Raw content of Bio::EnsEMBL::Variation::DBSQL::BaseGenotypeAdaptor
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# Ensembl module for Bio::EnsEMBL::Variation::DBSQL::BaseGenotypeAdaptor
#
# Copyright (c) 2005 Ensembl
#
# You may distribute this module under the same terms as perl itself
#
#
=head1 NAME
Bio::EnsEMBL::Variation::DBSQL::BaseGenotypeAdaptor
=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, retrieve all Genotypes from MultipleGenotype table
$genotypes = $ig_adaptor->fetch_all_by_Variation($variation_id);
#using the adaptor of the subclass and given a slice, returns all genotypes in the region
$genotypes = $ig_adaptor->fetch_sll_by_Slice($slice);
=head1 DESCRIPTION
This adaptor provides database connectivity for IndividualGenotype objects.
IndividualGenotypes may be retrieved from the Ensembl variation database by
several means using this module.
=head1 AUTHOR - Daniel Rios
=head1 CONTACT
Post questions to the Ensembl development list ensembl-dev@ebi.ac.uk
=head1 METHODS
=cut
package Bio::EnsEMBL::Variation::DBSQL::BaseGenotypeAdaptor;
use strict;
use warnings;
use vars qw(@ISA);
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::Variation::IndividualGenotypeFeature;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::Utils::Sequence qw(reverse_comp);
@ISA = ('Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor');
=head2 fetch_all_by_Variation
Arg [1] : Bio::EnsEMBL::Variation $variation
Example : my $var = $variation_adaptor->fetch_by_name( "rs1121" )
$igtypes = $igtype_adaptor->fetch_all_by_Variation( $var )
Description: Retrieves a list of individual genotypes for the given Variation.
If none are available an empty listref is returned.
Returntype : listref Bio::EnsEMBL::Variation::IndividualGenotype
Exceptions : none
Caller : general
Status : At Risk
=cut
sub fetch_all_by_Variation {
my $self = shift;
my $variation = shift;
if(!ref($variation) || !$variation->isa('Bio::EnsEMBL::Variation::Variation')) {
throw('Bio::EnsEMBL::Variation::Variation argument expected');
}
if(!defined($variation->dbID())) {
warning("Cannot retrieve genotypes for variation without set dbID");
return [];
}
my $res;
if (!$self->_multiple){
push @{$res},@{$self->generic_fetch("ig.variation_id = " . $variation->dbID())}; #to select data from individual_genotype_single_bp
$self->_multiple(1);
}
push @{$res}, @{$self->generic_fetch("ig.variation_id = " . $variation->dbID())}; #to select data from individual_genotype_multiple_bp
return $res;
}
sub _tables{
my $self = shift;
return (['individual_genotype_single_bp','ig'],['variation_feature','vf']) if (!$self->_multiple);
return (['individual_genotype_multiple_bp','ig'],['variation_feature','vf']) if ($self->_multiple);
}
sub _columns{
return qw(ig.sample_id ig.variation_id ig.allele_1 ig.allele_2 vf.seq_region_id vf.seq_region_start vf.seq_region_end vf.seq_region_strand);
}
sub _default_where_clause {
my $self = shift;
return 'vf.variation_id = ig.variation_id';
}
sub _objs_from_sth{
my ($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 = $self->db()->dnadb()->get_SliceAdaptor();
my @results;
my %slice_hash;
my %sr_name_hash;
my %sr_cs_hash;
my %individual_hash;
my %variation_hash;
my ($sample_id, $variation_id, $seq_region_id, $seq_region_start,
$seq_region_end, $seq_region_strand, $allele_1, $allele_2);
$sth->bind_columns(\$sample_id, \$variation_id, \$allele_1, \$allele_2,
\$seq_region_id, \$seq_region_start, \$seq_region_end, \$seq_region_strand);
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 $dest_slice_length;
if($dest_slice) {
$dest_slice_start = $dest_slice->start();
$dest_slice_end = $dest_slice->end();
$dest_slice_strand = $dest_slice->strand();
$dest_slice_length = $dest_slice->length();
}
FEATURE: while($sth->fetch()) {
#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} = $slice->coord_system();
}
#
# remap the feature coordinates to another coord system
# if a mapper was provided
#
if($mapper) {
my $sr_name = $sr_name_hash{$seq_region_id};
my $sr_cs = $sr_cs_hash{$seq_region_id};
($sr_name,$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,
$asm_cs_vers);
}
}
#
# If a destination slice was provided convert the coords
# If the dest_slice starts at 1 and is foward strand, nothing needs doing
#
if($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) {
next FEATURE;
}
}
$slice = $dest_slice;
}
#we have to consider if the variation is in the opposite strand, we should have it in the forward
if ($seq_region_strand == -1){
$seq_region_strand = 1;
reverse_comp(\$allele_1);
reverse_comp(\$allele_2);
$slice->{'strand'} = -1;
}
my $igtype = Bio::EnsEMBL::Variation::IndividualGenotypeFeature->new_fast({
'start' => $seq_region_start,
'end' => $seq_region_end,
'strand' => $seq_region_strand,
'slice' => $slice,
'allele1' => $allele_1,
'allele2' => $allele_2,
});
$individual_hash{$sample_id} ||= [];
$variation_hash{$sample_id} ||=[];
push @{$individual_hash{$sample_id}}, $igtype;
push @{$variation_hash{$variation_id}},$igtype;
push @results, $igtype;
}
# get all variations in one query (faster)
# and add to already created genotypes
my @var_ids = keys %variation_hash;
my $va = $self->db()->get_VariationAdaptor();
my $vars = $va->fetch_all_by_dbID_list(\@var_ids);
foreach my $v (@$vars) {
foreach my $igty (@{$variation_hash{$v->dbID()}}) {
$igty->variation($v);
}
}
# get all individual in one query (faster)
# and add to already created genotypes
my @ind_ids = keys %individual_hash;
my $ia = $self->db()->get_IndividualAdaptor();
my $inds = $ia->fetch_all_by_dbID_list(\@ind_ids);
foreach my $i (@$inds) {
foreach my $igty (@{$individual_hash{$i->dbID()}}) {
$igty->individual($i);
}
}
return \@results;
}
sub _multiple{
my $self = shift;
$self->{'_multiple'} = shift if (@_);
return $self->{'_multiple'};
}
1;
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