Raw content of Bio::EnsEMBL::DBSQL::SimpleFeatureAdaptor
<![CDATA[=head1 LICENSE
Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
=head1 NAME
Bio::EnsEMBL::DBSQL::SimpleFeatureAdaptor
=head1 SYNOPSIS
my $simple_feature_adaptor =
$database_adaptor->get_SimpleFeatureAdaptor();
@simple_features =
@{ $simple_feature_adaptor->fetch_all_by_Slice($slice) };
=head1 DESCRIPTION
Simple Feature Adaptor - database access for simple features
=head1 METHODS
=cut
package Bio::EnsEMBL::DBSQL::SimpleFeatureAdaptor;
use vars qw(@ISA);
use strict;
use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
use Bio::EnsEMBL::SimpleFeature;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
@ISA = qw(Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor);
=head2 store
Arg [1] : list of Bio::EnsEMBL::SimpleFeatures @sf
the simple features to store in the database
Example : $simple_feature_adaptor->store(@simple_feats);
Description: Stores a list of simple feature objects in the database
Returntype : none
Exceptions : thrown if @sf is not defined, if any of the features do not
have an attached slice.
or if any elements of @sf are not Bio::EnsEMBL::SimpleFeatures
Caller : general
Status : Stable
=cut
sub store{
my ($self,@sf) = @_;
if( scalar(@sf) == 0 ) {
throw("Must call store with list of SimpleFeatures");
}
my $sth = $self->prepare
("INSERT INTO simple_feature (seq_region_id, seq_region_start, " .
"seq_region_end, seq_region_strand, " .
"display_label, analysis_id, score) " .
"VALUES (?,?,?,?,?,?,?)");
my $db = $self->db();
my $analysis_adaptor = $db->get_AnalysisAdaptor();
FEATURE: foreach my $sf ( @sf ) {
if( !ref $sf || !$sf->isa("Bio::EnsEMBL::SimpleFeature") ) {
throw("SimpleFeature must be an Ensembl SimpleFeature, " .
"not a [".ref($sf)."]");
}
if($sf->is_stored($db)) {
warning("SimpleFeature [".$sf->dbID."] is already stored" .
" in this database.");
next FEATURE;
}
if(!defined($sf->analysis)) {
throw("An analysis must be attached to the features to be stored.");
}
#store the analysis if it has not been stored yet
if(!$sf->analysis->is_stored($db)) {
$analysis_adaptor->store($sf->analysis());
}
my $original = $sf;
my $seq_region_id;
($sf, $seq_region_id) = $self->_pre_store($sf);
$sth->bind_param(1,$seq_region_id,SQL_INTEGER);
$sth->bind_param(2,$sf->start,SQL_INTEGER);
$sth->bind_param(3,$sf->end,SQL_INTEGER);
$sth->bind_param(4,$sf->strand,SQL_TINYINT);
$sth->bind_param(5,$sf->display_label,SQL_VARCHAR);
$sth->bind_param(6,$sf->analysis->dbID,SQL_INTEGER);
$sth->bind_param(7,$sf->score,SQL_DOUBLE);
$sth->execute();
$original->dbID($sth->{'mysql_insertid'});
$original->adaptor($self);
}
}
=head2 _tablename
Arg [1] : none
Example : none
Description: PROTECTED implementation of superclass abstract method
returns the names, aliases of the tables to use for queries
Returntype : list of listrefs of strings
Exceptions : none
Caller : internal
Status : Stable
=cut
sub _tables {
my $self = shift;
return ['simple_feature', 'sf'];
}
=head2 _columns
Arg [1] : 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 : Stable
=cut
sub _columns {
my $self = shift;
return qw( sf.simple_feature_id
sf.seq_region_id sf.seq_region_start sf.seq_region_end
sf.seq_region_strand sf.display_label sf.analysis_id sf.score );
}
=head2 _objs_from_sth
Arg [1] : hash reference $hashref
Example : none
Description: PROTECTED implementation of superclass abstract method.
creates SimpleFeatures from an executed DBI statement handle.
Returntype : list reference to Bio::EnsEMBL::SimpleFeature objects
Exceptions : none
Caller : internal
Status : Stable
=cut
sub _objs_from_sth {
my ($self, $sth, $mapper, $dest_slice) = @_;
#
# This code is ugly because an attempt has been made to remove as many
# function calls as possible for speed purposes. Thus many caches and
# a fair bit of gymnastics is used.
#
my $sa = $self->db()->get_SliceAdaptor();
my $aa = $self->db->get_AnalysisAdaptor();
my @features;
my %analysis_hash;
my %slice_hash;
my %sr_name_hash;
my %sr_cs_hash;
my($simple_feature_id,$seq_region_id, $seq_region_start, $seq_region_end,
$seq_region_strand, $display_label, $analysis_id, $score);
$sth->bind_columns(\$simple_feature_id,\$seq_region_id, \$seq_region_start,
\$seq_region_end, \$seq_region_strand, \$display_label,
\$analysis_id, \$score);
my $asm_cs;
my $cmp_cs;
my $asm_cs_vers;
my $asm_cs_name;
my $cmp_cs_vers;
my $cmp_cs_name;
if($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;
my $dest_slice_end;
my $dest_slice_strand;
my $dest_slice_length;
my $dest_slice_sr_name;
my $dest_slice_seq_region_id;
if($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();
$dest_slice_seq_region_id =$dest_slice->get_seq_region_id();
}
my $count =0;
FEATURE: while($sth->fetch()) {
$count++;
#get the analysis object
my $analysis = $analysis_hash{$analysis_id} ||=
$aa->fetch_by_dbID($analysis_id);
#need to get the internal_seq_region, if present
$seq_region_id = $self->get_seq_region_id_internal($seq_region_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};
#
# remap the feature coordinates to another coord system
# if a mapper was provided
#
if($mapper) {
($seq_region_id,$seq_region_start,$seq_region_end,$seq_region_strand) =
$mapper->fastmap($sr_name, $seq_region_start, $seq_region_end,
$seq_region_strand, $sr_cs);
#skip features that map to gaps or coord system boundaries
next FEATURE if(!defined($seq_region_id));
#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 = $slice_hash{"ID:".$seq_region_id} ||=
$sa->fetch_by_seq_region_id($seq_region_id);
} else {
$slice = $slice_hash{"ID:".$seq_region_id} ||=
$sa->fetch_by_seq_region_id($seq_region_id);
}
}
#
# If a destination slice was provided convert the coords
# If the dest_slice starts at 1 and is foward strand, nothing needs doing
#
if($dest_slice) {
if($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;
$seq_region_strand *= -1;
}
}
#throw away features off the end of the requested slice
if($seq_region_end < 1 || $seq_region_start > $dest_slice_length ||
( $dest_slice_seq_region_id != $seq_region_id )) {
# print STDERR "IGNORED DUE TO CUTOFF $dest_slice_seq_region_id ne $seq_region_id . $sr_name\n";
next FEATURE;
}
$slice = $dest_slice;
}
push( @features,
$self->_create_feature_fast(
'Bio::EnsEMBL::SimpleFeature', {
'start' => $seq_region_start,
'end' => $seq_region_end,
'strand' => $seq_region_strand,
'slice' => $slice,
'analysis' => $analysis,
'adaptor' => $self,
'dbID' => $simple_feature_id,
'display_label' => $display_label,
'score' => $score
} ) );
}
return \@features;
}
=head2 list_dbIDs
Arg [1] : none
Example : @feature_ids = @{$simple_feature_adaptor->list_dbIDs()};
Description: Gets an array of internal ids for all simple features in the current db
Arg[1] : <optional> int. not 0 for the ids to be sorted by the seq_region.
Returntype : list of ints
Exceptions : none
Caller : ?
Status : Stable
=cut
sub list_dbIDs {
my ($self, $ordered) = @_;
return $self->_list_dbIDs("simple_feature", undef, $ordered);
}
1;
]]>