Raw content of Bio::EnsEMBL::ExternalData::Glovar::GlovarAdaptor
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# BioPerl module for Bio::EnsEMBL::ExternalData::Glovar::GlovarAdaptor
#
# Cared for by Tony Cox <avc@sanger.ac.uk>
#
# Copyright EnsEMBL
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
GlovarAdaptor - DESCRIPTION of Object
This object represents the Glovar database.
=head1 SYNOPSIS
$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!
=head1 DESCRIPTION
This module is an entry point into a glovar database,
Objects can only be read from the database, not written. (They are
loaded using a separate system).
=head1 CONTACT
Tony Cox <avc@sanger.ac.uk>
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
=cut
package Bio::EnsEMBL::ExternalData::Glovar::GlovarAdaptor;
use vars qw(@ISA);
use strict;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::External::ExternalFeatureAdaptor;
use Bio::EnsEMBL::SeqFeature;
use Bio::EnsEMBL::SNP;
use Bio::Annotation::DBLink;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
@ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor Bio::EnsEMBL::External::ExternalFeatureAdaptor);
=head2 fetch_clone_by_accession
Arg[1] : String $embl_acc - EMBL accession of the clone
Example : my ($nt_name, $id_seq, $clone_start, $clone_end, $clone_strand) = $glovar_adaptor->fetch_clone_by_accession('AL123456');
Description : Fetches clone info from Glovar by accession
Return type : List of
sequence name the clone is mapped to
dbID of this sequence
start coordinate of clone mapping
end coordinate of clone mapping
strand of clone mapping
Exceptions : thrown if data fetching error occurs
Caller : usually subclasses of GlovarAdaptor
=cut
sub fetch_clone_by_accession {
my ($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;
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