GlovarAdaptor documentation.

$glodb = Bio::EnsEMBL::ExternalData::Glovar::DBAdaptor->new(
-user => 'ensro',
-dbname => 'snp',
-host => 'go_host',
-driver => 'Oracle');
my $glovar_adaptor = $glodb->get_GlovarAdaptor;
$var_listref = $glovar_adaptor->fetch_all_by_Slice($slice); # grab the lot!

Arg[1] : String $embl_acc - EMBL accession of the clone
Example : my ($nt_name, $id_seq, $clone_start, $clone_end, $clone_strand) = $glovar_adaptor->fetch_clone_by_accession('AL123456');
Description : Fetches clone info from Glovar by accession
Return type : List of
sequence name the clone is mapped to
dbID of this sequence
start coordinate of clone mapping
end coordinate of clone mapping
strand of clone mapping
Exceptions : thrown if data fetching error occurs
Caller : usually subclasses of GlovarAdaptor

sub fetch_clone_by_accession {

    my ($self, $embl_acc) = @_;

    # get info on clone
    my $q1 = qq(
        SELECT
                ss.database_seqnname,
                csm.id_sequence,
                csm.start_coordinate,
                csm.end_coordinate,
                csm.contig_orientation,
                ss.database_source,
                ss.is_current
        FROM    clone_seq cs,
                clone_seq_map csm,
                snp_sequence ss
        WHERE   cs.database_seqname = '$embl_acc'
        AND     cs.id_cloneseq = csm.id_cloneseq
        AND     csm.id_sequence = ss.id_sequence
        AND     ss.is_current = 1
    );
    my $sth;
    eval {
        $sth = $self->prepare($q1);
        $sth->execute();
    }; 
    if ($@){
        warn("ERROR: SQL failed in " . (caller(0))[3] . "\n$@");
        return();
    }
    my ($nt_name, $id_seq, $clone_start, $clone_end, $clone_strand);
    my @cloneinfo;
    my %stats = map { $_ => 0 } qw(NT clone);
    while (my @res = $sth->fetchrow_array) {
        if ($res[0] =~ /NT_/) {
            $stats{'NT'}++;
        } else {
            $stats{'clone'}++;
        }
        @cloneinfo = @res;
    }
    if (($stats{'NT'} + $stats{'clone'}) > 1) {
        warning("Clone ($embl_acc) maps to more than one NTs ($stats{NT}) and/or clones ($stats{clones}).");
    }

    # return result list
    return (@cloneinfo);

}

sub track_name {

    my ($self) = @_;    
    die("ERROR: track_name called on Bio::EnsEMBL::ExternalData::Glovar::GlovarAdaptor!\n
        It should be implemented by a derived class!\n");
}

1;

}

fetch_clone_by_accession	Description	Code
track_name	No description	Code