Raw content of Bio::EnsEMBL::Variation::DBSQL::CompressedGenotypeAdaptor
<![CDATA[#
# Ensembl module for Bio::EnsEMBL::Variation::DBSQL::CompressedGenotypeAdaptor
#
# Copyright (c) 2005 Ensembl
#
# You may distribute this module under the same terms as perl itself
#
#
=head1 NAME
Bio::EnsEMBL::Variation::DBSQL::CompressedGenotypeAdaptor
=head1 SYNOPSIS
$db = Bio::EnsEMBL::Variation::DBSQL::DBAdaptor->new(...);
$iga = $db->get_IndividualGenotypeAdaptor();
#returns all genotypes in a certain Slice
$genotypes = $iga->fetch_by_Slice($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::CompressedGenotypeAdaptor;
use strict;
use warnings;
use vars qw(@ISA);
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::Variation::IndividualGenotype;
use Bio::EnsEMBL::Variation::DBSQL::BaseGenotypeAdaptor;
@ISA = qw(Bio::EnsEMBL::Variation::DBSQL::BaseGenotypeAdaptor);
use Data::Dumper;
=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;
my $res;
if(!ref($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 $vfa = $self->db->get_VariationFeatureAdaptor();
if (!$vfa){
throw("Cannot retrieve genotypes for variation without adaptor set");
return [];
}
my $variation_features = $vfa->fetch_all_by_Variation($variation);
#foreach of the hitting variation Features, get the Genotype information
foreach my $vf (@{$variation_features}){
map {$_->variation($variation); push @{$res}, $_} @{$self->fetch_all_by_Slice($vf->feature_Slice)};
}
#and include the genotypes from the multiple genotype table
$self->_multiple(1);
push @{$res}, @{$self->SUPER::fetch_all_by_Variation($variation)};
$self->_multiple(0);
return $res;
}
=head2 fetch_all_by_Slice
Arg [1] : Bio::EnsEMBL:Slice $slice
Arg [2] : (optional) Bio::EnsEMBL::Variation::Individual $individual
Example : my @IndividualGenotypesFeatures = @{$ca->fetch_all_by_Slice($slice)};
Description: Retrieves all IndividualGenotypeFeature features for a given slice for
a certain individual (if provided).
Returntype : reference to list Bio::EnsEMBL::Variation::IndividualGenotype
Exceptions : throw on bad argument
Caller : general
Status : At Risk
=cut
sub fetch_all_by_Slice{
my $self = shift;
my $slice = shift;
my $individual = shift;
my @results;
my $features;
my $constraint;
if (!$self->_multiple){
#if passed inividual, add constraint
if (defined $individual && defined $individual->dbID){
$constraint = ' c.sample_id = ' . $individual->dbID;
# $constraint = ' c.sample_id = ?';
# $self->bind_param_generic_fetch($individual->dbID,SQL_INTEGER);
$features = $self->SUPER::fetch_all_by_Slice_constraint($slice,$constraint);
}
else{
$features = $self->SUPER::fetch_all_by_Slice($slice);
}
#need to check the feature is within the Slice
foreach my $indFeature (@{$features}){
# print "feature_start ",$indFeature->start,"slice_end ",$slice->end,"slice_start ",$slice->start,"feature_end ",$indFeature->end,"\n" if ($indFeature->end==1);
if ($indFeature->start > 0 && ($slice->end-$slice->start +1) >= $indFeature->end){
if ($indFeature->slice->strand == -1){ #ignore the different strand transformation
# Position will change if the strand is negative so change the strand to 1 temporarily
$indFeature->slice->{'strand'} = 1;
my $newFeature = $indFeature->transfer($slice->seq_region_Slice);
$indFeature->slice->{'strand'} = -1;
$newFeature->slice->{'strand'} = -1;
$newFeature->variation($indFeature->variation);
push @results, $newFeature;
}
else{
push @results,$indFeature->transfer($slice->seq_region_Slice);
}
}
}
}
else{
#if passed inividual, add constraint
if (defined $individual && defined $individual->dbID){
$constraint = ' c.sample_id = ' . $individual->dbID;
# $constraint = ' c.sample_id = ?';
# $self->bind_param_generic_fetch($individual->dbID,SQL_INTEGER);
$features = $self->SUPER::fetch_all_by_Slice_constraint($slice,$constraint);
}
else{
$features = $self->SUPER::fetch_all_by_Slice($slice);
}
#and include the genotypes from the multiple genotype table
push @results, $features;
}
return \@results;
}
sub _tables{
my $self = shift;
return (['compressed_genotype_single_bp','c']) if (!$self->_multiple);
return $self->SUPER::_tables if ($self->_multiple);
}
sub _columns{
my $self = shift;
return qw(sample_id seq_region_id seq_region_start seq_region_end seq_region_strand genotypes) if (!$self->_multiple);
return $self->SUPER::_columns if ($self->_multiple);
}
sub _objs_from_sth{
my ($self, $sth, $mapper, $dest_slice) = @_;
return $self->SUPER::_objs_from_sth($sth,$mapper,$dest_slice) if ($self->_multiple);
#
# 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 = $self->db()->dnadb()->get_SliceAdaptor();
my @results;
my %slice_hash;
my %sr_name_hash;
my %sr_cs_hash;
my %individual_hash;
my ($sample_id, $seq_region_id, $seq_region_start,
$seq_region_end, $seq_region_strand, $genotypes);
$sth->bind_columns(\$sample_id, \$seq_region_id,
\$seq_region_start, \$seq_region_end, \$seq_region_strand,
\$genotypes);
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_start = $seq_region_start - $dest_slice_start + 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;
}
#create the different Features for all the Genotypes compressed in the genotype field
my $blob = substr($genotypes,2);
my @genotypes = unpack("naa" x (length($blob)/4),$blob);
unshift @genotypes, substr($genotypes,1,1); #add the second allele of the first genotype
unshift @genotypes, substr($genotypes,0,1); #add the first allele of the first genotype
unshift @genotypes, 0; #the first SNP is in the position indicated by the seq_region1
my ($snp_start, $allele_1, $allele_2);
for (my $i=0; $i < @genotypes -1;$i+=3){
#number of gaps
if ($i == 0){
$snp_start = $seq_region_start; #first SNP is in the beginning of the region
}
else{
if ($genotypes[$i] == -1){ #remove duplicates !!
$snp_start += 1;
next;
}
$snp_start += ($genotypes[$i] +1);
}
#genotype
$allele_1 = $genotypes[$i+1];
$allele_2 = $genotypes[$i+2];
my $igtype = Bio::EnsEMBL::Variation::IndividualGenotype->new_fast({
'start' => $snp_start,
'end' => $snp_start,
'strand' => $seq_region_strand,
'slice' => $slice,
'allele1' => $allele_1,
'allele2' => $allele_2,
'adaptor' => $self
});
$individual_hash{$sample_id} ||= [];
push @{$individual_hash{$sample_id}}, $igtype;
push @results, $igtype;
}
}
# 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 _default_where_clause {
my $self = shift;
return '' if (!$self->_multiple);
return $self->SUPER::_default_where_clause if ($self->_multiple);
}
1;
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