[BioSQL-l] [Newbie] find_by_query() usage ?

[Mark Hoebeke]

Hi all,

I just managed to load some whole genomes into my BioSQL compliant
database, but now I run into troubles when trying to retrieve them
with the following script Perl script:

<snip>
my $dbadap= Bio::DB::BioDB->new(
				-database => 'biosql',
				-dbname => $dbname,
				-user => $dbuser,
				-host => $dbhost,
				-driver => $dbdriver);

my $objadap=$dbadap->get_object_adaptor("Bio::SeqI");

my $query=Bio::DB::Query::BioQuery->new(); 

my $result=$objadap->find_by_query();

foreach my $obj ($result->each_Object()) {
    print "Id : $obj->display_id\n";
}
</snip>

This script fails in the find_bu_query() method call, with an error
message like this (topmost exeception) :
	
DBD::Pg::st execute failed: ERROR:  parser: parse error at or near "." at character 8 at /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 1083.

A quick investigation traced to problem to be in the SQL generation
code as the query string is as follows :

     SELECT .bioentry_id, .display_id, .identifier, .accession,
     .description, .entry_version, .biodatabase_id, .taxon_id FROM

Obvisously, the table name(s) is (are) missing in the query string.

I guess the creation of the Bio::DB::Query::BioQuery instance may be
wrong. I read through the POD files, and the sample scripts to find an
example based on the find_by_query() method but found none.

Thanks for any pointers showing how to use the find_by_query method.

Mark

P.S. : sorry if this message is more related to BioPerl than to BioSQL...

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