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

Hilmar Lapp hlapp at gmx.net
Thu Feb 3 23:51:41 EST 2005

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.


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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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757

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