# # EnsEMBL module for Bio::EnsEMBL::Funcgen::DBSQL::BaseFeatureAdaptor # =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. =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 . =head1 NAME Bio::EnsEMBL::Funcgen::DBSQL::BaseFeatureAdaptor - Funcgen Feature Adaptor base class =head1 SYNOPSIS Abstract class - should not be instantiated. Implementation of abstract methods must be performed by subclasses. =head1 DESCRIPTION This is a base adaptor for Funcgen feature adaptors. This base class is simply a way to redefine some methods to use with the Funcgen DB. =cut package Bio::EnsEMBL::Funcgen::DBSQL::BaseFeatureAdaptor; use strict; use warnings; use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor; use Bio::EnsEMBL::Funcgen::DBSQL::BaseAdaptor; use Bio::EnsEMBL::Utils::Cache; use Bio::EnsEMBL::Utils::Exception qw( throw deprecate ); use Bio::EnsEMBL::Utils::Argument qw( rearrange ); use Bio::EnsEMBL::Utils::Scalar qw( assert_ref ); use base qw(Bio::EnsEMBL::Funcgen::DBSQL::BaseAdaptor Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor); use vars qw(@EXPORT); #require Exporter is done in BaseAdaptor @EXPORT = (@{$DBI::EXPORT_TAGS{'sql_types'}}); ### To do ### #Add Translation method for fetch by FeatureSets methods? #Test and implement feature mapping between coord systems #Correct/Document methods!!! #Implement externaldb db_name version registry my %warnings; =head2 generic_fetch Arg [1] : (optional) string $constraint An SQL query constraint (i.e. part of the WHERE clause) Arg [2] : (optional) Bio::EnsEMBL::AssemblyMapper $mapper A mapper object used to remap features as they are retrieved from the database Arg [3] : (optional) Bio::EnsEMBL::Slice $slice A slice that features should be remapped to Example : $fts = $a->generic_fetch('contig_id in (1234, 1235)', 'Swall'); Description: Wrapper method for core BaseAdaptor, build seq_region cache for features Returntype : ARRAYREF of Bio::EnsEMBL::SeqFeature in contig coordinates Exceptions : none Caller : FeatureAdaptor classes Status : at risk =cut sub generic_fetch { my $self = shift; #need to wrap _generic_fetch to always generate the #seq_region_cache other wise non-slice based fetch methods fail #build seq_region cache here once for entire query #Using default schema_build here #So would need to set dnadb appropriately #This is cleaning tmp cache values such that #nested feature fetches cause failure e.g. when regfeats retrieve their reg_attrs #We need a way of always generating the tmp cache, or having it persist? #This is because we haven't built the tmp cache in non_slice based methods i.e. we haven't run get_seq_region_id_by_Slice #This is the same for all non-Slice based methods #And the is no way around it as we are not providing that info about the new DB by passing a slice! #The only way to get around this is to make the tmp_cache persistant # $self->build_seq_region_cache(); return $self->SUPER::generic_fetch(@_); } # TODO compare this to core methods and remove new_assembly support? # sub _pre_store { my ($self, $feature, $new_assembly) = @_; if (!ref($feature) || !$feature->isa('Bio::EnsEMBL::Feature')) { throw('Expected Feature argument.'); } $self->_check_start_end_strand($feature->start(),$feature->end(), $feature->strand()); my $db = $self->db(); my $slice = $feature->slice(); if (!ref($slice) || !$slice->isa('Bio::EnsEMBL::Slice')) { throw('Feature must be attached to Slice to be stored.'); } # make sure feature coords are relative to start of entire seq_region if ($slice->start != 1 || $slice->strand != 1) { #move feature onto a slice of the entire seq_region $slice = $slice->adaptor->fetch_by_region($slice->coord_system->name(), $slice->seq_region_name(), undef, #start undef, #end undef, #strand $slice->coord_system->version()); $feature = $feature->transfer($slice); if (!$feature) { throw('Could not transfer Feature to slice of ' . 'entire seq_region prior to storing'); } } my $seq_region_id = $slice->adaptor->get_seq_region_id($slice); if(!$seq_region_id) { throw('Feature is associated with seq_region which is not in this DB.'); } return ($feature, $seq_region_id); } # May need to clone _get_by_Slice in here # if coord system mapping is required sub fetch_all_by_Gene_FeatureSets{ my ($self, $gene, $fsets, $dblinks) = @_; if (! ( ref($gene) && $gene->isa('Bio::EnsEMBL::Gene'))) { throw("You must pass a valid Bio::EnsEMBL::Gene object"); } my @features = @{$self->fetch_all_by_stable_Storable_FeatureSets($gene, $fsets)}; if ($dblinks) { foreach my $transcript (@{$gene->get_all_Transcripts}) { push @features, @{$self->fetch_all_by_Transcript_FeatureSets($transcript, $fsets, $dblinks)}; } } return \@features; } sub fetch_all_by_Transcript_FeatureSets{ my ($self, $transc, $fsets, $dblinks) = @_; if (! ( ref($transc) && $transc->isa('Bio::EnsEMBL::Transcript'))) { throw("You must pass a valid Bio::EnsEMBL::Transcript object"); } my @features = @{$self->fetch_all_by_stable_Storable_FeatureSets($transc, $fsets)}; if ($dblinks) { my $translation = $transc->translation; push @features, @{$self->fetch_all_by_stable_Storable_FeatureSets($translation, $fsets)} if $translation; } return \@features; } =head2 fetch_all_by_display_label Arg [1] : String $label - display label of feature to fetch Example : my $feat = $adaptor->fetch_all_by_display_label('abd-A_dpp:REDFLY:TF000092'); Description: Returns the features with the given display label. Returntype : ARRAYREF of Bio::EnsEMBL::Funcgen::Feature objects Exceptions : none Caller : general Status : At risk =cut #There is no result_feature.display_label attribute. #Move this to individual feature adaptors to avoid over-riding? sub fetch_all_by_display_label { my ($self, $label) = @_; throw('You must defined a display_label argument') if ! defined $label; my $table_syn = $self->_main_table->[1]; my $constraint = "${table_syn}.display_label = ?"; $self->bind_param_generic_fetch($label, SQL_VARCHAR); return $self->generic_fetch($constraint); } =head2 _count_features_by_field_id Arg [1] : string - table field to count Arg [2] : string/int - id to count Example : my $probe_feature_count = $pfa->count_feature_by_field_id('probe_id', $probe_id); Description: Returns a count of the features with the acciated field id Returntype : string/int - count of features Exceptions : Throws args are not set Caller : FeatureAdaptors Status : At risk =cut #This does not assume one record per feature #But does assume primary key if ${table_name}_id #Can't move to core due to cs issues, but could mirror implementation. sub _count_features_by_field_id { my ($self, $count_field, $count_id) = @_; #Any other params here? if (! ($count_field && $count_id)) { throw('You must provide a count name and a count id to count by'); } my ($table_name, $table_syn) = @{$self->_main_table}; my $table_id = "${table_name}_id"; my @cs_ids = @{$self->_get_coord_system_ids}; my $sql = "SELECT count(distinct($table_id)) from $table_name $table_syn, seq_region sr where ${table_syn}.${count_field}=? and ${table_syn}.seq_region_id in(select distinct(seq_region_id) from seq_region where coord_system_id in(".join(',', @cs_ids).'))'; my $sth = $self->prepare($sql); $sth->bind_param(1, $count_id, SQL_INTEGER); $sth->execute; return $sth->fetchrow_array; } =head2 force_reslice Arg [1] : Optional - Boolean Example : if($self->force_reslice){ # Reslice features past ends of destination Slice } Description: Sets/Returns force_reslice boolean Returntype : Boolean Exceptions : None Caller : FeatureAdaptors::_objs_from_sth Status : At risk =cut sub force_reslice{ my $self = shift; my $force = shift; if (defined $force) { $self->{force_reslice} = $force; } return $self->{force_reslice}; } # Currently over-riding this method in SetFeatureAdaptor # But might be nice to remove that and genericise this by getting # the analysis_id table via a method which can be over-ridden e.g. # SetFeatureAdaptor::_analysis_id_table_syn which would return the relevant set table name and syn # BaseFeatureAdaptor::_analysis_id_table_syn would simply return the _main_table syn # #Should this use the cache via AnalysisAdpator::fetch_by_logic_name? #As _logic_name_to_constriant does? #_logic_name_to_constraint returns undef if logic_name is not known # allowing caller to return [] early. # How would this work in compose_constraint? # simply delete this first if exists # How does this work wrt redundancy between constraints and optional_constraints # For generic methods, there is a slight redundancy in calling # the _main_table method # Can we call this in compose_constraint and pass to contrain method sub _constrain_logic_names { my $self = shift; my $logic_names = shift; assert_ref($logic_names, 'ARRAY'); if(! @$logic_names){ throw('Must pass an Arrayref of logic_name strings to contrain by'); } for my $lname(@$logic_names){ if(! defined $lname){ throw('Found undefined logic_name value'); } } my $syn = $self->_main_table->[1]; $self->_tables([['analysis', 'a']]); my $constraint = $syn.'.analysis_id = a.analysis_id and a.logic_name in ("'. join('", "', @$logic_names).'")'; return ($constraint, {}); #{} = not further constraint conf } 1;