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Bio-EnsEMBL-112.0_54
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/ Bio::EnsEMBL::DBSQL::RNAProductAdaptor

LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] 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.

CONTACT

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NAME

Bio::EnsEMBL::DBSQL::RNAProductAdaptor - Provides a means to fetch and store RNAProduct objects from a database.

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.

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" );

...

METHODS

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

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

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

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

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

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

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

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

_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

_fetch_direct_query Arg [1] : reference to an array consisting of: - the name of the column to use in the WHERE clause, - the value fields from that column are to be equal to, - the data type of that column (e.g. SQL_INTEGER) Description: PRIVATE internal method shared between public fetch methods in order to avoid duplication of SQL-query logic. NOT SAFE to be handed directly to users because in its current form it can be trivially exploited to inject arbitrary SQL. Returntype : ArrayRef of either Bio::EnsEMBL::RNAProducts or undefs Exceptions : throws if RNAProduct type is absent or unknown Caller : internal Status : At Risk (In Development)

_obj_from_sth Arg [1] : DBI statement handle Description: PRIVATE internal method shared between public SQL-query methods in order to avoid duplication of object-creation logic. Returntype : ArrayRef of either Bio::EnsEMBL::RNAProducts or undefs Exceptions : throws if RNAProduct type is absent or unknown Caller : internal Status : At Risk (In Development)

_tables

Arg [1]    : none
Description: PROTECTED implementation of superclass abstract method.
             Returns the names, aliases of the tables to use for queries.
Returntype : list of listrefs of strings
Exceptions : none
Caller     : internal
Status     : Stable