[Bioperl-l] Obsolete method call in Bio/DB/SQL/SeqAdaptor.pm?

[Mike Muratet]

Hilmar

I think part of the discussion that went by was what to use? 0.1 is the
latest version at bioperl.org. Is there an alternative? (Roll your own?)

Thanks

Mike

On Thu, 3 Feb 2005, Hilmar Lapp wrote:

> Mike, you should not use the bioperl-db-0.1 release if you want to use 
> the current biosql schema.
> 
> Also, load_seqdatabase.pl does not have a --pipeline option in the 0.1 
> release. In fact, it almost changed 100% as did much of the rest of 
> bioperl-db. Download bioperl-db from cvs to get the latest revision.
> 
> 	-hilmar
> 
> On Thursday, February 3, 2005, at 07:59  AM, Mike Muratet wrote:
> 
> > Greetings
> >
> > I thought I remembered seeing this go by, but I couldn't find it in the
> > archive, so I'll bring it up.
> >
> > I downloaded what I think is the latest bioperl-db-0.1. Initialization 
> > of
> > the database went off without a glitch, and I loaded a bunch of 
> > records in
> > Swissprot format. I then tried to load some simple fasta files and got 
> > a
> > 'no method' message in SeqAdaptor.pm at line 477. It uses the 
> > seq_version
> > method instead of the current version method. I'm guessing that the
> > 'store' method that contains the error gets called for fasta file and 
> > some
> > other method gets called for swissprot. Anyway, I changed the code and 
> > it
> > works.
> >
> > Except...
> >
> > The bioentry table has a key biodatabase_id that includes 
> > biodatabase_id,
> > accession, and entry version. The fasta files have only a number on the
> > header line to identify them and apparently either SeqIO or Seq loads 
> > this
> > into the display id and leaves the accession undefined so that all of 
> > the
> > records have the same key (e.g., 4-unknown-UNK) which is a Bozo no-no 
> > (for
> > you old enough to remember who Bozo is). I'm using bioperl 1.4. 
> > Shouldn't
> > the accession get set to display_id if accession doesn't exist? Failing
> > that, would it make sense to modify the store method in SeqAdaptor to 
> > use
> > the display_id in the key if the accession is undefined?
> >
> > Thanks
> >
> > Mike
> >
> >
> > _______________________________________________
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> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
> -- 
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
> 
> 
>