[Bioperl-l] Modern BioPerl vs. Ensembl

[Adam Witney]

>
> 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

	• ensembl
	• ensembl-compara
	• ensembl-variation
	• 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)

cheers

adam