Raw content of Bio::EnsEMBL::Compara::DBSQL::AnchorSeqAdaptor
<![CDATA[package Bio::EnsEMBL::Compara::DBSQL::AnchorSeqAdaptor;
use strict;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
our @ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
sub store {
my ($self, @args) = @_;
my ($anchor_id, $dnafrag_id, $start, $end, $strand, $mlssid, $test_mlssid, $sequence) =
rearrange([qw(ANCHOR_ID, DNAFRAG_ID, START, END, STRAND, MLSSID, SEQUENCE, LENGTH)], @args);
my $dcs = $self->dbc->disconnect_when_inactive();
$self->dbc->disconnect_when_inactive(0);
$self->dbc->do("LOCK TABLE anchor_sequence WRITE");
my $length = length($sequence);
my $sth = $self->prepare("INSERT INTO anchor_sequence (sequence,
length, dnafrag_id, start, end, strand, anchor_id, method_link_species_set_id) VALUES (?,?,?,?,?,?,?,?)");
$sth->execute($sequence, $length, $dnafrag_id, $start, $end, $strand, $anchor_id, $mlssid);
$sth->finish;
$self->dbc->do("UNLOCK TABLES");
$self->dbc->disconnect_when_inactive($dcs);
}
sub get_anchor_sequences {
my ($self, $anc_ids_from_to) = @_;
my $sth = $self->prepare("SELECT a.anchor_id, df.genome_db_id, a.dnafrag_id, a.start, a.end, a.strand, a.sequence
FROM anchor_sequence a INNER JOIN dnafrag df ON a.dnafrag_id = df.dnafrag_id WHERE a.anchor_id
BETWEEN ? AND ? order by a.anchor_id");
# my $sth = $self->prepare("SELECT anchor_id, anchor_seq_id, dnafrag_id, start, end, strand, sequence
# FROM anchor_sequence WHERE anchor_id BETWEEN ? AND ? order by anchor_id");
$sth->execute($anc_ids_from_to->[0], $anc_ids_from_to->[1]);
my $anchor_array_ref = $sth->fetchall_arrayref;
return $anchor_array_ref;
}
1;
]]>