[Bioperl-l] bioperl-live: audit of FIXME/???/TODO/etc and undef/die

Chris Fields cjfields at uiuc.edu
Wed Sep 20 00:44:02 EDT 2006


Ouch!  That many?

Chris

On Sep 19, 2006, at 11:38 PM, Torsten Seemann wrote:

> David,
>
>>  From running the deobfuscator on bioperl-live, I've found some   
>> formatting inconsistencies in the POD of some modules which are  
>> hard  for the deobfuscator to parse. I've corrected some of these  
>> in my  working (checked-out) copy of bioperl-live.
>
> Please check them in.
>
> I have written a script to audit all Perl modules to ensure the  
> NAME in the POD matches the Perl module and has the correct  
> capitilization.
>
> % cd bioperl-live/maintenance
> % ./check_NAMEs.pl
>
> Here's the current buggy ones, before your commits AFAIK.
>
> Bio::IdCollectionI
> Bio::Location::SplitLocationI
> Bio::Search::Result::PullResultI
> Bio::Search::HSP::HmmpfamHSP
> Bio::Search::Hit::HmmpfamHit
> Bio::Expression::FeatureGroup::FeatureGroupMas50
> Bio::Expression::FeatureSet::FeatureSetMas50
> Bio::DB::EUtilities::Cookie
> Bio::DB::GFF::Adaptor::berkeleydb
> Bio::DB::GFF::Adaptor::biofetch_oracle
> Bio::DB::GFF::Adaptor::dbi::pg_fts
> Bio::DB::GFF::Adaptor::memory::feature_serializer
> Bio::DB::SeqFeature::Store::bdb
> Bio::DB::SeqFeature::Store::DBI::Iterator
> Bio::Matrix::PSM::SiteMatrixI
> Bio::Matrix::PSM::ProtPsm
> Bio::Matrix::PSM::IO::psiblast
> Bio::Matrix::PSM::IO::transfac
> Bio::Matrix::PSM::IO::meme
> Bio::Graphics::Util
> Bio::Graphics::Glyph::ex
> Bio::Graphics::Glyph::three_letters
> Bio::Graphics::Glyph::arrow
> Bio::Graphics::Glyph::ruler_arrow
> Bio::Graphics::Glyph::flag
> Bio::Phenotype::Measure
> Bio::Phenotype::PhenotypeI
> Bio::Phenotype::Phenotype
> Bio::Phenotype::Correlate
> Bio::Phenotype::OMIM::MiniMIMentry
> Bio::Phenotype::OMIM::OMIMparser
> Bio::Phenotype::OMIM::OMIMentry
> Bio::Phenotype::OMIM::OMIMentryAllelicVariant
> Bio::SeqIO::qual
> Bio::SeqIO::genbank
> Bio::OntologyIO::simplehierarchy
> Bio::OntologyIO::InterProParser
> Bio::OntologyIO::soflat
> Bio::OntologyIO::dagflat
> Bio::OntologyIO::obo
> Bio::OntologyIO::goflat
> Bio::OntologyIO::Handlers::InterProHandler
> Bio::Tools::pICalculator
> Bio::Tools::ECnumber
> Bio::SeqFeature::Gene::GeneStructureI
> Bio::SeqFeature::Gene::Poly_A_site
> Bio::Seq::SeqFastaSpeedFactory
> Bio::Ontology::RelationshipI
> Bio::Ontology::TermI
> Bio::Ontology::InterProTerm
> Bio::Ontology::RelationshipType
> Bio::Ontology::OBOterm
> Bio::Ontology::OBOEngine
> Bio::Ontology::PathI
> Bio::Ontology::OntologyEngineI
> Bio::Ontology::Path
> Bio::Ontology::GOterm
> Bio::Ontology::Term
> Bio::Ontology::SimpleGOEngine
> Bio::Ontology::Relationship
> Bio::Ontology::SimpleGOEngine::GraphAdaptor
> Bio::Ontology::SimpleGOEngine::GraphAdaptor02
>
> -- 
> Dr Torsten Seemann               http://www.vicbioinformatics.com
> Victorian Bioinformatics Consortium, Monash University, Australia
>

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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