[Bioperl-l] Modern BioPerl vs. Ensembl

[Andreas Kähäri]

[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                     -{ }-