Merge pull request #371 from Ensembl/feature/rna-products

Add support for mature RNA products of transcripts (e.g. MicroRNA) to the API and schema

misc-scripts/stable_id_lookup/README

@@ -12,6 +12,7 @@ core	  Exon
 	  Translation
 	  Operon
 	  OperonTranscript
+	  RNAProduct
 
 
 For Gene, Transcript and Translation, an archive_id_lookup is also created, containing all previously used ids

misc-scripts/stable_id_lookup/populate_stable_id_lookup.pl

@@ -37,6 +37,7 @@ my %group_objects = (
     Transcript  => 1,
     Translation => 1,
     Operon      => 1,
+    RNAProduct  => 1,
 
 # OperonTranscript => 1, # these are in transcript table anyway
     GeneArchive        => 1,
@@ -417,7 +418,7 @@ sub load_ids {
 
       my $rows_inserted = build_insert_sql( $select_sql, $dbh_read, $dbh_write, $is_archive );
     }
-    elsif ( $object_name =~ /Translation/ ) {
+    elsif ( $object_name =~ / RNAProduct | Translation /x ) {
       my $sth = $dbh_read->prepare("SELECT COUNT(*) FROM $object");
       $sth->execute();
       my ($count) = $sth->fetchrow_array;

modules/Bio/EnsEMBL/DBSQL/AttributeAdaptor.pm

@@ -291,6 +291,22 @@ sub store_on_Transcript {
   return;
 }
 
+sub store_on_RNAProduct {
+  my ($self, $object, $attributes) = @_;
+
+  my $object_id;
+  if (!ref($object)) {
+    $object_id = $object;
+  }
+  else {
+    $object_id = $object->dbID();
+  }
+
+  $self->store_on_Object($object_id, $attributes, 'rnaproduct');
+
+  return;
+}
+
 sub store_on_Translation {
   my ($self, $object, $attributes) = @_;
 
@@ -417,6 +433,18 @@ sub remove_from_Transcript {
 
 }
 
+sub remove_from_RNAProduct {
+  my ($self, $object, $code) = @_;
+
+  assert_ref($object, 'Bio::EnsEMBL::RNAProduct');
+
+  my $object_id = $object->dbID();
+  $self->remove_from_Object($object_id, 'rnaproduct', $code);
+
+  return;
+
+}
+
 sub remove_from_Translation {
   my ($self, $object, $code) = @_;
 
@@ -576,6 +604,22 @@ sub fetch_all_by_Translation {
 
 }
 
+sub fetch_all_by_RNAProduct {
+  my ($self, $object, $code) = @_;
+
+  my $object_id;
+
+  if (defined($object)) {
+    assert_ref($object, 'Bio::EnsEMBL::RNAProduct');
+    $object_id = $object->dbID();
+  }
+
+  my $results = $self->fetch_all_by_Object($object_id, 'rnaproduct', $code);
+
+  return $results;
+
+}
+
 sub fetch_all_by_DnaDnaAlignFeature {
   my ($self, $object, $code) = @_;
 

modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm

@@ -421,6 +421,7 @@ sub get_available_adaptors {
     PredictionTranscript                => 'Bio::EnsEMBL::DBSQL::PredictionTranscriptAdaptor',
     ProteinAlignFeature                 => 'Bio::EnsEMBL::DBSQL::ProteinAlignFeatureAdaptor',
     ProteinFeature                      => 'Bio::EnsEMBL::DBSQL::ProteinFeatureAdaptor',
+    RNAProduct                          => 'Bio::EnsEMBL::DBSQL::RNAProductAdaptor',
     RepeatConsensus                     => 'Bio::EnsEMBL::DBSQL::RepeatConsensusAdaptor',
     RepeatFeature                       => 'Bio::EnsEMBL::DBSQL::RepeatFeatureAdaptor',
     SeqRegionSynonym                    => 'Bio::EnsEMBL::DBSQL::SeqRegionSynonymAdaptor',

modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm

@@ -1329,6 +1329,37 @@ sub fetch_all_by_Translation {
 }
 
 
+=head2 fetch_all_by_RNAProduct
+
+  Arg [1]    : Bio::EnsEMBL::RNAProduct $rp
+               (The rnaproduct to fetch database entries for)
+  Arg [2]    : optional external database name. SQL wildcards are accepted
+  Arg [3]    : optional externaldb type. SQL wildcards are accepted
+  Example    : @db_entries = @{$db_entry_adptr->fetch_all_by_RNAProduct($rp)};
+  Description: Retrieves external database entries for an EnsEMBL rnaproduct
+  Returntype : listref of Bio::EnsEMBL::DBEntries; may be of type IdentityXref if
+               there is mapping data, or OntologyXref if there is linkage data.
+  Exceptions : throws if rnaproduct object not passed
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub fetch_all_by_RNAProduct {
+  my ($self, $rp, $ex_db_reg, $ex_db_type) = @_;
+
+  if (!ref($rp) || !$rp->isa('Bio::EnsEMBL::RNAProduct')) {
+    throw('Bio::EnsEMBL::RNAProduct argument expected.');
+  }
+  if (!$rp->dbID()){
+    warning("Cannot fetch_all_by_RNAProduct without a dbID");
+    return [];
+  }
+
+  return $self->_fetch_by_object_type($rp->dbID(), 'RNAProduct', $ex_db_reg, $ex_db_type);
+}
+
+
 
 =head2 remove_from_object
 
@@ -1850,6 +1881,29 @@ sub list_translation_ids_by_external_db_id {
     return $self->_type_by_external_db_id( $external_db_id, 'Translation', undef, $linkage_type ),
 }
 
+
+=head2 list_rnaproduct_ids_by_extids
+
+  Arg [1]    : string $external_name
+  Arg [2]    : (optional) string $external_db_name
+  Arg [3]    : Boolean override, see _type_by_external_id
+  Example    : @rp_ids = $dbea->list_rnaproduct_ids_by_extids('GO:0004835');
+  Description: Gets a list of rnaproduct IDs by external display IDs
+  Returntype : list of Ints
+  Exceptions : none
+  Caller     : unknown
+  Status     : Stable
+
+=cut
+
+sub list_rnaproduct_ids_by_extids {
+  my ($self, $external_name, $external_db_name, $override) = @_;
+
+  return $self->_type_by_external_id($external_name, 'RNAProduct', undef,
+				     $external_db_name, $override);
+}
+
+
 =head2 _type_by_external_id
 
   Arg [1]    : string $name - dbprimary_acc

modules/Bio/EnsEMBL/DBSQL/RNAProductAdaptor.pm

+=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 <http://lists.ensembl.org/mailman/listinfo/dev>.
+
+  Questions may also be sent to the Ensembl help desk at
+  <http://www.ensembl.org/Help/Contact>.
+
+=cut
+
+=head1 NAME
+
+Bio::EnsEMBL::DBSQL::RNAProductAdaptor - Provides a means to fetch and store
+RNAProduct objects from a database.
+
+=head1 DESCRIPTION
+
+This adaptor provides a means to retrieve and store
+Bio::EnsEMBL::RNAProduct objects from/in a database.
+
+RNAProduct objects only truly make sense in the context of their
+transcripts so the recommended means to retrieve RNAProducts is
+by retrieving the Transcript object first, and then fetching the
+RNAProduct.
+
+=head1 SYNOPSIS
+
+  use Bio::EnsEMBL::Registry;
+
+  Bio::EnsEMBL::Registry->load_registry_from_db(
+    -host => 'ensembldb.ensembl.org',
+    -user => 'anonymous'
+  );
+
+  $rnaproduct_adaptor =
+    Bio::EnsEMBL::Registry->get_adaptor( "human", "core",
+    "rnaproduct" );
+
+  ...
+
+=head1 METHODS
+
+=cut
+
+package Bio::EnsEMBL::DBSQL::RNAProductAdaptor;
+
+use strict;
+use warnings;
+
+use Bio::EnsEMBL::DBSQL::BaseAdaptor;
+use Bio::EnsEMBL::MicroRNA;
+use Bio::EnsEMBL::RNAProduct;
+use Bio::EnsEMBL::Utils::Exception qw( throw warning );
+use Bio::EnsEMBL::Utils::Scalar qw( assert_ref );
+
+
+use parent qw( Bio::EnsEMBL::DBSQL::BaseAdaptor );
+
+
+
+=head2 fetch_all_by_Transcript
+
+  Arg [1]    : Bio::EnsEMBL::Transcript $transcript
+  Example    : $rps = $rnaproduct_adaptor->fetch_by_Transcript($transcript);
+  Description: Retrieves RNAProducts via their associated transcript.
+               If no RNAProducts are found, an empty list is returned.
+  Returntype : arrayref of Bio::EnsEMBL::RNAProducts
+  Exceptions : throw on incorrect argument
+  Caller     : Transcript
+  Status     : Stable
+
+=cut
+
+sub fetch_all_by_Transcript {
+  my ($self, $transcript) = @_;
+
+  assert_ref($transcript, 'Bio::EnsEMBL::Transcript');
+
+  return $self->_fetch_direct_query(['rp.transcript_id', $transcript->dbID(), SQL_INTEGER]);
+}
+
+
+=head2 fetch_all_by_external_name
+
+  Arg [1]    : String $external_name
+               An external identifier of the RNAProduct to be obtained
+  Arg [2]    : (optional) String $external_db_name
+               The name of the external database from which the
+               identifier originates.
+  Arg [3]    : Boolean override. Force SQL regex matching for users
+               who really do want to find all 'NM%'
+  Example    : my @rnaproducts =
+                  @{ $rp_a->fetch_all_by_external_name('MIMAT0000416') };
+               my @more_rnaproducts =
+                  @{ $rp_a->fetch_all_by_external_name('hsa-miR-1-__') };
+  Description: Retrieves all RNAProducts which are associated with
+               an external identifier such as a GO term, miRBase
+               identifer, etc. Usually there will only be a single
+               RNAProduct returned in the list reference, but not
+               always. If no RNAProducts with the external identifier
+               are found, a reference to an empty list is returned.
+               SQL wildcards % and _ are supported in the $external_name
+               but their use is somewhat restricted for performance reasons.
+               Users that really do want % and _ in the first three characters
+               should use argument 3 to prevent optimisations
+  Returntype : listref of Bio::EnsEMBL::RNAProduct
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub fetch_all_by_external_name {
+  my ($self, $external_name, $external_db_name, $override) = @_;
+
+  my $entry_adaptor = $self->db->get_DBEntryAdaptor();
+
+  my @ids = $entry_adaptor->list_rnaproduct_ids_by_extids($external_name,
+                                                          $external_db_name,
+                                                          $override);
+
+  my $transcript_adaptor = $self->db()->get_TranscriptAdaptor();
+
+  my @reference;
+  my @non_reference;
+  foreach my $id (@ids) {
+    my $transcript = $transcript_adaptor->fetch_by_rnaproduct_id($id);
+
+    if ( defined($transcript) ) {
+      my $rnaproduct = $self->fetch_by_dbID($id);
+      if ( $transcript->slice()->is_reference() ) {
+        push(@reference, $rnaproduct);
+      }
+      else {
+        push(@non_reference, $rnaproduct);
+      }
+    }
+  }
+
+  return [@reference, @non_reference];
+}
+
+
+=head2 fetch_all_by_type
+
+  Arg [1]    : string $type_code
+  Example    : $rps = $rp_a->fetch_all_by_type('miRNA');
+  Description: Retrieves RNAProducts via their type (e.g. miRNA, circRNA).
+               If no matching RNAProducts are found, an empty list is
+               returned.
+  Returntype : arrayref of Bio::EnsEMBL::RNAProducts
+  Exceptions : throws if type code is undefined
+  Caller     : ?
+  Status     : In Development
+
+=cut
+
+sub fetch_all_by_type {
+  my ($self, $type_code) = @_;
+
+  if ( !defined $type_code ) {
+    throw("type code argument is required");
+  }
+
+  return ($self->_fetch_direct_query(['pt.code', $type_code, SQL_VARCHAR]));
+}
+
+
+=head2 fetch_by_dbID
+
+  Arg [1]    : int $dbID
+               The internal identifier of the RNAProduct to obtain
+  Example    : $rnaproduct = $rnaproduct_adaptor->fetch_by_dbID(1234);
+  Description: This fetches a RNAProduct object via its internal id.
+               This is only debatably useful since RNAProducts do
+               not make much sense outside of the context of their
+               Transcript.  Consider using fetch_by_Transcript instead.
+  Returntype : Bio::EnsEMBL::RNAProduct, or undef if the RNAProduct is not
+               found.
+  Caller     : ?
+  Status     : Stable
+
+=cut
+
+sub fetch_by_dbID {
+  my ($self, $dbID) = @_;
+
+  if ( !defined $dbID ) {
+    throw("dbID argument is required");
+  }
+
+  return ($self->_fetch_direct_query(['rp.rnaproduct_id', $dbID, SQL_INTEGER]))->[0];
+}
+
+
+=head2 fetch_by_stable_id
+
+  Arg [1]    : string $stable_id
+               The stable identifier of the RNAProduct to obtain
+  Example    : $rnaproduct = $rnaproduct_adaptor->fetch_by_stable_id("ENSS00001");
+  Description: This fetches a RNAProduct object via its stable id.
+  Returntype : Bio::EnsEMBL::RNAProduct, or undef if the RNAProduct is not
+               found.
+  Caller     : ?
+  Status     : Stable
+
+=cut
+
+sub fetch_by_stable_id {
+  my ($self, $stable_id) = @_;
+
+  if ( !defined $stable_id ) {
+    throw("stable id argument is required");
+  }
+
+  return ($self->_fetch_direct_query(['rp.stable_id', $stable_id, SQL_VARCHAR]))->[0];
+}
+
+
+=head2 list_dbIDs
+
+  Arg [1]    : none
+  Example    : @rnaproduct_ids = @{$rnaproduct_adaptor->list_dbIDs()};
+  Description: Gets an array of internal ids for all RNAProducts in the current db
+  Returntype : list of ints
+  Exceptions : none
+  Caller     : ?
+  Status     : Stable
+
+=cut
+
+sub list_dbIDs {
+   my ($self) = @_;
+
+   return $self->_list_dbIDs("rnaproduct");
+}
+
+
+=head2 remove
+
+  Arg [1]    : Bio::EnsEMBL::RNAProduct $rnaproduct
+               The RNAProduct to be removed from the database
+  Example    : $rpID = $rp_adaptor->remove($rnaproduct, $transcript->dbID());
+  Description: Removes a RNAProduct, along with all associated information
+               from the database.
+  Returntype : none
+  Exceptions : throw on incorrect arguments
+  Caller     : ?
+  Status     : Stable
+
+=cut
+
+sub remove {
+  my ($self, $rnaproduct) = @_;
+
+  if (!ref($rnaproduct) || !$rnaproduct->isa('Bio::EnsEMBL::RNAProduct')) {
+    throw("$rnaproduct is not a EnsEMBL rnaproduct");
+  }
+
+  my $db = $self->db();
+
+  # Do nothing if the object is not stored to begin with
+  if (!$rnaproduct->is_stored($db)) {
+    return;
+  }
+
+  # Remove xrefs
+  my $dbe_adaptor = $db->get_DBEntryAdaptor();
+  for my $dbe (@{ $rnaproduct->get_all_DBEntries() }) {
+    $dbe_adaptor->remove_from_object($dbe, $rnaproduct, 'RNAProduct');
+  }
+
+  # Remove attributes
+  my $attr_adaptor = $db->get_AttributeAdaptor();
+  $attr_adaptor->remove_from_RNAProduct($rnaproduct);
+
+  # Remove rnaproduct itself
+  my $sth = $self->prepare("DELETE FROM rnaproduct WHERE rnaproduct_id = ?");
+  $sth->bind_param(1, $rnaproduct->dbID(), SQL_INTEGER);
+  $sth->execute();
+  $sth->finish();
+
+  # Mark the object as local
+  $rnaproduct->dbID(undef);
+  $rnaproduct->adaptor(undef);
+
+  return;
+}
+
+
+=head2 store
+
+  Arg [1]    : Bio::EnsEMBL::RNAProduct $rnaproduct
+               The RNAProduct to be written to the database
+  Arg [2]    : Int $transcript_dbID
+               The identifier of the transcript that this RNAProduct is
+               associated with
+  Example    : $rpID = $rp_adaptor->store($rnaproduct, $transcript->dbID());
+  Description: Stores a RNAProduct in the database and returns the new
+               internal identifier for the stored RNAProduct.
+  Returntype : Int
+  Exceptions : throw on incorrect arguments
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub store {
+  my ($self, $rnaproduct, $transcript_dbID) = @_;
+
+  if (!ref($rnaproduct) || !$rnaproduct->isa('Bio::EnsEMBL::RNAProduct')) {
+    throw("$rnaproduct is not a EnsEMBL rnaproduct - not storing");
+  }
+
+  my $db = $self->db();
+
+  # Avoid creating duplicate entries
+  if ($rnaproduct->is_stored($db)) {
+    return $rnaproduct->dbID();
+  }
+
+  my ( $start_exon_dbID, $end_exon_dbID );
+  if ( $rnaproduct->start_Exon() ) {
+    $start_exon_dbID = $rnaproduct->start_Exon()->dbID();
+  }
+  if ( $rnaproduct->end_Exon() ) {
+    $end_exon_dbID = $rnaproduct->end_Exon()->dbID();
+  }
+
+  # Store rnaproduct
+
+  my @columns = qw{ transcript_id seq_start start_exon_id seq_end end_exon_id };
+
+  my @canned_columns = ( 'rnaproduct_type_id' );
+  my @canned_values
+    = ( '(SELECT rnaproduct_type_id FROM rnaproduct_type WHERE code=?)' );
+
+  if (defined($rnaproduct->stable_id())) {
+    push @columns, 'stable_id', 'version';
+
+    my $created = $db->dbc->from_seconds_to_date($rnaproduct->created_date());
+    if ($created) {
+      push @canned_columns, 'created_date';
+      push @canned_values,  $created;
+    }
+
+    my $modified = $db->dbc->from_seconds_to_date($rnaproduct->modified_date());
+    if ($modified) {
+      push @canned_columns, 'modified_date';
+      push @canned_values,  $modified;
+    }
+  }
+
+  my $column_string = join(', ', @columns, @canned_columns);
+  my $value_string  = join(', ', (q{?}) x @columns, @canned_values);
+  my $store_rnaproduct_sql
+    = "INSERT INTO rnaproduct ( $column_string ) VALUES ( $value_string )";
+  my $rp_st = $self->prepare($store_rnaproduct_sql);
+
+  $rp_st->bind_param(  1, $transcript_dbID,         SQL_INTEGER);
+  $rp_st->bind_param(  2, $rnaproduct->start(),     SQL_INTEGER);
+  $rp_st->bind_param(  3, $start_exon_dbID,         SQL_INTEGER);
+  $rp_st->bind_param(  4, $rnaproduct->end(),       SQL_INTEGER);
+  $rp_st->bind_param(  5, $end_exon_dbID,           SQL_INTEGER);
+  if (defined($rnaproduct->stable_id())) {
+    $rp_st->bind_param(6, $rnaproduct->stable_id(), SQL_VARCHAR);
+    $rp_st->bind_param(7, $rnaproduct->version(),   SQL_INTEGER);
+  }
+  $rp_st->bind_param(  8, $rnaproduct->type_code(), SQL_VARCHAR);
+  $rp_st->execute();
+  $rp_st->finish();
+
+  # Retrieve the newly assigned dbID
+  my $rp_dbID = $self->last_insert_id('rnaproduct_id', undef, 'rnaproduct');
+
+  # Store attributes
+  $rnaproduct->synchronise_attributes();
+  my $attr_adaptor = $db->get_AttributeAdaptor();
+  $attr_adaptor->store_on_RNAProduct($rp_dbID,
+                                     $rnaproduct->get_all_Attributes());
+
+  # Store xrefs
+  my $dbe_adaptor = $db->get_DBEntryAdaptor();
+  for my $dbe (@{ $rnaproduct->get_all_DBEntries() }) {
+    $dbe_adaptor->store($dbe, $rp_dbID, 'RNAProduct', 1);
+  }
+
+  # Link the rnaproduct object to its data row
+  $rnaproduct->dbID($rp_dbID);
+  $rnaproduct->adaptor($self);
+
+  return $rp_dbID;
+}
+
+
+=head2 _list_dbIDs
+
+  Arg[1]      : String $table
+  Arg[2]      : String $column
+  Example     : $rnaproduct_adaptor->_list_dbIDs('rnaproduct', 'rnaproduct_id');
+  Description : Local reimplementation to ensure multi-species RNAProducts
+                are limited to their species alone
+  Returntype  : ArrayRef of specified IDs
+  Caller      : Internal
+  Status      : Unstable
+
+=cut
+
+sub _list_dbIDs {
+  my ($self, $table, $column) = @_;
+  my $ids;
+  if($self->is_multispecies()) {
+    $column ||= "${table}_id";
+    my $sql = <<"SQL";
+SELECT `rp`.`${column}` FROM rnaproduct rp
+JOIN transcript t USING (transcript_id)