Raw content of Bio::EnsEMBL::ExternalData::Glovar::GlovarSTSAdaptor
<![CDATA[=head1 NAME
Bio::EnsEMBL::ExternalData::Glovar::GlovarSTSAdaptor -
Database adaptor for Glovar STSs
=head1 SYNOPSIS
$glodb = Bio::EnsEMBL::ExternalData::Glovar::DBAdaptor->new(
-user => 'ensro',
-pass => 'secret',
-dbname => 'snp',
-host => 'go_host',
-driver => 'Oracle'
);
my $glovar_adaptor = $glodb->get_GlovarSTSAdaptor;
$var_listref = $glovar_adaptor->fetch_all_by_clone_accession(
'AL100005', 'AL100005', 1, 10000);
=head1 DESCRIPTION
This module is an entry point into a Glovar database. It allows you to retrieve
STSs from Glovar.
=head1 AUTHOR
Tony Cox <avc@sanger.ac.uk>
Patrick Meidl <pm2@sanger.ac.uk>
=head1 CONTACT
Post questions to the EnsEMBL development list ensembl-dev@ebi.ac.uk
=cut
package Bio::EnsEMBL::ExternalData::Glovar::GlovarSTSAdaptor;
use strict;
use Bio::EnsEMBL::ExternalData::Glovar::STS;
use Bio::EnsEMBL::ExternalData::Glovar::GlovarAdaptor;
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::ExternalData::Glovar::GlovarAdaptor);
=head2 fetch_all_by_clone_accession
Arg[1] : clone internal ID
Arg[2] : clone embl accession
Arg[3] : clone start coordinate
Arg[4] : clone end coordinate
Example : @list = @{$glovar_adaptor->fetch_all_by_clone_accession(
'AL100005', 'AL100005', 1, 10000)};
Description: Retrieves STSs on a clone in clone coordinates.
Returntype : Listref of Bio::EnsEMBL::ExternalData::Glovar::STS objects
Exceptions : none
Caller : $self->fetch_all_by_Clone
=cut
sub fetch_all_by_clone_accession {
my ($self, $embl_acc, $embl_version, $cl_start, $cl_end) = @_;
# get info on clone
my @cloneinfo = $self->fetch_clone_by_accession($embl_acc);
return([]) unless (@cloneinfo);
my ($nt_name, $id_seq, $clone_start, $clone_end, $clone_strand) = @cloneinfo;
# now get the STSs on this clone
# get only features in the desired region of the clone
my ($q_start, $q_end);
if ($clone_strand == 1) {
$q_start = $clone_start + $cl_start - 1;
$q_end = $clone_start + $cl_end + 1;
} else{
$q_start = $clone_end - $cl_end - 1;
$q_end = $clone_end - $cl_start + 1;
}
# also get STS which don't start within the clone region, but overlap it
# (assumes a max STS length of 1000 bp)
$q_start -= 1000;
# NOTE:
# This query only gets ExoSeq STSs (sts_summary.assay_type = 8).
my $q2 = qq(
SELECT
ss.id_sts as internal_id,
ss.sts_name as sts_name,
ms.start_coordinate as sts_start,
ms.end_coordinate as sts_end,
ms.is_revcomp as sts_strand,
length(ss.sense_oligoprimer) as sen_len,
length(ss.antisense_oligoprimer) as anti_len,
sod.description as pass_status,
sad.description as assay_type,
ss.is_private as private
FROM
mapped_sts ms,
sts_summary ss,
sts_outcome_dict sod,
snpassaydict sad
WHERE ms.id_sequence = ?
AND ms.id_sts = ss.id_sts
AND ss.assay_type = sad.id_dict
AND ss.pass_status = sod.id_dict
AND ms.start_coordinate BETWEEN $q_start AND $q_end
);
my $sth;
eval {
$sth = $self->prepare($q2);
$sth->execute($id_seq);
};
if ($@){
warn("ERROR: SQL failed in " . (caller(0))[3] . "\n$@");
return([]);
}
my @features = ();
while (my $row = $sth->fetchrow_hashref()) {
return([]) unless keys %{$row};
warn "WARNING: private STS!" if $row->{'PRIVATE'};
## calculate coords depending on clone orientation
my ($start, $end);
$row->{'STS_END'} ||= $row->{'STS_START'};
if ($clone_strand == 1) {
$start = $row->{'STS_START'} - $clone_start + 1;
$end = $row->{'STS_END'} - $clone_start + 1;
} else {
$start = $clone_end - $row->{'STS_END'} + 1;
$end = $clone_end - $row->{'STS_START'} + 1;
}
my $strand = (1 - 2 * $row->{'STS_STRAND'}) * $clone_strand;
# the following lines correct for an off by one error in mapped_sts
# 1 should be substracted from all coords once db has been fixed
push @features, Bio::EnsEMBL::ExternalData::Glovar::STS->new_fast({
'analysis' => 'glovar_sts',
'display_id' => $row->{'STS_NAME'},
'dbID' => $row->{'INTERNAL_ID'},
'start' => $start,
'end' => $end,
'strand' => $strand,
'seqname' => $embl_acc,
'sense_length' => $row->{'SEN_LEN'},
'antisense_length' => $row->{'ANTI_LEN'},
'pass_status' => $row->{'PASS_STATUS'},
'assay_type' => $row->{'ASSAY_TYPE'},
});
}
return(\@features);
}
=head2 coordinate_systems
Arg[1] : none
Example : my @coord_systems = $glovar_adaptor->coordinate_systems;
Description : This method returns a list of coordinate systems which are
implemented by this class. A minimum of one valid coordinate
system must be implemented. Valid coordinate systems are:
'SLICE', 'ASSEMBLY', 'CONTIG', and 'CLONE'.
Return type : list of strings
Exceptions : none
Caller : internal
=cut
sub coordinate_systems {
return ('CLONE');
}
=head2 track_name
Arg[1] : none
Example : my $track_name = $sts_adaptor->track_name;
Description : returns the track name
Return type : String - track name
Exceptions : none
Caller : Bio::EnsEMBL::Slice,
Bio::EnsEMBL::ExternalData::ExternalFeatureAdaptor
=cut
sub track_name {
my ($self) = @_;
return("GlovarSTS");
}
1;
]]>