[Bioperl-l] Modern BioPerl vs. Ensembl

[George Hartzell]

Adam Witney writes:
 > >
 > > 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...
 > 
 > I just downloaded
 > 
 > 	$,1s"(B ensembl
 > 	$,1s"(B ensembl-compara
 > 	$,1s"(B ensembl-variation
 > 	$,1s"(B ensembl-functgenomics
 > 
 > from their website and did a regex on the files for
 > 
 > /^use (Bio::.+);/
 > 
 > which reveals (filtering out Bio::EnsEMBL::*):
 > 
 > Bio::AlignIO
 > Bio::Annotation::DBLink
 > Bio::Das::ProServer::SourceAdaptor
 > Bio::Das::ProServer::SourceAdaptor::Transport::generic
 > Bio::Index::Fastq
 > Bio::LocatableSeq
 > Bio::Location::Simple
 > Bio::MAGE::Experiment::Experiment
 > Bio::MAGE::XMLUtils
 > Bio::Perl
 > Bio::PrimarySeq
 > Bio::PrimarySeqI
 > Bio::Root::Root
 > Bio::Root::RootI
 > Bio::Search::HSP::EnsemblHSP
 > Bio::Seq
 > Bio::SeqFeature::FeaturePair
 > Bio::SeqFeature::Generic
 > Bio::SeqFeatureI
 > Bio::SeqIO
 > Bio::SimpleAlign
 > Bio::Species
 > Bio::Tools::CodonTable
 > Bio::Tools::Run::Phylo::PAML::Codeml
 > Bio::TreeIO
 > 
 > does that help? (I have the list broken down by which module/script  
 > contains which if that helps also)

What would be most useful to me would be to understand where they
*need* to use release 1.2.3.  Is there something magical about their
use of e.g. Bio::Seq.

It's worth noting that your technique won't pick up various modules
that are loaded on demand by e.g. Bio::SearchIO.

g.