Raw content of Bio::EnsEMBL::Compara::DBSQL::SyntenyRegionAdaptor
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# Ensembl module for Bio::EnsEMBL::Compara::SyntenyRegionAdaptor
#
# Cared for by Abel Ureta-Vidal <abel@ebi.ac.uk>
#
# Copyright GRL and EBI
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::EnsEMBL::Compara::DBSQL::SyntenyRegionAdaptor - Object to access data in the synteny_region
and dnafrag_region tables
=head1 SYNOPSIS
=head2 Get the adaptor from the Registry
use Bio::EnsEMBL::Registry;
my $reg = "Bio::EnsEMBL::Registry";
$reg->load_registry_from_db(
-host => "ensembldb.ensembl.org",
-user => "anonymous");
my $synteny_region_adaptor = $reg->get_adaptor(
"Multi", "compara", "SyntenyRegion");
=head2 Store method
$synteny_region_adaptor->store($synteny_region);
=head2 Fetching methods
my $synteny_region = $synteny_region_adaptor->fetch_by_dbID(1);
my $synteny_regions = $synteny_region_adaptor->
fetch_by_MethodLinkSpeciesSet_DnaFrag(
$mlss, $dnafrag, $start, $end);
=head2 Example script
use strict;
use Bio::EnsEMBL::Registry;
my $reg = "Bio::EnsEMBL::Registry";
$reg->load_registry_from_db(
-host=>"ensembldb.ensembl.org", -user=>"anonymous", -software_version => 38);
my $method_link_species_set_adaptor = $reg->get_adaptor(
"Multi", "compara", "MethodLinkSpeciesSet");
my $human_mouse_synteny_method_link_species_set =
$method_link_species_set_adaptor->
fetch_by_method_link_type_registry_aliases(
"SYNTENY", ["human", "mouse"]);
my $genome_db_adaptor = $reg->get_adaptor(
"Multi", "compara", "GenomeDB");
my $genome_db = $genome_db_adaptor->
fetch_by_name_assembly("Homo sapiens", undef);
my $dnafrag_adaptor = $reg->get_adaptor(
"Multi", "compara", "DnaFrag");
my $dnafrag = $dnafrag_adaptor->
fetch_by_GenomeDB_and_name($genome_db, "3");
my $synteny_region_adaptor = $reg->get_adaptor(
"Multi", "compara", "SyntenyRegion");
my $synteny_regions = $synteny_region_adaptor->
fetch_by_MethodLinkSpeciesSet_DnaFrag(
$human_mouse_synteny_method_link_species_set,
$dnafrag, 100000, 200000);
foreach my $this_synteny_region (@$synteny_regions) {
my $these_dnafrag_regions = $this_synteny_region->children();
foreach my $this_dnafrag_region (@$these_dnafrag_regions) {
print $this_dnafrag_region->dnafrag->genome_db->name, ": ", $this_dnafrag_region->slice->name, "\n";
}
print "\n";
}
=head1 DESCRIPTION
This object is intended for accessing data in the synteny_region and dnafrag_region tables.
=head1 INHERITANCE
This class inherits all the methods and attributes from Bio::EnsEMBL::DBSQL::BaseAdaptor
=head1 SEE ALSO
- Bio::EnsEMBL::Compara::SyntenyRegion
- Bio::EnsEMBL::Compara::DnaFragRegion
- Bio::EnsEMBL::Compara::MethodLinkSpeciesSet
- Bio::EnsEMBL::Compara::GenomeDB
=head1 CONTACT
Ensembl - ensembl-dev@ebi.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::Compara::DBSQL::SyntenyRegionAdaptor;
use strict;
use Bio::EnsEMBL::Utils::Exception;
use Bio::EnsEMBL::Compara::SyntenyRegion;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
our @ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
=head2 fetch_by_dbID
Arg 1 : int $synteny_region_id
Example : my $this_synteny_region = $synteny_region_adaptor->
fetch_by_dbID($synteny_region_id)
Description: Fetches the corresponding Bio::EnsEMBL::Compara::SyntenyRegion
object.
Returntype : Bio::EnsEMBL::Compara::SyntenyRegion object
Exception : Thrown if the argument is not defined
Caller :
=cut
sub fetch_by_dbID{
my ($self,$dbID) = @_;
if( !defined $dbID ) {
throw("fetch_by_dbID with no dbID!");
}
my $sth = $self->prepare("select synteny_region_id, method_link_species_set_id from synteny_region where synteny_region_id = $dbID");
$sth->execute;
my ($synteny_region_id, $method_link_species_set_id) = $sth->fetchrow_array();
my $sr = new Bio::EnsEMBL::Compara::SyntenyRegion;
$sr->dbID($synteny_region_id);
$sr->method_link_species_set_id($method_link_species_set_id);
my $dfra = $self->db->get_DnaFragRegionAdaptor;
my $dfrs = $dfra->fetch_by_synteny_region_id($dbID);
while (my $dfr = shift @{$dfrs}) {
$sr->add_child($dfr);
}
return $sr;
}
=head2 store
Arg 1 : Bio::EnsEMBL::Compara::SyntenyRegion object
Example : $synteny_region_adaptor->store($synteny_region)
Description: Stores a Bio::EnsEMBL::Compara::SyntenyRegion object into
the database as well as the underlying
Bio::EnsEMBL::Compara::DnaFragRegion objects
Returntype : int (the synteny_region_id)
Exception : Thrown if the argument is not a
Bio::EnsEMBL::Compara::SyntenyRegion object
Caller :
=cut
sub store{
my ($self,$sr) = @_;
if( !ref $sr || !$sr->isa("Bio::EnsEMBL::Compara::SyntenyRegion") ) {
throw("$sr is not a SyntenyRegion object");
}
my $sth = $self->prepare("insert into synteny_region (method_link_species_set_id) VALUES (?)");
$sth->execute($sr->method_link_species_set_id);
my $synteny_region_id = $sth->{'mysql_insertid'};
$sr->dbID($synteny_region_id);
$sr->adaptor($self);
my $dfra = $self->db->get_DnaFragRegionAdaptor;
foreach my $dfr (@{$sr->children}) {
$dfr->synteny_region_id($synteny_region_id);
$dfra->store($dfr);
}
return $sr->dbID;
}
=head2 fetch_all_by_MethodLinkSpeciesSet_Slice
Arg 1 : Bio::EnsEMBL::Compara::MethodLinkSpeciesSet $method_link_species_set
Arg 2 : Bio::EnsEMBL::Slice $original_slice
Example : my $synteny_regions =
$synteny_region_adaptor->fetch_all_by_MethodLinkSpeciesSet_Slice(
$method_link_species_set, $original_slice);
Description: Retrieve the corresponding
Bio::EnsEMBL::Compara::SyntenyRegion objects.
Returntype : ref. to an array of Bio::EnsEMBL::Compara::SyntenyRegion objects.
Exceptions : Returns ref. to an empty array if no matching
Bio::EnsEMBL::Compara::SyntenyRegion object can be retrieved
Caller : $object->method_name
Status : Medium risk
=cut
sub fetch_all_by_MethodLinkSpeciesSet_Slice {
my ($self, $method_link_species_set, $reference_slice) = @_;
my $all_synteny_regions = []; # Returned value
## method_link_species_set will be checked in the fetch_all_by_MethodLinkSpeciesSet_DnaFrag method
## Check original_slice
unless(UNIVERSAL::isa($reference_slice, 'Bio::EnsEMBL::Slice')) {
throw("[$reference_slice] should be a Bio::EnsEMBL::Slice object\n");
}
my $dnafrag_adaptor = $self->db->get_DnaFragAdaptor;
my $projection_segments = $reference_slice->project('toplevel');
return [] if(!@$projection_segments);
foreach my $this_projection_segment (@$projection_segments) {
my $this_slice = $this_projection_segment->to_Slice;
my $this_dnafrag = $dnafrag_adaptor->fetch_by_Slice($this_slice);
next if (!$this_dnafrag);
my $these_synteny_regions = $self->fetch_all_by_MethodLinkSpeciesSet_DnaFrag(
$method_link_species_set,
$this_dnafrag,
$this_slice->start,
$this_slice->end,
);
push (@$all_synteny_regions, @$these_synteny_regions);
}
return $all_synteny_regions;
}
=head2 fetch_by_MethodLinkSpeciesSet_DnaFrag
Status : Deprecated. Use fetch_all_by_MethodLinkSpeciesSet_DnaFrag
instead
=cut
sub fetch_by_MethodLinkSpeciesSet_DnaFrag {
my $self = shift(@_);
return $self->fetch_all_by_MethodLinkSpeciesSet_DnaFrag(@_);
}
=head2 fetch_all_by_MethodLinkSpeciesSet_DnaFrag
Arg 1 : Bio::EnsEMBL::Compara::MethodLinkSpeciesSet $mlss
Arg 2 : Bio::EnsEMBL::Compara::DnaFrag $dnafrag
Arg 3 (opt): int $start
Arg 4 (opt): int $end
Example : my $these_synteny_regions = $synteny_region_adaptor->
fetch_all_by_MethodLinkSpeciesSet_DnaFrag(
$mlss, $dnafrag, 100000, 200000);
Description: Fetches the Bio::EnsEMBL::Compara::SyntenyRegion
objects in this region for the set of species
defined by the $mlss.
Returntype : listref of Bio::EnsEMBL::Compara::SyntenyRegion objects
Exception : Thrown if the argument is not defined
Caller :
Status : Stable
=cut
sub fetch_all_by_MethodLinkSpeciesSet_DnaFrag {
my ($self, $mlss, $dnafrag, $start, $end) = @_;
if (!UNIVERSAL::isa($mlss, "Bio::EnsEMBL::Compara::MethodLinkSpeciesSet")) {
throw("[$mlss] is not a Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object");
}
if (!UNIVERSAL::isa($dnafrag, "Bio::EnsEMBL::Compara::DnaFrag")) {
throw("[$dnafrag] is not a Bio::EnsEMBL::Compara::DnaFrag object");
}
my $sql = "select sr.synteny_region_id from synteny_region sr, dnafrag_region dfr where sr.method_link_species_set_id = ? and sr.synteny_region_id=dfr.synteny_region_id and dfr.dnafrag_id = ?";
if (defined $start) {
$sql .= " and dfr.dnafrag_end >= $start";
}
if (defined $end) {
$sql .= " and dfr.dnafrag_start <= $end";
}
my $sth = $self->prepare($sql);
$sth->execute($mlss->dbID, $dnafrag->dbID);
my $synteny_region_id;
$sth->bind_columns(\$synteny_region_id);
my @srs;
while ($sth->fetch) {
my $sr = new Bio::EnsEMBL::Compara::SyntenyRegion;
$sr->dbID($synteny_region_id);
$sr->method_link_species_set_id($mlss->dbID);
my $dfra = $self->db->get_DnaFragRegionAdaptor;
my $dfrs = $dfra->fetch_by_synteny_region_id($synteny_region_id);
while (my $dfr = shift @{$dfrs}) {
$sr->add_child($dfr);
}
push @srs, $sr;
}
return \@srs;
}
=head2 fetch_all_by_MethodLinkSpeciesSet
Arg 1 : Bio::EnsEMBL::Compara::MethodLinkSpeciesSet $mlss
Example : my $these_synteny_regions = $synteny_region_adaptor->
fetch_all_by_MethodLinkSpeciesSet($mlss);
Description: Fetches the Bio::EnsEMBL::Compara::SyntenyRegion
objects for the set of species defined by the $mlss.
Returntype : listref of Bio::EnsEMBL::Compara::SyntenyRegion objects
Exception : Thrown if the argument is not defined
Caller :
Status : Stable
=cut
sub fetch_all_by_MethodLinkSpeciesSet {
my ($self, $mlss) = @_;
if (!UNIVERSAL::isa($mlss, "Bio::EnsEMBL::Compara::MethodLinkSpeciesSet")) {
throw("[$mlss] is not a Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object");
}
my $sql = "select sr.synteny_region_id from synteny_region sr where sr.method_link_species_set_id = ?";
my $sth = $self->prepare($sql);
$sth->execute($mlss->dbID);
my $synteny_region_id;
$sth->bind_columns(\$synteny_region_id);
my @srs;
while ($sth->fetch) {
my $sr = new Bio::EnsEMBL::Compara::SyntenyRegion;
$sr->dbID($synteny_region_id);
$sr->method_link_species_set_id($mlss->dbID);
my $dfra = $self->db->get_DnaFragRegionAdaptor;
my $dfrs = $dfra->fetch_by_synteny_region_id($synteny_region_id);
while (my $dfr = shift @{$dfrs}) {
$sr->add_child($dfr);
}
push @srs, $sr;
}
return \@srs;
}
1;
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