Raw content of Bio::EnsEMBL::Funcgen::DBSQL::ExternalFeatureAdaptor
<![CDATA[#
# Ensembl module for Bio::EnsEMBL::DBSQL::Funcgen::ExternalFeatureAdaptor
#
# You may distribute this module under the same terms as Perl itself
=head1 NAME
Bio::EnsEMBL::DBSQL::Funcgen::ExternalFeatureAdaptor - A database adaptor for fetching and
storing ExternalFeature objects.
=head1 SYNOPSIS
my $afa = $db->get_ExternalFeatureAdaptor();
my $features = $afa->fetch_all_by_Slice($slice);
=head1 DESCRIPTION
The ExternalFeatureAdaptor is a database adaptor for storing and retrieving
ExternalFeature objects.
=head1 AUTHOR
This module was created by Nathan Johnson.
This module is part of the Ensembl project: /
=head1 CONTACT
Post comments or questions to the Ensembl development list: ensembl-dev@ebi.ac.uk
=head1 METHODS
=cut
use strict;
use warnings;
package Bio::EnsEMBL::Funcgen::DBSQL::ExternalFeatureAdaptor;
use Bio::EnsEMBL::Utils::Exception qw( throw warning );
use Bio::EnsEMBL::Funcgen::ExternalFeature;
use Bio::EnsEMBL::Funcgen::DBSQL::SetFeatureAdaptor;
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Funcgen::DBSQL::SetFeatureAdaptor);
=head2 _tables
Args : None
Example : None
Description: PROTECTED implementation of superclass abstract method.
Returns the names and aliases of the tables to use for queries.
Returntype : List of listrefs of strings
Exceptions : None
Caller : Internal
Status : At Risk
=cut
sub _tables {
my $self = shift;
return (
[ 'external_feature', 'ef' ],
[ 'feature_set', 'fs' ],#this is required for fetching on analysis, external_db (cell_type or feature_type).
);
}
=head2 _columns
Args : None
Example : None
Description: PROTECTED implementation of superclass abstract method.
Returns a list of columns to use for queries.
Returntype : List of strings
Exceptions : None
Caller : Internal
Status : At Risk
=cut
sub _columns {
my $self = shift;
return qw(
ef.external_feature_id ef.seq_region_id
ef.seq_region_start ef.seq_region_end
ef.seq_region_strand ef.display_label
ef.feature_type_id ef.feature_set_id
);
}
=head2 _objs_from_sth
Arg [1] : DBI statement handle object
Example : None
Description: PROTECTED implementation of superclass abstract method.
Creates ExternalFeature objects from an executed DBI statement
handle.
Returntype : Listref of Bio::EnsEMBL::ExternalFeature objects
Exceptions : None
Caller : Internal
Status : At Risk
=cut
sub _objs_from_sth {
my ($self, $sth, $mapper, $dest_slice) = @_;
#For EFG this has to use a dest_slice from core/dnaDB whether specified or not.
#So if it not defined then we need to generate one derived from the species_name and schema_build of the feature we're retrieving.
my ($sa, @features, $seq_region_id, %fset_hash, %slice_hash, %sr_name_hash, %sr_cs_hash, %ftype_hash);
$sa = $dest_slice->adaptor->db->get_SliceAdaptor() if($dest_slice);#don't really need this if we're using DNADBSliceAdaptor?
$sa ||= $self->db->get_SliceAdaptor();
my $fset_adaptor = $self->db->get_FeatureSetAdaptor();
my $ftype_adaptor = $self->db->get_FeatureTypeAdaptor();
my (
$external_feature_id, $efg_seq_region_id,
$seq_region_start, $seq_region_end,
$seq_region_strand, $fset_id,
$display_label, $ftype_id
);
$sth->bind_columns(
\$external_feature_id, \$efg_seq_region_id,
\$seq_region_start, \$seq_region_end,
\$seq_region_strand, \$display_label,
\$ftype_id, \$fset_id,
);
#abstract to BaseFeatureAdaptor?
my ($asm_cs, $cmp_cs, $asm_cs_name, $asm_cs_vers, $cmp_cs_name, $cmp_cs_vers);
if ($mapper) {
$asm_cs = $mapper->assembled_CoordSystem();
$cmp_cs = $mapper->component_CoordSystem();
$asm_cs_name = $asm_cs->name();
$asm_cs_vers = $asm_cs->version();
$cmp_cs_name = $cmp_cs->name();
$cmp_cs_vers = $cmp_cs->version();
}
my ($dest_slice_start, $dest_slice_end, $dest_slice_strand, $dest_slice_length, $dest_slice_sr_name);
if ($dest_slice) {
$dest_slice_start = $dest_slice->start();
$dest_slice_end = $dest_slice->end();
$dest_slice_strand = $dest_slice->strand();
$dest_slice_length = $dest_slice->length();
$dest_slice_sr_name = $dest_slice->seq_region_name();
}
FEATURE: while ( $sth->fetch() ) {
#Need to build a slice adaptor cache here?
#Would only ever want to do this if we enable mapping between assemblies??
#Or if we supported the mapping between cs systems for a given schema_build,
#which would have to be handled by the core api
#get core seq_region_id
$seq_region_id = $self->get_core_seq_region_id($efg_seq_region_id);
if(! $seq_region_id){
warn "Cannot get slice for eFG seq_region_id $efg_seq_region_id\n".
"The region you are using is not present in the current dna DB";
next;
}
#Get the FeatureSet/Type objects
$fset_hash{$fset_id} = $fset_adaptor->fetch_by_dbID($fset_id) if(! exists $fset_hash{$fset_id});
$ftype_hash{$ftype_id} = $ftype_adaptor->fetch_by_dbID($ftype_id) if(! exists $ftype_hash{$ftype_id});
# Get the slice object
my $slice = $slice_hash{'ID:'.$seq_region_id};
if (! $slice) {
$slice = $sa->fetch_by_seq_region_id($seq_region_id);
$slice_hash{'ID:'.$seq_region_id} = $slice;
$sr_name_hash{$seq_region_id} = $slice->seq_region_name();
$sr_cs_hash{$seq_region_id} = $slice->coord_system();
}
my $sr_name = $sr_name_hash{$seq_region_id};
my $sr_cs = $sr_cs_hash{$seq_region_id};
#abstract to BaseFeatureAdaptor?
# Remap the feature coordinates to another coord system if a mapper was provided
if ($mapper) {
throw("Not yet implmented mapper, check equals are Funcgen calls too!");
($sr_name, $seq_region_start, $seq_region_end, $seq_region_strand)
= $mapper->fastmap($sr_name, $seq_region_start, $seq_region_end, $seq_region_strand, $sr_cs);
# Skip features that map to gaps or coord system boundaries
next FEATURE if !defined $sr_name;
# Get a slice in the coord system we just mapped to
if ( $asm_cs == $sr_cs || ( $cmp_cs != $sr_cs && $asm_cs->equals($sr_cs) ) ) {
$slice = $slice_hash{"NAME:$sr_name:$cmp_cs_name:$cmp_cs_vers"}
||= $sa->fetch_by_region($cmp_cs_name, $sr_name, undef, undef, undef, $cmp_cs_vers);
} else {
$slice = $slice_hash{"NAME:$sr_name:$asm_cs_name:$asm_cs_vers"}
||= $sa->fetch_by_region($asm_cs_name, $sr_name, undef, undef, undef, $asm_cs_vers);
}
}
# If a destination slice was provided convert the coords
# If the destination slice starts at 1 and is forward strand, nothing needs doing
if ($dest_slice) {
unless ($dest_slice_start == 1 && $dest_slice_strand == 1) {
if ($dest_slice_strand == 1) {
$seq_region_start = $seq_region_start - $dest_slice_start + 1;
$seq_region_end = $seq_region_end - $dest_slice_start + 1;
} else {
my $tmp_seq_region_start = $seq_region_start;
$seq_region_start = $dest_slice_end - $seq_region_end + 1;
$seq_region_end = $dest_slice_end - $tmp_seq_region_start + 1;
$seq_region_strand *= -1;
}
}
# Throw away features off the end of the requested slice
next FEATURE if $seq_region_end < 1 || $seq_region_start > $dest_slice_length
|| ( $dest_slice_sr_name ne $sr_name );
$slice = $dest_slice;
}
push @features, Bio::EnsEMBL::Funcgen::ExternalFeature->new_fast
({
'start' => $seq_region_start,
'end' => $seq_region_end,
'strand' => $seq_region_strand,
'slice' => $slice,
'analysis' => $fset_hash{$fset_id}->analysis(),
'adaptor' => $self,
'dbID' => $external_feature_id,
'display_label' => $display_label,
'feature_set' => $fset_hash{$fset_id},
'feature_type' => $ftype_hash{$ftype_id},
});
}
return \@features;
}
=head2 store
Args : List of Bio::EnsEMBL::Funcgen::ExternalFeature objects
Example : $ofa->store(@features);
Description: Stores given ExternalFeature objects in the database. Should only
be called once per feature because no checks are made for
duplicates. Sets dbID and adaptor on the objects that it stores.
Returntype : Arrayref of stored ExternalFeatures
Exceptions : Throws if a list of ExternalFeature objects is not provided or if
the Analysis, CellType and FeatureType objects are not attached or stored
Caller : General
Status : At Risk
=cut
sub store{
my ($self, @efs) = @_;
if (scalar(@efs) == 0) {
throw('Must call store with a list of ExternalFeature objects');
}
my $sth = $self->prepare("
INSERT INTO external_feature (
seq_region_id, seq_region_start,
seq_region_end, seq_region_strand,
display_label, feature_type_id,
feature_set_id
) VALUES (?, ?, ?, ?, ?, ?, ?)
");
my $db = $self->db();
FEATURE: foreach my $ef (@efs) {
if(! (ref($ef) && $ef->isa('Bio::EnsEMBL::Funcgen::ExternalFeature') )) {
throw('Feature must be an ExternalFeature object');
}
if ( $ef->is_stored($db) ) {
#does not accomodate adding Feature to >1 feature_set
warning('ExternalFeature [' . $ef->dbID() . '] is already stored in the database');
next FEATURE;
}
#Have to do this for Analysis separately due to inheritance, removed defined as constrained in Feature->new
#Redundancy with Analysis in FeatureSet
if ( ! $ef->analysis->is_stored($db)) {
throw('A stored Bio::EnsEMBL::Analysis must be attached to the ExternalFeature objects to be stored.');
}
#won't this implicitly check for stored analysis? Not at present, we should probably do this
if (! $ef->feature_set->is_stored($db)) {
throw('A stored Bio::EnsEMBL::Funcgen::FeatureSet must be attached to the ExternalFeature objects to be stored.');
}
my $seq_region_id;
($ef, $seq_region_id) = $self->_pre_store($ef);
$sth->bind_param(1, $seq_region_id, SQL_INTEGER);
$sth->bind_param(2, $ef->start(), SQL_INTEGER);
$sth->bind_param(3, $ef->end(), SQL_INTEGER);
$sth->bind_param(4, $ef->strand(), SQL_TINYINT);
$sth->bind_param(5, $ef->display_label(), SQL_VARCHAR);
$sth->bind_param(6, $ef->feature_type->dbID(), SQL_INTEGER);
$sth->bind_param(7, $ef->feature_set->dbID(), SQL_INTEGER);
$sth->execute();
$ef->dbID( $sth->{'mysql_insertid'} );
$ef->adaptor($self);
$self->store_associated_feature_types($ef) if (defined $ef->{'associated_feature_types'});
}
return \@efs;
}
1;
]]>