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

Mike Muratet muratem at eng.uah.edu
Thu Feb 3 10:59:41 EST 2005


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


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?



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