[BioSQL-l] bioperl-db bugs
Chris Fields
cjfields at uiuc.edu
Wed Mar 5 23:24:03 UTC 2008
Hilmar,
I think I have two bioperl-db bugs sorted out, but I'm trying to
determine whether the solution is a side-effect, a feature, or a bug.
Dmitry has filed two bug reports which are somewhat related:
http://bugzilla.open-bio.org/show_bug.cgi?id=2280
http://bugzilla.open-bio.org/show_bug.cgi?id=2281
I have added my comments to it, but maybe you can shed some more light
on this. What he is trying to do is copy a persistent Seq object to a
different namespace; load_seqdatabase.pl won't let him do that
directly using the same sequence file. If he changes the namespace()
and store()s it using a script, the seq is moved to the new namespace,
not updated.
My reasoning is this is a feature (by not changing the primary_key,
you don't store a new sequence but update the current one). However,
if the primary_key is unset (undef), then it appears you can copy the
sequence over (from Dmitry's script, with my addition noted):
...
my $ns1 = 'space1';
my $ns2 = 'space2';
my $seqadp = $db->get_object_adaptor('Bio::SeqI');
my $aux_seq = Bio::Seq::RichSeq->new(
-accession_number => 'NC_005982',
-version => 1,
-namespace => $ns1);
my $seq = $seqadp->find_by_unique_key($aux_seq);
# store the found sequence in the second biodatabase:
my $pseq = $seqadp->create_persistent($ns2);
$pseq->namespace('bioperl2');
$pseq->primary_key(undef); # my addition, which appears to work
$pseq->store();
$seqadp->commit;
...
My question: is this an intended effect? The ability to assign undef
to primary_key seems intentional based on the method code, but I'm a
bit uncertain here.
chris
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