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Bio-EnsEMBL-112.0_52
River stage zero No dependents
/ Bio::EnsEMBL::DBSQL::OperonTranscriptAdaptor

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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  Questions may also be sent to the Ensembl help desk at
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NAME

Bio::EnsEMBL::DBSQL::OperonAdaptor - Database adaptor for the retrieval and storage of OperonTranscript objects

SYNOPSIS

my $operon_transcript_adaptor = Bio::EnsEMBL::DBSQL::OperonTranscriptAdaptor->new($dba); $operon_transcript_adaptor->store($operon_transcript); my $operon_transcript2 = $operon_transcript_adaptor->fetch_by_dbID( $operon->dbID() ); my $operon_transcripts = $operon_transcript_adaptor->fetch_all_by_gene( $gene );

DESCRIPTION

This is a database aware adaptor for the retrieval and storage of operon transcript objects.

METHODS

list_dbIDs

  Example    : @ot_ids = @{$ot_adaptor->list_dbIDs()};
  Description: Gets an array of internal ids for all operon_transcripts in the current 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     : Stable

list_stable_ids

  Example    : @stable_ot_ids = @{$ot_adaptor->list_stable_ids()};
  Description: Gets an listref of stable ids for all operon_transcripts in the current db
  Returntype : reference to a list of strings
  Exceptions : none
  Caller     : general
  Status     : Stable

fetch_by_stable_id

  Arg [1]    : String $id 
               The stable ID of the operon_transcript to retrieve
  Example    : $operon_transcript = $operon_transcript_adaptor->fetch_by_stable_id('T16152-16153-4840');
  Description: Retrieves a operon_transcript object from the database via its stable id.
               The operon_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 operon_transcript is not found
               undef is returned instead.
  Returntype : Bio::EnsEMBL::OperonTranscript or undef
  Exceptions : if we cant get the operon_transcript in given coord system
  Caller     : general
  Status     : Stable

fetch_by_stable_id_version

  Arg [1]    : String $id 
               The stable ID of the operon_transcript to retrieve
  Arg [2]    : Integer $version
               The version of the stable_id to retrieve
  Example    : $operon_transcript = $operon_transcript_adaptor->fetch_by_stable_id('T16152-16153-4840', 2);
  Description: Retrieves an operon_transcript object from the database via its stable id and version.
               The operon_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 operon_transcript is not found
               undef is returned instead.
  Returntype : Bio::EnsEMBL::OperonTranscript or undef
  Exceptions : if we cant get the operon_transcript in given coord system
  Caller     : general
  Status     : Stable

fetch_by_name

  Arg [1]    : String $label - name of operon transcript to fetch
  Example    : my $operon_transcript = $operonAdaptor->fetch_by_name("ECK0012121342");
  Description: Returns the operon 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::OperonTranscript
  Exceptions : none
  Caller     : general
  Status     : Stable

fetch_all

  Example     : $operon_transcripts = $operon_adaptor->fetch_all();
  Description : Retrieves all operon transcripts stored in the database.
  Returntype  : listref of Bio::EnsEMBL::OperonTranscript
  Caller      : general
  Status      : At Risk

fetch_all_versions_by_stable_id

  Arg [1]     : String $stable_id 
                The stable ID of the operon_transcript to retrieve
  Example     : $operon_transcript = $operon_transcript_adaptor->fetch_all_versions_by_stable_id
                  ('ENSG00000148944');
  Description : Similar to fetch_by_stable_id, but retrieves all versions of a
                operon_transcript stored in the database.
  Returntype  : listref of Bio::EnsEMBL::OperonTranscript
  Exceptions  : if we cant get the operon_transcript in given coord system
  Caller      : general
  Status      : At Risk

fetch_all_by_Slice

  Arg [1]    : Bio::EnsEMBL::Slice $slice
               The slice to fetch operon_transcripts on.
  Arg [2]    : (optional) string $logic_name
               the logic name of the type of features to obtain
  Arg [3]    : (optional) boolean $load_transcripts
               if true, transcripts will be loaded immediately rather than
               lazy loaded later.
  Arg [4]    : (optional) string $source
               the source name of the features to obtain.
  Arg [5]    : (optional) string biotype
                the biotype of the features to obtain.
  Example    : @operon_transcripts = @{$operon_transcript_adaptor->fetch_all_by_Slice()};
  Description: Overrides superclass method to optionally load transcripts
               immediately rather than lazy-loading them later.  This
               is more efficient when there are a lot of operon_transcripts whose
               transcripts are going to be used.
  Returntype : reference to list of operon_transcripts 
  Exceptions : thrown if exon cannot be placed on transcript slice
  Caller     : Slice::get_all_OperonTranscripts
  Status     : Stable

fetch_by_Operon

  Arg [1]    : Bio::EnsEMBL::Operon
  Example    : $ot = $ot_adaptor->fetch_by_Operon($operon);
  Description: Retrieves all operon transcripts belonging to an operon
  Returntype : arrayref of Bio::EnsEMBL::OperonTranscript
  Exceptions : none
  Caller     : general
  Status     : Stable

fetch_by_operon_id

  Arg [1]    : Int id
  Example    : $ot = $ot_adaptor->fetch_by_operon_transcript($operon);
  Description: Retrieves all operon transcripts belonging to an operon
  Returntype : arrayref of Bio::EnsEMBL::OperonTranscript
  Exceptions : none
  Caller     : general
  Status     : Stable

fetch_genes_by_operon_transcript

  Arg [1]    : Bio::EnsEMBL::OperonTranscript
  Example    : $ot = $ot_adaptor->fetch_genes_by_operon_transcript($operon_transcript);
  Description: Retrieves all genes attached to an operon transcript
  Returntype : arrayref of Bio::EnsEMBL::Gene
  Exceptions : none
  Caller     : general
  Status     : Stable

fetch_genes_by_operon_transcript_id

  Arg [1]    : Int id
  Example    : $ot = $ot_adaptor->fetch_genes_by_operon_transcript($operon_transcript_id);
  Description: Retrieves all genes attached to an operon transcript
  Returntype : arrayref of Bio::EnsEMBL::Gene
  Exceptions : none
  Caller     : general
  Status     : Stable

fetch_all_by_gene

  Arg [1]    : Bio::EnsEMBL::Gene
  Example    : $ots = $ot_adaptor->fetch_all_by_gene($gene);
  Description: Retrieves all operon transcripts attached to a given gene
  Returntype : arrayref of Bio::EnsEMBL::OperonTranscript
  Exceptions : none
  Caller     : general
  Status     : Stable

fetch_all_by_gene_id

  Arg [1]    : Int id of Bio::EnsEMBL::Gene
  Example    : $ots = $ot_adaptor->fetch_all_by_gene($gene);
  Description: Retrieves all operon transcripts attached to a given gene
  Returntype : arrayref of Bio::EnsEMBL::OperonTranscript
  Exceptions : none
  Caller     : general
  Status     : Stable

store

  Arg [1]    : Bio::EnsEMBL::OperonTranscript $gene
               The gene to store in the database
  Arg [2]    : ignore_release in xrefs [default 1] set to 0 to use release info 
               in external database references
  Example    : $gene_adaptor->store($gene);
  Description: Stores a gene in the database.
  Returntype : the database identifier (dbID) of the newly stored gene
  Exceptions : thrown if the $gene is not a Bio::EnsEMBL::OperonTranscript or if 
               $gene does not have an analysis object
  Caller     : general
  Status     : Stable

store_genes_on_OperonTranscript

  Arg [1]    : Bio::EnsEMBL::OperonTranscript $ot
               the operon_transcript to store genes on
  Arg [2]    : arrayref of Bio::EnsEMBL::Gene $gene
               the genes to store on operon transcript
  Example    : $ot_adaptor->store_genes_on_OperonTranscript(\@genes);
  Description: Associates genes with operon transcript
  Returntype : none
  Exceptions : throw on incorrect arguments 
               warning if operon_transcript is not stored in this database
  Caller     : general, store
  Status     : Stable

remove

  Arg [1]    : Bio::EnsEMBL::OperonTranscript $ot
               the operon_transcript to remove from the database
  Example    : $ot_adaptor->remove($ot);
  Description: Removes a operon transcript completely from the database.
  Returntype : none
  Exceptions : throw on incorrect arguments 
               warning if operon_transcript is not stored in this database
  Caller     : general
  Status     : Stable