=head1 LICENSE Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2019] EMBL-European Bioinformatics Institute Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. =cut =head1 CONTACT Please email comments or questions to the public Ensembl developers list at . Questions may also be sent to the Ensembl help desk at . =cut # # Ensembl module for Bio::EnsEMBL::Variation::DBSQL::DBAdaptor # # =head1 NAME Bio::EnsEMBL::DBSQL::DBAdaptor =head1 SYNOPSIS =head1 DESCRIPTION This module provides a connection to an Ensembl variation database and provides a means to obtain ObjectAdaptors. =head1 METHODS =cut use strict; use warnings; package Bio::EnsEMBL::Variation::DBSQL::DBAdaptor; use Bio::EnsEMBL::DBSQL::DBAdaptor; use Bio::EnsEMBL::Utils::Exception qw(throw warning); use Bio::EnsEMBL::Utils::Argument qw(rearrange); our @ISA = ('Bio::EnsEMBL::DBSQL::DBAdaptor'); our $DEFAULT_INCLUDE_FAILED_VARIATIONS = 0; our $DEFAULT_INCLUDE_NON_SIGNIFICANT_PHENOTYPES = 0; our $DEFAULT_SHIFT_HGVS_VARIANTS_3PRIME = 1; sub get_available_adaptors{ my %pairs = ( 'Allele' => 'Bio::EnsEMBL::Variation::DBSQL::AlleleAdaptor', 'AlleleFeature' => 'Bio::EnsEMBL::Variation::DBSQL::AlleleFeatureAdaptor', 'AlleleSynonym' => 'Bio::EnsEMBL::Variation::DBSQL::AlleleSynonymAdaptor', 'Attribute' => 'Bio::EnsEMBL::Variation::DBSQL::AttributeAdaptor', 'CADDAnnotation' => 'Bio::EnsEMBL::Variation::DBSQL::CADDAnnotationAdaptor', 'GenotypeCode' => 'Bio::EnsEMBL::Variation::DBSQL::GenotypeCodeAdaptor', 'GERPAnnotation' => 'Bio::EnsEMBL::Variation::DBSQL::GERPAnnotationAdaptor', 'Individual' => 'Bio::EnsEMBL::Variation::DBSQL::IndividualAdaptor', 'LDFeatureContainer' => 'Bio::EnsEMBL::Variation::DBSQL::LDFeatureContainerAdaptor', 'MetaCoordContainer' => 'Bio::EnsEMBL::DBSQL::MetaCoordContainer', 'MetaContainer' => 'Bio::EnsEMBL::Variation::DBSQL::MetaContainer', 'MotifFeatureVariation' => 'Bio::EnsEMBL::Variation::DBSQL::MotifFeatureVariationAdaptor', 'Phenotype' => 'Bio::EnsEMBL::Variation::DBSQL::PhenotypeAdaptor', 'PhenotypeFeature' => 'Bio::EnsEMBL::Variation::DBSQL::PhenotypeFeatureAdaptor', 'Population' => 'Bio::EnsEMBL::Variation::DBSQL::PopulationAdaptor', 'PopulationGenotype' => 'Bio::EnsEMBL::Variation::DBSQL::PopulationGenotypeAdaptor', 'ProteinFunctionPredictionMatrix' => 'Bio::EnsEMBL::Variation::DBSQL::ProteinFunctionPredictionMatrixAdaptor', 'Publication' => 'Bio::EnsEMBL::Variation::DBSQL::PublicationAdaptor', 'ReadCoverage' => 'Bio::EnsEMBL::Variation::DBSQL::ReadCoverageAdaptor', 'RegulatoryFeatureVariation' => 'Bio::EnsEMBL::Variation::DBSQL::RegulatoryFeatureVariationAdaptor', 'Sample' => 'Bio::EnsEMBL::Variation::DBSQL::SampleAdaptor', 'SampleGenotype' => 'Bio::EnsEMBL::Variation::DBSQL::SampleGenotypeAdaptor', 'SampleGenotypeFeature' => 'Bio::EnsEMBL::Variation::DBSQL::SampleGenotypeFeatureAdaptor', 'Source' => 'Bio::EnsEMBL::Variation::DBSQL::SourceAdaptor', 'StrainSlice' => 'Bio::EnsEMBL::Variation::DBSQL::StrainSliceAdaptor', 'StructuralVariation' => 'Bio::EnsEMBL::Variation::DBSQL::StructuralVariationAdaptor', 'StructuralVariationFeature' => 'Bio::EnsEMBL::Variation::DBSQL::StructuralVariationFeatureAdaptor', 'StructuralVariationPopulationFrequency' => 'Bio::EnsEMBL::Variation::DBSQL::StructuralVariationPopulationFrequencyAdaptor', 'StructuralVariationSample' => 'Bio::EnsEMBL::Variation::DBSQL::StructuralVariationSampleAdaptor', 'Study' => 'Bio::EnsEMBL::Variation::DBSQL::StudyAdaptor', 'SupportingStructuralVariation' => 'Bio::EnsEMBL::Variation::DBSQL::SupportingStructuralVariationAdaptor', 'TranscriptVariation' => 'Bio::EnsEMBL::Variation::DBSQL::TranscriptVariationAdaptor', 'Variation' => 'Bio::EnsEMBL::Variation::DBSQL::VariationAdaptor', 'VariationFeature' => 'Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor', 'VariationSet' => 'Bio::EnsEMBL::Variation::DBSQL::VariationSetAdaptor', 'VCFCollection' => 'Bio::EnsEMBL::Variation::DBSQL::VCFCollectionAdaptor', 'TranscriptHaplotype' => 'Bio::EnsEMBL::Variation::DBSQL::TranscriptHaplotypeAdaptor', ); return (\%pairs); } =head2 include_failed_variations Arg [1] : int $newval (optional) Example : #Get a DBAdaptor for the human variation database my $dba = $registry->get_DBAdaptor('human','variation'); #Configure the DBAdaptor to return failed variations when using #fetch methods in the various object adaptors $dba->include_failed_variations(1); #Get a variation set adaptor my $vs_adaptor = $dba->get_VariationSetAdaptor(); #Get a variation set for the 1000 genomes high coverage Yoruba trio data my $vs = $vs_adaptor->fetch_by_name('1000 genomes - High coverage - Trios - YRI'); # Get the iterator for the variations belonging to this variation set. #This will now include variations that has been flagged as being failed. #The default behaviour is not to return these. my $it = $vs->get_Variation_Iterator(); # Iterate over the variations while ($it->has_next()) { # Get the next variation object in the iterator my $v = $it->next(); # Check if the variation is flagged as failed if ($v->is_failed()) { # Do something... } # If not, check if any of its subsnps have been flagged as failed elsif ($v->has_failed_alleles()) { #Do something else... } else { #Do something else... } } Description: Getter/Setter for the behaviour of the adaptors connected through this DBAdaptor when it comes to variations and alleles that have been flagged as failed. The default behaviour is not to return these variations or alleles in e.g. the 'fetch_all_by...'-type methods. If this flag is set, those methods will instead also return failed variations and alleles. Note that a variation is considered failed when the variation itself is failed. If only some alleles belonging to the variation are failed, the entire variation will not be considered to be failed. Returntype : int Exceptions : none Caller : general Status : Stable =cut sub include_failed_variations { my $self = shift; my $include = shift; #If the flag should be modified, do that if (defined($include)) {$self->{'include_failed_variations'} = $include;} #In case the flag has not been set at all, set it to the default value unless (exists($self->{'include_failed_variations'})) {$self->{'include_failed_variations'} = $DEFAULT_INCLUDE_FAILED_VARIATIONS;} return $self->{'include_failed_variations'}; } # API-internal method for getting the constraint to filter out variations not shown by default # (those failing standard QC which are not cited). # Assumes that the variation table has been (left) joined to the query and that the table # alias is either supplied or equals 'v' sub _exclude_failed_variations_constraint { my $self = shift; my $table_alias = shift; # If not specified, assume that the variation table alias is 'v' $table_alias ||= 'v'; return $table_alias . ".display =1"; } # API-internal method for getting the constraint to filter out failed structural variations. Assumes that the # failed_structural_variation table has been (left) joined to the query and that the table alias is either supplied # or equals 'fsv' sub _exclude_failed_structural_variations_constraint { my $self = shift; my $table_alias = shift; # If not specified, assume that the failed_structural_variation table alias is 'fsv' $table_alias ||= 'fsv'; return $self->_exclude_failed_constraint('structural_variation_id',$table_alias); } # API-internal method for getting the constraint to filter out failed alleles. Assumes that the # failed_allele table has been (left) joined to the query and that the table alias is either supplied # or equals 'fa' sub _exclude_failed_alleles_constraint { my $self = shift; my $table_alias = shift; # If not specified, assume that the failed_variation table alias is 'fv' $table_alias ||= 'fa'; return $self->_exclude_failed_constraint('allele_id',$table_alias); } sub _exclude_failed_constraint { my $self = shift; my $key_column = shift; my $table_alias = shift; #If we should include failed objects, no extra condition is needed return qq{ 1 } if ($self->include_failed_variations()); # Otherwise, add a constraint on the alias table to have the key_column NULL my $constraint = qq{ ( $table_alias.$key_column IS NULL ) }; return $constraint; } =head2 include_non_significant_phenotype_associations Arg [1] : int $newval (optional) Example : # Get a DBAdaptor for the human variation database my $dba = $registry->get_DBAdaptor('human','phenotypefeature'); # Configure the DBAdaptor to return non significant phenotype associations when using # fetch methods in the various object adaptors $dba->include_non_significant_phenotype_associations(1); Description: Getter/Setter for the behaviour of the adaptors connected through this DBAdaptor when it comes to phenotype feature. The default behaviour is to return the phenotype features with significance results only e.g. the 'fetch_all_by...'-type methods. If this flag is set, those methods will instead also return phenotype features with non significant results. Returntype : int Exceptions : none Caller : general Status : Stable =cut sub include_non_significant_phenotype_associations { my $self = shift; my $include = shift; # If the flag should be modified, do that if (defined($include)) {$self->{'include_non_significant_phenotypes'} = $include;} # In case the flag has not been set at all, set it to the default value unless (exists($self->{'include_non_significant_phenotypes'})) {$self->{'include_non_significant_phenotypes'} = $DEFAULT_INCLUDE_NON_SIGNIFICANT_PHENOTYPES;} return $self->{'include_non_significant_phenotypes'}; } =head2 shift_hgvs_variants_3prime Arg [1] : int $newval (optional) Example : #Get a DBAdaptor for the human variation database my $dba = $registry->get_DBAdaptor('human','variation'); #Configure the DBAdaptor to return failed variations when using #fetch methods in the various object adaptors $dba->shift_hgvs_variants_3prime(1); #Proceed to extract HGVS annotation as normal Description: Getter/Setter for the behaviour of the adaptors connected through this DBAdaptor when it comes to HGVS transcript and protein level annotation. The default behaviour is to keep the positions as input. Formal HGVS annotation requires any variant to be described at the most 3 prime location possible which changes the variation consequence in a very small number of cases. Returntype : int Exceptions : none Caller : general Status : at risk =cut sub shift_hgvs_variants_3prime{ my $self = shift; my $move_3prime = shift; #If the flag should be modified, do that if (defined($move_3prime)) {$self->{'shift_hgvs_variants_3prime'} = $move_3prime;} #In case the flag has not been set at all, set it to the default value unless (exists($self->{'shift_hgvs_variants_3prime'})) {$self->{'shift_hgvs_variants_3prime'} = $DEFAULT_SHIFT_HGVS_VARIANTS_3PRIME;} return $self->{'shift_hgvs_variants_3prime'}; } =head2 use_vcf Arg [1] : int $newval (optional) Example : # Get a LD feature container adaptor my $ldfca = $registry->get_DBAdaptor('human','variation','ldfeaturecontainer'); # tell the adaptor to include genotypes from VCF files $ldfca->db->use_vcf(1); # fetch LD container as normal my $ldfc = $ldfca->fetch_by_Slice($slice, $population); Description: Getter/Setter the use_vcf property. Switching this to a non-zero value instructs the API to look in configured VCF files for genotype-based data. Setting to 1 tells the API to use both the DB and VCF; setting to 2 tells the API to use only VCF. Returntype : int Exceptions : none Caller : general Status : at risk =cut sub use_vcf { my $self = shift; my ($new_use, $vcf_config_file) = @_; # default to 0 $self->{use_vcf} = 0 if !exists($self->{use_vcf}); # allow user to switch $self->{use_vcf} = $new_use if defined($new_use); $self->vcf_config_file($vcf_config_file) if defined($vcf_config_file); return $self->{use_vcf} } sub vcf_config { my $self = shift; if(!exists($self->{vcf_config})) { if(@_) { $self->{vcf_config} = shift; } else { $self->{vcf_config} = {}; } } return $self->{vcf_config}; } sub vcf_config_file { my $self = shift; $self->{vcf_config_file} = shift if @_; return $self->{vcf_config_file}; } sub vcf_root_dir { my $self = shift; $self->{vcf_root_dir} = shift if @_; return $self->{vcf_root_dir}; } sub gerp_root_dir { my $self = shift; $self->{gerp_root_dir} = shift if @_; return $self->{gerp_root_dir}; } sub vcf_tmp_dir { my $self = shift; $self->{vcf_tmp_dir} = shift if @_; return $self->{vcf_tmp_dir}; } 1;