[Bioperl-l] load_seqdatabase.pl --pipeline

Peter Müller pan.mueller at yahoo.de
Wed Apr 16 08:34:51 EDT 2008


Dear list,

a want to add gene symbols to unigene-cluster which were in a biosql database and lacks this information.

So one way is to make a post-update script:
my $adp = $db->get_object_adaptor('Bio::ClusterI');
my $pseq = $adp->find_by_primary_key(n);
$adp->remove($pseq);
$pseq->gene('symbol');
$adp->store($pseq);
$adp->commit();

O.k., this works (I ask me why to remove the cluster first - bug or feature...?)

Second way - perhaps:
Using the --pipeline option, but it looks like useable only for seq-objects (Bio::Factory::SeqProcessoI) right?

regards
pan



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