[Bioperl-l] bioperl-db: It's aaaaaaliiiiiive

[Ewan Birney]

On Tue, 10 Apr 2001, Jason Stajich wrote:

> Did we lose some modules?

We lost some modules. The Bio/DB/SQL/SeqAdaptor was a cvs add
omission. Will fix now.



> 
> 105 tetra ../bio/bioperl/bioperl-db> perl Makefile.PL
> Generated sub tests. go make show_tests to see available subtests
> Checking if your kit is complete...
> Warning: the following files are missing in your kit:
>         Bio/DB/BasicUpdateableDB.pm
>         t/add_basic.t
>         t/add_ensembl.t
>         t/remove_basic.t
>         t/remove_ensembl.t
> Please inform the author.
> Writing Makefile for Bio
> 
> t/species...........dubious                                                  
>         Test returned status 2 (wstat 512, 0x200)
> DIED. FAILED tests 1-6
>         Failed 6/6 tests, 0.00% okay
> t/swiss.............ls Can't locate Bio/DB/SQL/SeqAdaptor.pm in @INC
> [snip]
> 
> 117 tetra ../bio/bioperl/bioperl-db> ls Bio/DB/SQL/SeqAdaptor.pm
> Bio/DB/SQL/SeqAdaptor.pm not found
> 
> -Jason
> 
> On Mon, 9 Apr 2001, Ewan Birney wrote:
> 
> > 
> > I have been bringing bioperl-db up to full storage of Bio::SeqI objects.
> > It handles:
> > 
> >    Bio::SeqI and the following components:
> > 
> > Bio::PrimarySeqI, Bio::SeqFeature::Generic (and in general
> > Bio::SeqFeatureI compliant features - but of course they will be stored
> > "as if" they are Bio::SeqFeature::Generic), Bio::Location::Split/Simple
> > (no Fuzzies, but should be easish to add in. hohohoho. No remote features.
> > I want to see how the EMBL schema handles local/remote features before I
> > take that on), Bio::Annotation::DBLink, Bio::Annotation::Comment, no
> > Bio::Annotation::Reference and Bio::Species yet.
> > 
> > 
> > Bio::Species and some other db info is kept as singletons. Bio::SeqI
> > implementing objects is implemented in a "lazy" fashion of delaying object
> > gets until it needs it, but then cach'ing the get. This works only really
> > as a read-only concept.
> > 
> > 
> > I have done two GenBank round-trips and it looks pretty good. Mainly
> > whitespace problems in the diff. The lack of full fuzzy support is felt
> > for those pesky '<' and '>' on CDS lines.
> > 
> > 
> > 
> > 
> > But - hey - it works and the code is super-clean, conforming to the
> > Ensembl adaptor scheme and well tested with a total of 102 tests already.
> > 
> > 
> > 
> > So - does anyone want to take it for a drive? I think you'll like
> > it.... ;)
> > 
> > 
> > 
> > ewan
> > 
> > 
> > 
> > 
> > -----------------------------------------------------------------
> > Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> > <birney@ebi.ac.uk>. 
> > -----------------------------------------------------------------
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> > 
> 
> Jason Stajich
> jason@chg.mc.duke.edu
> Center for Human Genetics
> Duke University Medical Center 
> http://www.chg.duke.edu/ 
> 
> 
> 

-----------------------------------------------------------------
Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney@ebi.ac.uk>. 
-----------------------------------------------------------------