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
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NAME
Bio::EnsEMBL::DBSQL::TranslationAdaptor - Provides a means to fetch and store Translation objects from a database.
DESCRIPTION
This adaptor provides a means to retrieve and store Bio::EnsEMBL::Translation objects from/in a database.
Translation objects only truly make sense in the context of their transcripts so the recommended means to retrieve Translations is by retrieving the Transcript object first, and then fetching the Translation.
SYNOPSIS
Bio::EnsEMBL::Registry->load_registry_from_db(
-host => 'ensembldb.ensembl.org',
-user => 'anonymous'
);
$transcript_adaptor =
Bio::EnsEMBL::Registry->get_adaptor( "human", "core",
"transcript" );
$translation_adaptor =
Bio::EnsEMBL::Registry->get_adaptor( "human", "core",
"translation" );
my $transcript = $transcript_adaptor->fetch_by_dbID(131243);
my $translation =
$translation_adaptor->fetch_by_Transcript($transcript);
print("Translation Start Site: "
. $translation->start_Exon()->stable_id() . " "
. $translation->start()
. "\n" );
print("Translation Stop: "
. $translation->end_Exon()->stable_id() . " "
. $translation->end() );
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METHODS
fetch_all_alternative_by_Transcript
Arg [1] : Bio::EnsEMBL::Transcript $transcript
Example :
@tl = @{
$translation_adaptor->fetch_all_alternative_by_Transcript(
$transcript)
};
Description: Retrieves all alternative translations associated with a
particular transcript. If no alternative translation is
found, a reference to an empty list is returned.
Returntype : listref of Bio::EnsEMBL::Translation
Exceptions : throw on incorrect argument
Caller : Transcript
Status : Stable
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fetch_by_Transcript
Arg [1] : Bio::EnsEMBL::Transcript $transcript
Example : $tl = $translation_adaptor->fetch_by_Transcript($transcript);
Description: Retrieves a Translation via its associated transcript.
If the Translation is not found, undef is returned.
Returntype : Bio::EnsEMBL::Translation
Exceptions : throw on incorrect argument
Caller : Transcript
Status : Stable
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fetch_all_by_external_name
Arg [1] : string $external_name
The external identifier for the translation(s) 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 @translations =
@{ $trl_adaptor->fetch_all_by_external_name('BRCA2') };
my @many_translations =
@{ $trl_adaptor->fetch_all_by_external_name('BRCA%') };
Description: Retrieves a list of translations fetched via an
external identifier. Note that this may not be a
particularly useful method, because translations
do not make much sense out of the context of
their transcript. It may be better to use the TranscriptAdaptor::fetch_all_by_external_name instead.
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 optimisationsReturntype : reference to a list of Translations
Exceptions : none
Caller : general
Status : Medium Risk
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fetch_all_by_GOTerm
Arg [1] : Bio::EnsEMBL::OntologyTerm
The GO term for which translations should be fetched.
Example: @translations = @{
$translation_adaptor->fetch_all_by_GOTerm(
$go_adaptor->fetch_by_accession('GO:0030326') ) };
Description : Retrieves a list of translations that are
associated with the given GO term, or with any of
its descendent GO terms.
Return type : listref of Bio::EnsEMBL::Translation
Exceptions : Throws of argument is not a GO term
Caller : general
Status : Stable
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fetch_all_by_GOTerm_accession
Arg [1] : String
The GO term accession for which genes should be
fetched.
Example :
@genes =
@{ $gene_adaptor->fetch_all_by_GOTerm_accession('GO:0030326') };
Description : Retrieves a list of genes that are associated with
the given GO term, or with any of its descendent
GO terms. The genes returned are in their native
coordinate system, i.e. in the coordinate system
in which they are stored in the database. If
another coordinate system is required then the
Gene::transfer or Gene::transform method can be
used.
Return type : listref of Bio::EnsEMBL::Gene
Exceptions : Throws of argument is not a GO term accession
Caller : general
Status : Stable
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store
Arg [1] : Bio::EnsEMBL::Translation $translation
The translation object to be stored in the database
Example : $transl_id = $translation_adaptor->store($translation);
Description: Stores a translation object in the database
Returntype : int - the new dbID of the stored translation
Exceptions : thrown if the dbID of the start_Exon or end_Exon is not
defined.
thrown if only partial stable id information is present (e.g.
identifier but not version number)
Caller : Transcript::store
Status : Stable
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remove
Arg [1] : Bio::EnsEMBL::Translation $translation
Example : $translation_adaptor->remove($translation);
Description: Removes a translation completely from the database, and all
associated information including protein features etc.
Returntype : none
Exceptions : throw on incorrect arguments
warning if translation is not in this database
Caller : TranscriptAdaptor::remove
Status : Stable
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list_dbIDs
Arg [1] : none
Example : @translation_ids = @{$translation_adaptor->list_dbIDs()};
Description: Gets an array of internal ids for all translations in the current db
Returntype : list of ints
Exceptions : none
Caller : ?
Status : Stable
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list_stable_ids
Arg [1] : none
Example : @transl_stable_ids = @{$transl_adaptor->list_stable_dbIDs()};
Description: Gets an array of stable ids for all translations in the current
db
Returntype : reference to a list of strings
Exceptions : none
Caller : general
Status : Stable
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_list_dbIDs
Arg[1] : String $table
Arg[2] : String $column
Example : $transl_adaptor->_list_dbIDs('translation','translation_id');
Description : Local reimplementation to ensure multi-species translations
are limited to their species alone
Returntype : ArrayRef of specified IDs
Caller : Internal
Status : Unstable
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fetch_by_dbID
Arg [1] : int $dbID
The internal identifier of the Translation to obtain
Example : $translation = $translation_adaptor->fetch_by_dbID(1234);
Description: This fetches a Translation object via its internal id.
This is only debatably useful since translations do
not make much sense outside of the context of their
Transcript. Consider using fetch_by_Transcript instead.
Returntype : Bio::EnsEMBL::Translation, or undef if the translation is not
found.
Exceptions : warning if an additional (old style) Transcript argument is
provided
Caller : ?
Status : Stable
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fetch_by_stable_id
Arg [1] : string $stable_id
The stable identifier of the Translation to obtain
Example : $translation = $translation_adaptor->fetch_by_stable_id("ENSP00001");
Description: This fetches a Translation object via its stable id.
This is only debatably useful since translations do
not make much sense outside of the context of their
Transcript. Consider using fetch_by_Transcript instead.
Returntype : Bio::EnsEMBL::Translation or undef if the translation is not
found.
Exceptions : warning if an additional (old style) Transcript argument is
provided
Caller : ?
Status : Stable
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fetch_by_stable_id_version
Arg [1] : String $id
The stable ID of the gene to retrieve
Arg [2] : Integer $version
The version of the stable_id to retrieve
Example : $gene = $gene_adaptor->fetch_by_stable_id('ENSG00000148944', 14);
Description: Retrieves a gene object from the database via its stable id and version.
The gene will be retrieved in its native coordinate system (i.e.
in the coordinate system it is stored in the database). It may
be converted to a different coordinate system through a call to
transform() or transfer(). If the gene or exon is not found
undef is returned instead.
Returntype : Bio::EnsEMBL::Gene or undef
Exceptions : if we cant get the gene in given coord system
Caller : general
Status : Stable
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fetch_all_by_Transcript_list
Arg [1] : reference to list of Bio::EnsEMBL::Transcripts $transcripts
The list of $transcripts to obtain Translation object for.
Example : @translations = @{$tla->fetch_all_by_Transcript_list([$t1,$t2]);
Description: Fetches all translations associated with the list of transcripts
passed to this method. The passed transcripts will also have
their translation set by this method.
Returntype : Reference to list of Bio::EnsEMBL::Translations
Exceptions : None
Caller : general
Status : Stable
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fetch_all
Example : $translations = $translation_adaptor->fetch_all();
Description : Retrieves all canonical and alternative translations
stored in the database.
Returntype : listref of Bio::EnsEMBL::Translation
Caller : general
Status : At Risk
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