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

[Jason Stajich]

Did we lose some modules?

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>. 
> -----------------------------------------------------------------
> 
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Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center 
http://www.chg.duke.edu/