Raw content of Bio::EnsEMBL::Variation::DBSQL::SampleAdaptor
<![CDATA[#
# Ensembl module for Bio::EnsEMBL::Variation::DBSQL::SampleAdaptor
#
# Copyright (c) 2005 Ensembl
#
# You may distribute this module under the same terms as perl itself
#
#
=head1 NAME
Bio::EnsEMBL::Variation::DBSQL::SampleAdaptor
=head1 SYNOPSIS
Abstract class - should not be instantiated. Implementation of
abstract methods must be performed by subclasses.
Base adaptors provides:
#using the adaptor of the subclass, given the id of the sample, returns all synonyms in database
$synonyms = $sample_adaptor->fetch_synonyms($sample_id);
#using the adaptor of the subclass and given the name of the synonym, returns the sample
$sample = $sample_adaptor->fetch_sample_by_synonym($sample_synonym_id);
=head1 DESCRIPTION
This is a base class implementing common methods in population, individual and strain. This base
class is simply a way of merging similar concepts that should have the same ID
=head1 AUTHOR - Daniel Rios
=head1 CONTACT
Post questions to the Ensembl development list ensembl-dev@ebi.ac.uk
=head1 METHODS
=cut
use strict;
use warnings;
package Bio::EnsEMBL::Variation::DBSQL::SampleAdaptor;
use vars qw(@ISA @EXPORT);
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
our @ISA = ('Bio::EnsEMBL::DBSQL::BaseAdaptor');
@EXPORT = (@{$DBI::EXPORT_TAGS{'sql_types'}});
=head2 fetch_synonyms
Arg [1] : $sample_id
Arg [2] (optional) : $source
Example : my $dbSNP_synonyms = $pop_adaptor->fetch_synonyms($sample_id,$dbSNP);
my $all_synonyms = $pop_adaptor->fetch_synonyms($sample_id);
Description: Retrieves synonyms for the source provided. Otherwise, return all the synonyms for the sample
Returntype : list of strings
Exceptions : none
Caller : Bio:EnsEMBL:Variation::Sample
Status : At Risk
=cut
sub fetch_synonyms{
my $self = shift;
my $dbID = shift;
my $source = shift;
my $sample_synonym;
my $synonyms;
my $sql;
if (defined $source){
$sql = qq{SELECT ss.name FROM sample_synonym ss, source s WHERE ss.sample_id = ? AND ss.source_id = s.source_id AND s.name = "$source"}
}
else{
$sql = qq{SELECT name FROM sample_synonym WHERE sample_id = ?};
}
my $sth = $self->prepare($sql);
$sth->bind_param(1,$dbID,SQL_INTEGER);
$sth->execute();
$sth->bind_columns(\$sample_synonym);
while ($sth->fetch){
push @{$synonyms},$sample_synonym;
}
return $synonyms;
}
=head2 fetch_sample_by_synonym
Arg [1] : $sample_synonym
Example : my $pop = $pop_adaptor->fetch_sample_by_synonym($sample_synonym,$source);
Description : Retrieves sample for the synonym given in the source. If no source is provided, retrieves all the synonyms
Returntype : list of Bio::EnsEMBL::Variation::Sample
Exceptions : none
Caller : general
Status : At Risk
=cut
sub fetch_sample_by_synonym{
my $self = shift;
my $synonym_name = shift;
my $source = shift;
my $sql;
my $sample;
my $sample_array;
if (defined $source){
$sql = qq{SELECT sample_id FROM sample_synonym ss, source s WHERE ss.name = ? and ss.source_id = s.source_id AND s.name = "$source"};
}
else{
$sql = qq{SELECT sample_id FROM sample_synonym WHERE name = ?};
}
my $sample_id;
my $sth = $self->prepare($sql);
$sth->bind_param(1,$synonym_name,SQL_VARCHAR);
$sth->execute();
$sth->bind_columns(\$sample_id);
while ($sth->fetch()){
push @{$sample_array}, $sample_id;
}
return $sample_array;
}
=head2 fetch_by_dbID
Arg [1] : int $id
The unique sample identifier for the sample to be obtained
Example : $population = $population_adaptor->fetch_by_dbID(1234);
Description: Returns the feature sample from the database defined by the
the id $id.
Returntype : Bio::EnsEMBL::Variation::Sample
Exceptions : thrown if $id arg is not provided
does not exist
Caller : general
Status : At Risk
=cut
sub fetch_by_dbID{
my ($self,$id) = @_;
throw("id argument is required") if(!defined $id);
#construct a constraint like 't1.table1_id = 123'
my @tabs = $self->_tables;
my ($name, $syn) = @{$tabs[0]};
#the constraint must contain the sample_id, that it is used either for individuals or populations
my $constraint = "${syn}.sample_id = ?";
$self->bind_param_generic_fetch($id,SQL_INTEGER);
#Should only be one
my ($feat) = @{$self->generic_fetch($constraint)};
return undef if(!$feat);
return $feat;
}
=head2 fetch_all_by_dbID_list
Arg [1] : listref of ints $id_list
The unique database identifiers for the samples to be obtained
Example : @individuals = @{$individual_adaptor->fetch_by_dbID_list([1234, 2131, 982]))};
Description: Returns the samples created from the database defined by the
the ids in contained in the id list $id_list. If none of the
samples are found in the database a reference to an empty
list is returned.
Returntype : listref of Bio::EnsEMBL::Variation::Sample
Exceptions : thrown if $id arg is not provided
does not exist
Caller : general
Status : At Risk
=cut
sub fetch_all_by_dbID_list {
my ($self,$id_list_ref) = @_;
if(!defined($id_list_ref) || ref($id_list_ref) ne 'ARRAY') {
throw("id_list list reference argument is required");
}
return [] if(!@$id_list_ref);
my @out;
#construct a constraint like 't1.table1_id = 123'
my @tabs = $self->_tables;
my ($name, $syn) = @{$tabs[0]};
# mysql is faster and we ensure that we do not exceed the max query size by
# splitting large queries into smaller queries of 200 ids
my $max_size = 200;
my @id_list = @$id_list_ref;
while(@id_list) {
my @ids;
if(@id_list > $max_size) {
@ids = splice(@id_list, 0, $max_size);
} else {
@ids = splice(@id_list, 0);
}
my $id_str;
if(@ids > 1) {
$id_str = " IN (" . join(',', @ids). ")";
} else {
$id_str = " = ?";
$self->bind_param_generic_fetch($ids[0],SQL_INTEGER);
}
my $constraint = "${syn}.sample_id $id_str";
push @out, @{$self->generic_fetch($constraint)};
}
return \@out;
}
1;
]]>