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Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute
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<http://www.ensembl.org/Help/Contact>.NAME
Bio::EnsEMBL::DBSQL::TranscriptAdaptor - An adaptor which performs database interaction relating to the storage and retrieval of Transcripts
SYNOPSIS
use Bio::EnsEMBL::Registry;
Bio::EnsEMBL::Registry->load_registry_from_db(
-host => 'ensembldb.ensembl.org',
-user => 'anonymous'
);
$transcript_adaptor =
Bio::EnsEMBL::Registry->get_adaptor( 'Human', 'Core',
'Transcript' );
$transcript = $transcript_adaptor->fetch_by_dbID(1234);
$transcript =
$transcript_adaptor->fetch_by_stable_id('ENST00000201961');
$slice =
$slice_adaptor->fetch_by_region( 'Chromosome', '3', 1, 1000000 );
@transcripts = @{ $transcript_adaptor->fetch_all_by_Slice($slice) };
($transcript) =
@{ $transcript_adaptor->fetch_all_by_external_name('NP_065811.1') };DESCRIPTION
This adaptor provides a means to retrieve and store information related to Transcripts. Primarily this involves the retrieval or storage of Bio::EnsEMBL::Transcript objects from a database.
See Bio::EnsEMBL::Transcript for details of the Transcript class.
fetch_by_stable_id
Arg [1] : String $stable_id
The stable id of the transcript to retrieve
Example : my $tr = $tr_adaptor->fetch_by_stable_id('ENST00000309301');
Description: Retrieves a transcript via its stable id.
Returntype : Bio::EnsEMBL::Transcript
Exceptions : none
Caller : general
Status : Stablefetch_by_stable_id_version
Arg [1] : String $id
The stable ID of the transcript to retrieve
Arg [2] : Integer $version
The version of the stable_id to retrieve
Example : $tr = $tr_adaptor->fetch_by_stable_id('ENST00000309301', 3);
Description: Retrieves a transcript object from the database via its
stable id and version.
The transcript 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 transcript is not found
undef is returned instead.
Returntype : Bio::EnsEMBL::Transcript or undef
Exceptions : if we cant get the transcript in given coord system
Caller : general
Status : Stablefetch_all_versions_by_stable_id
Arg [1] : String $stable_id
The stable ID of the transcript to retrieve
Example : my $tr = $tr_adaptor->fetch_all_version_by_stable_id
('ENST00000309301');
Description : Similar to fetch_by_stable_id, but retrieves all versions of a
transcript stored in the database.
Returntype : listref of Bio::EnsEMBL::Transcript objects
Exceptions : if we cant get the gene in given coord system
Caller : general
Status : At Riskfetch_by_rnaproduct_id
Arg [1] : Int $id
The internal identifier of the RNAProduct whose transcript
is to be retrieved
Example : my $tr = $tr_adaptor->fetch_by_rnaproduct_id($rnap->dbID);
Description: Given the internal identifier of a RNAProduct this method
retrieves the transcript associated with that RNAProduct.
If the transcript cannot be found undef is returned instead.
Returntype : Bio::EnsEMBL::Transcript or undef
Exceptions : none
Caller : general
Status : Stablefetch_by_translation_stable_id
Arg [1] : String $transl_stable_id
The stable identifier of the translation of the transcript to
retrieve
Example : my $tr = $tr_adaptor->fetch_by_translation_stable_id
('ENSP00000311007');
Description: Retrieves a Transcript object using the stable identifier of
its translation.
Returntype : Bio::EnsEMBL::Transcript or undef
Exceptions : none
Caller : general
Status : Stablefetch_by_translation_stable_id_version
Arg [1] : String $transl_stable_id
The stable identifier of the translation of the transcript to
retrieve
Arg [2] : Integer $version
The version of the translation of the transcript to retrieve
Example : my $tr = $tr_adaptor->fetch_by_translation_stable_id_version
('ENSP00000311007', 2);
Description: Retrieves a Transcript object using the stable identifier and
version of its translation.
Returntype : Bio::EnsEMBL::Transcript or undef
Exceptions : none
Caller : general
Status : Stablefetch_by_translation_id
Arg [1] : Int $id
The internal identifier of the translation whose transcript
is to be retrieved
Example : my $tr = $tr_adaptor->fetch_by_translation_id($transl->dbID);
Description: Given the internal identifier of a translation this method
retrieves the transcript associated with that translation.
If the transcript cannot be found undef is returned instead.
Returntype : Bio::EnsEMBL::Transcript or undef
Exceptions : none
Caller : general
Status : Stablefetch_all_by_Gene
Arg [1] : Bio::EnsEMBL::Gene $gene
The gene to fetch transcripts of
Example : my $gene = $gene_adaptor->fetch_by_stable_id('ENSG0000123');
my @transcripts = { $tr_adaptor->fetch_all_by_Gene($gene) };
Description: Retrieves Transcript objects for given gene. Puts Genes slice
in each Transcript.
Returntype : Listref of Bio::EnsEMBL::Transcript objects
Exceptions : none
Caller : Gene->get_all_Transcripts()
Status : Stablefetch_all_by_Slice
Arg [1] : Bio::EnsEMBL::Slice $slice
The slice to fetch transcripts on
Arg [2] : (optional) Boolean $load_exons
If true, exons will be loaded immediately rather than
lazy loaded later
Arg [3] : (optional) String $logic_name
The logic name of the type of features to obtain
ARG [4] : (optional) String $constraint
An extra contraint.
Example : my @transcripts = @{ $tr_adaptor->fetch_all_by_Slice($slice) };
Description: Overrides superclass method to optionally load exons
immediately rather than lazy-loading them later. This
is more efficient when there are a lot of transcripts whose
exons are going to be used.
Returntype : Listref of Bio::EnsEMBL::Transcript objects
Exceptions : thrown if exon cannot be placed on transcript slice
Caller : Slice::get_all_Transcripts
Status : Stablefetch_all_by_external_name
Arg [1] : String $external_name
An external identifier of the transcript 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 @transcripts =
@{ $tr_adaptor->fetch_all_by_external_name( 'NP_065811.1') };
my @more_transcripts =
@{$tr_adaptor->fetch_all_by_external_name( 'NP_0658__._')};
Description: Retrieves all transcripts which are associated with
an external identifier such as a GO term, Swissprot
identifer, etc. Usually there will only be a single
transcript returned in the list reference, but not
always. Transcripts are returned in their native
coordinate system, i.e. the coordinate system in which
they are stored in the database. If they are required
in another coordinate system the Transcript::transfer or
Transcript::transform method can be used to convert them.
If no transcripts 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::Transcript
Exceptions : none
Caller : general
Status : Stablefetch_all_by_GOTerm
Arg [1] : Bio::EnsEMBL::OntologyTerm
The GO term for which transcripts should be fetched.
Example: @transcripts = @{
$transcript_adaptor->fetch_all_by_GOTerm(
$go_adaptor->fetch_by_accession('GO:0030326') ) };
Description : Retrieves a list of transcripts that are
associated with the given GO term, or with any of
its descendent GO terms. The transcripts 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 Transcript::transfer or
Transcript::transform method can be used.
Return type : listref of Bio::EnsEMBL::Transcript
Exceptions : Throws of argument is not a GO term
Caller : general
Status : Stablefetch_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 : Stablefetch_by_display_label
Arg [1] : String $label - display label of transcript to fetch
Example : my $tr = $tr_adaptor->fetch_by_display_label("BRCA2");
Description: Returns the transcript which has the given display label or
undef if there is none. If there are more than 1, only the first
is reported.
Returntype : Bio::EnsEMBL::Transcript
Exceptions : none
Caller : general
Status : Stablefetch_all_by_exon_stable_id
Arg [1] : String $stable_id
The stable id of an exon in a transcript
Example : my $tr = $tr_adaptor->fetch_all_by_exon_stable_id
('ENSE00000309301');
Description: Retrieves a list of transcripts via an exon stable id.
Returntype : Listref of Bio::EnsEMBL::Transcript objects
Exceptions : none
Caller : general
Status : Stablefetch_all_by_source
Arg [1] : String $source
listref of $sources
The source of the transcript to retrieve. You can have as an argument a reference
to a list of sources
Example : $transcripts = $transcript_adaptor->fetch_all_by_source('havana');
$transcripts = $transcript_adaptor->fetch_all_by_source(['ensembl', 'vega']);
Description: Retrieves an array reference of transcript objects from the database via its source or sources.
The transcript 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 : listref of Bio::EnsEMBL::Transcript
Exceptions : if we cant get the gene in given coord system
Caller : general
Status : Stablesource_constraint
Arg [1] : String $source
listref of $sources
The source of the transcript to retrieve. You can have as an argument a reference
to a list of sources
Description: Used internally to generate a SQL constraint to restrict a transcript query by source
Returntype : String
Exceptions : If source is not supplied
Caller : general
Status : Stablecount_all_by_source
Arg [1] : String $source
listref of $source
The source of the transcript to retrieve. You can have as an argument a reference
to a list of sources
Example : $cnt = $transcript_adaptor->count_all_by_source('ensembl');
$cnt = $transcript_adaptor->count_all_by_source(['havana', 'vega']);
Description : Retrieves count of transcript objects from the database via its source or sources.
Returntype : integer
Caller : general
Status : Stablecount_all_by_Slice
Arg [1] : Bio::EnsEMBL::Slice $slice
The slice to count transcripts on.
Arg [2] : (optional) biotype(s) string or arrayref of strings
the biotype of the features to count.
Arg [1] : (optional) string $source
the source name of the features to count.
Example : $cnt = $transcript_adaptor->count_all_by_Slice();
Description: Method to count transcripts on a given slice, filtering by biotype and source
Returntype : integer
Exceptions : thrown if exon cannot be placed on transcript slice
Status : Stable
Caller : generalfetch_all_by_biotype
Arg [1] : String $biotype
listref of $biotypes
The biotype of the transcript to retrieve. You can have as an argument a reference
to a list of biotypes
Example : $gene = $transcript_adaptor->fetch_all_by_biotype('protein_coding');
$gene = $transcript_adaptor->fetch_all_by_biotypes(['protein_coding', 'sRNA', 'miRNA']);
Description: Retrieves an array reference of transcript objects from the database via its biotype or biotypes.
The transcript 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 : listref of Bio::EnsEMBL::Transcript
Exceptions : if we cant get the gene in given coord system
Caller : general
Status : Stablebiotype_constraint
Arg [1] : String $biotypes
listref of $biotypes
The biotype of the transcript to retrieve. You can have as an argument a reference
to a list of biotypes
Description: Used internally to generate a SQL constraint to restrict a transcript query by biotype
Returntype : String
Exceptions : If biotype is not supplied
Caller : general
Status : Stablecount_all_by_biotype
Arg [1] : String $biotype
listref of $biotypes
The biotype of the transcript to retrieve. You can have as an argument a reference
to a list of biotypes
Example : $cnt = $transcript_adaptor->count_all_by_biotype('protein_coding');
$cnt = $transcript_adaptor->count_all_by_biotypes(['protein_coding', 'sRNA', 'miRNA']);
Description : Retrieves count of transcript objects from the database via its biotype or biotypes.
Returntype : integer
Caller : general
Status : Stablestore
Arg [1] : Bio::EnsEMBL::Transcript $transcript
The transcript to be written to the database
Arg [2] : Int $gene_dbID
The identifier of the gene that this transcript is associated
with
Arg [3] : DEPRECATED (optional) Int $analysis_id
The analysis_id to use when storing this gene. This is for
backward compatibility only and used to fall back to the gene
analysis_id if no analysis object is attached to the transcript
(which you should do for new code).
Arg [4] : prevent coordinate recalculation if you are persisting
transcripts with this gene
Example : $transID = $tr_adaptor->store($transcript, $gene->dbID);
Description: Stores a transcript in the database and returns the new
internal identifier for the stored transcript.
Returntype : Int
Exceptions : none
Caller : general
Status : Stableget_Interpro_by_transid
Arg [1] : String $trans_stable_id
The stable if of the transcript to obtain
Example : @i = $tr_adaptor->get_Interpro_by_transid($trans->stable_id());
Description: Gets interpro accession numbers by transcript stable id.
A hack really - we should have a much more structured
system than this.
Returntype : listref of strings (Interpro_acc:description)
Exceptions : none
Caller : domainview? , GeneView
Status : Stableis_Transcript_canonical()
Arg [1] : Bio::EnsEMBL::Transcript $transcript
The transcript to query with
Example : $tr_adaptor->is_Transcript_canonical($transcript);
Description : Returns a boolean if the given transcript is considered
canonical with respect to a gene
Returntype : Boolean
Exceptions : None
Caller : Bio::EnsEMBL::Transcript
Status : Betaremove
Arg [1] : Bio::EnsEMBL::Transcript $transcript
The transcript to remove from the database
Arg [2] : Boolean, update Gene coordinates after removal. WARNING: this does not alter any other copies of the
gene currently in memory. Other copies will retain their original coordinates. Either refetch them
or go directly through Gene->remove_Transcript first, then remove the Transcript here.
Example : $tr_adaptor->remove($transcript);
Description: Removes a transcript completely from the database, and all
associated information.
This method is usually called by the GeneAdaptor::remove method
because this method will not preform the removal of genes
which are associated with this transcript. Do not call this
method directly unless you know there are no genes associated
with the transcript!
Returntype : none
Exceptions : throw on incorrect arguments
warning if transcript is not in this database
Caller : GeneAdaptor::remove
Status : Stableupdate
Arg [1] : Bio::EnsEMBL::Transcript $transcript
The transcript to update
Example : $tr_adaptor->update($transcript);
Description: Updates a transcript in the database.
Returntype : None
Exceptions : thrown if the $transcript is not a Bio::EnsEMBL::Transcript.
warn if the method is called on a transcript that does not exist
in the database.
Should warn if trying to update the number of attached exons, but
this is a far more complex process and is not yet implemented.
Caller : general
Status : Stablelist_dbIDs
Example : @transcript_ids = @{ $t_adaptor->list_dbIDs };
Description: Gets a list of internal ids for all transcripts in the db.
Arg[1] : <optional> int. not 0 for the ids to be sorted by the seq_region. Returntype : Listref of Ints
Exceptions : none
Caller : general
Status : Stablelist_stable_ids
Example : @stable_trans_ids = @{ $transcript_adaptor->list_stable_ids };
Description: Gets a list of stable ids for all transcripts in the current
database.
Returntype : Listref of Strings
Exceptions : none
Caller : general
Status : Stablefetch_all_by_exon_supporting_evidence
Arg [1] : String $hit_name
Name of supporting feature
Arg [2] : String $feature_type
one of "dna_align_feature" or "protein_align_feature"
Arg [3] : (optional) Bio::Ensembl::Analysis
Example : $tr = $tr_adaptor->fetch_all_by_exon_supporting_evidence
('XYZ', 'dna_align_feature');
Description: Gets all the transcripts with exons which have a specified hit
on a particular type of feature. Optionally filter by analysis.
Returntype : Listref of Bio::EnsEMBL::Transcript objects
Exceptions : If feature_type is not of correct type.
Caller : general
Status : Stablefetch_all_by_transcript_supporting_evidence
Arg [1] : String $hit_name
Name of supporting feature
Arg [2] : String $feature_type
one of "dna_align_feature" or "protein_align_feature"
Arg [3] : (optional) Bio::Ensembl::Analysis
Example : $transcripts = $transcript_adaptor->fetch_all_by_transcript_supporting_evidence('XYZ', 'dna_align_feature');
Description: Gets all the transcripts with evidence from a specified hit_name on a particular type of feature, stored in the
transcript_supporting_feature table. Optionally filter by analysis. For hits stored in the supporting_feature
table (linked to exons) use fetch_all_by_exon_supporting_evidence instead.
Returntype : Listref of Bio::EnsEMBL::Transcript objects
Exceptions : If feature_type is not of correct type.
Caller : general
Status : Stable