (more easily  
maintainable) parts.  The exact nature of these is still a bit fuzzy  
(we have to sort out dependencies) but we do plan on making a bundle  
package to assemble a complete old-style 'monolithic' bioperl, just a  
bit more customizable.

It's very likely the versioning scheme will stay the same for the core  
(root) set of modules, but the others may end up having their own  
versioning for monitoring dependencies.

chris

On Aug 25, 2009, at 8:43 AM, Andreas Kähäri wrote:

> [cut]
>>
>> It would be nice if someone at Ensembl could compile a list of
>> BioPerl dependencies. At least that would give a feel for the scope
>> of the problem...
>>
>> Will
>
> Hi Will, and list,
>
> These are the BioPerl modules that the Ensembl Core API "use" or
> otherwise directly call (scanned our current HEAD code):
>
>  Bio::Annotation::DBLink
>    in Bio::EnsEMBL::DBEntry
>
>  Bio::Tools::CodonTable
>    in Bio::EnsEMBL::Utils::TranscriptAlleles
>    in Bio::EnsEMBL::PredictionTranscript
>    in Bio::EnsEMBL::Transcript.pm
>
>  Bio::LocatableSeq
>    in Bio::EnsEMBL::DnaDnaAlignFeature
>
>  Bio::PrimarySeqI
>    in Bio::EnsEMBL::Slice
>
>  Bio::Root::IO
>    in Bio::EnsEMBL::Utils::Converter
>
>  Bio::Root::Root
>    in Bio::EnsEMBL::Utils::EasyArgv
>
>  Bio::Seq
>    in Bio::EnsEMBL::Utils::PolyA
>    in Bio::EnsEMBL::Intron
>    in Bio::EnsEMBL::Exon
>    in Bio::EnsEMBL::Transcript
>    in Bio::EnsEMBL::Translation
>    in Bio::EnsEMBL::Utils::TranscriptAlleles
>
>  Bio::SeqFeature::FeaturePair
>    in Bio::EnsEMBL::Utils::Converter::ens_bio_featurePair
>
>  Bio::SeqFeature::Generic
>    in Bio::EnsEMBL::Utils::Converter::ens_bio_featurePair
>
>  Bio::SeqFeatureI
>    in Bio::EnsEMBL::SeqFeatureI
>
>  Bio::SimpleAlign
>    in Bio::EnsEMBL::DnaDnaAlignFeature
>
>  Bio::Species
>    in Bio::EnsEMBL::DBSQL::MetaContainer
>
>
> I have not looked at the other Ensembl APIs (Variation, FuncGen,
> Compara, Web, Pipeline, etc.), and I might possibly have missed
> references to some BioPerl modules.  I have also not indicated
> the relative importance of any of these modules (clearly Bio::Seq
> is central, but I don't know how widely the code that accesses
> Bio::SeqFeature::Generic is used) or investigated if any of the
> references to BioPerl modules occur in deprecated code.
>
> As far as I know, there are currently no plans to get rid of these
> dependencies.  Or there might be, only they are not very far up the
> priority list right now.  I would be happy to look at conservative
> patches, but can not promise snappy response times.
>
>
> Regards,
> Andreas
>
> -- 
> Andreas Kähäri, Ensembl Software Developer             -{ }-
> European Bioinformatics Institute (EMBL-EBI)           -{ }-
> Wellcome Trust Genome Campus, Hinxton                  -{ }-
> Cambridge CB10 1SD, United Kingdom                     -{ }-
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