=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::GERPAnnotationAdaptor # # =head1 NAME Bio::EnsEMBL::DBSQL::GERPAnnotationAdaptor =head1 SYNOPSIS my $reg = 'Bio::EnsEMBL::Registry'; # set path to configuration file ## explicit use # get GERP Annotation Adaptor my $gerp_annotation_adaptor = $reg->get_adaptor('human', 'variation', 'GERPAnnotation'); my $va = $reg->get_adaptor('human', 'variation', 'variation'); my $v = $va->fetch_by_name('rs699'); my $vf = $v->get_all_VariationFeatures->[0]; # iterate over GERP annotation collections foreach my $gerp_annotation (@{$gerp_annotation_adaptor->fetch_all}) # get GERP score for this VariationFeature my $gerp_score = $gerp_annotation->get_score_by_VariationFeature($vf); } =head1 DESCRIPTION This module creates a set of objects that can read GERP scores from BigWig files. =head1 METHODS =cut use strict; use warnings; package Bio::EnsEMBL::Variation::DBSQL::GERPAnnotationAdaptor; use Bio::EnsEMBL::Utils::Exception qw(throw warning); use Bio::EnsEMBL::Utils::Argument qw(rearrange); use Bio::EnsEMBL::Utils::Scalar qw(assert_ref); use Bio::EnsEMBL::Variation::GERPAnnotation; use Bio::EnsEMBL::Variation::Source; use Bio::EnsEMBL::Variation::DBSQL::BaseAdaptor; use base qw(Bio::EnsEMBL::Variation::DBSQL::BaseAnnotationAdaptor); our @EXPORT_OK = qw($CONFIG_FILE); our $CONFIG_FILE; =head2 new Arg [-CONFIG]: string - path to JSON configuration file Example : my $gaa = Bio::EnsEMBL::Variation::DBSQL::GERPAnnotationAdaptor->new( -config => '/path/to/annotation_config.json' ); Description: Constructor. Instantiates a new GERPAnnotationAdaptor object. Returntype : Bio::EnsEMBL::Variation::DBSQL::GERPAnnotationAdaptor Exceptions : none Caller : general Status : Stable =cut sub new { my $caller = shift; my $class = ref($caller) || $caller; $Bio::EnsEMBL::Variation::DBSQL::BaseAnnotationAdaptor::CONFIG_FILE = $CONFIG_FILE if ($CONFIG_FILE); my $self = $class->SUPER::new(@_); my $config = $self->config; my $root_dir = $self->root_dir; my $tmpdir = $self->tmpdir; foreach my $hash(@{$config->{collections}}) { next unless (defined $hash->{annotation_type} && lc $hash->{annotation_type} eq 'gerp'); # check the species and assembly if we can if($self->db) { my $species = $hash->{species}; my $assembly = $hash->{assembly}; # check species throw("ERROR: No species defined in collection ".$hash->{id}."\n") unless defined($species); next unless lc($self->db->species) =~ lc($species); # check assembly if($assembly) { next unless lc($self->db->dnadb->get_CoordSystemAdaptor->fetch_all->[0]->version) eq lc($assembly); } else { warn("WARNING: No assembly defined in collection ".$hash->{id}."\n"); } } my $filename_template = $self->_get_filename_template($hash); ## create source object if source info available my $source = Bio::EnsEMBL::Variation::Source->new_fast({ name => $hash->{source_name} || $hash->{id}, version => $hash->{source_version}, url => $hash->{source_url}, description => $hash->{description} || $hash->{id}, }); $self->add_GERPAnnotation( Bio::EnsEMBL::Variation::GERPAnnotation->new( -id => $hash->{id}, -description => $hash->{description}, -type => $hash->{type}, -use_as_source => $hash->{use_as_source}, -filename_template => $filename_template, -chromosomes => $hash->{chromosomes}, -assembly => $hash->{assembly} || undef, -source => $source || undef, -strict_name_match => $hash->{strict_name_match}, -use_seq_region_synonyms => $hash->{use_seq_region_synonyms}, -created =>$hash->{created} || undef, -updated =>$hash->{updated} || undef, -is_remapped => $hash->{is_remapped} || 0, -adaptor => $self, -tmpdir => $hash->{tmpdir} || $tmpdir, )); } return $self; } =head2 fetch_by_id Example : my $collection = $gerp_annotation_adaptor->fetch_by_id('gerp_conservation_scores'); Description: Fetches GERPAnnotation with given ID Returntype : Bio::EnsEMBL::Variation::GERPAnnotation Exceptions : none Caller : general Status : Stable =cut sub fetch_by_id { my $self = shift; return $self->SUPER::fetch_by_id(@_); } =head2 fetch_all Example : my $collections = $gerp_annotation_adaptor->fetch_all(); Description: Fetches all configured GERPAnnotations Returntype : Arrayref of Bio::EnsEMBL::Variation::GERPAnnotations Exceptions : none Caller : general Status : Stable =cut sub fetch_all { my $self = shift; return $self->SUPER::fetch_all(@_); } =head2 add_GERPAnnotation Example : $gerp_annotation_adaptor->add_GERPAnnotation($collection); Description: Add a GERPAnnotation to the cached list on this adaptor Returntype : Bio::EnsEMBL::Variation::GERPAnnotation Exceptions : throw on invalid or missing collection throw on attempt to add collection with duplicated ID Caller : general Status : Stable =cut sub add_GERPAnnotation { my $self = shift; my $collection = shift; # check class assert_ref($collection, 'Bio::EnsEMBL::Variation::GERPAnnotation'); # check ID my $id = $collection->id; throw("ERROR: Collection with ID $id already exists\n") if $self->fetch_by_id($id); $self->{collections}->{$id} = $collection; push @{$self->{order}}, $id; return $collection; } =head2 remove_GERPAnnotation_by_ID Example : $gerp_annotation_adaptor->remove_GERPAnnotation_by_ID($id); Description: Remove a GERPAnnotation from the cached list on this adaptor Returntype : bool (0 = ID does not exist; 1 = deleted OK) Exceptions : none Caller : general Status : Stable =cut sub remove_GERPAnnotation_by_ID { my $self = shift; my $id = shift; return 0 unless $self->fetch_by_id($id); delete $self->{collections}->{$id}; @{$self->{order}} = grep {$_ ne $id} @{$self->{order}}; return 1; } =head2 root_dir Example : $root_dir = $gerp_annotation_adaptor->root_dir; Description: Sets and returns the root directory. Returntype : String Exceptions : None Caller : General Status : Stable =cut sub root_dir { my ($self, $root_dir) = @_; if (!$root_dir) { if (!$self->{root_dir}) { if($self->db && $self->db->gerp_root_dir) { $self->{root_dir} = $self->db->gerp_root_dir.'/'; } } } else { $self->{root_dir} = $root_dir; } return $self->{root_dir} || ''; } 1;