LICENSE

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

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NAME

Bio::EnsEMBL::DBSQL::PredictionTranscriptAdaptor - Performs database interaction related to PredictionTranscripts

SYNOPSIS

# get a prediction transcript adaptor from the database
$pta = $database_adaptor->get_PredictionTranscriptAdaptor();

# get a slice on a region of chromosome 1
$sa = $database_adaptor->get_SliceAdaptor();

$slice = $sa->fetch_by_region( 'chromosome', 'x', 100000, 200000 );

# get all the prediction transcripts from the slice region
$prediction_transcripts = @{ $pta->fetch_all_by_Slice($slice) };

METHODS

fetch_by_stable_id

Arg [1]    : string $stable_id
             The stable id of the transcript to retrieve
Example    : $trans = $trans_adptr->fetch_by_stable_id('GENSCAN00000001234');
Description: Retrieves a prediction transcript via its display_label.
             This method is called fetch_by_stable_id for polymorphism with
             the TranscriptAdaptor.  Prediction transcript display_labels are
             not necessarily stable in that the same identifier may be reused
             for a completely different prediction transcript in a subsequent
             database release.
Returntype : Bio::EnsEMBL::PredictionTranscript
Caller     : general
Status     : Stable

fetch_all_by_Slice

Arg [1]    : Bio::EnsEMBL::Slice $slice
             The slice to fetch transcripts on.
Arg [3]    : (optional) boolean $load_exons
             if true, exons will be loaded immediately rather than
             lazy loaded later.
Example    : $transcripts = $
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 : reference to list of transcripts
Exceptions : thrown if exon cannot be placed on transcript slice
Caller     : Slice::get_all_Transcripts
Status     : Stable

fetch_by_prediction_exon_id

Arg [1]    : Int $prediction_exon_id
             Unique database identifier for the prediction exon
             whose prediction transcript should be retrieved.
Example    : $prediction_transcript = $prediction_transcript_adaptor->fetch_by_exon_id(1241);
Description: Retrieves a prediction transcript from the database via the database identifier
             of one of its exons.
Returntype : Bio::EnsEMBL::PredictionTranscript
Exceptions : none
Caller     : general
Status     : Stable

_objs_from_sth

Arg [1]    : DBI:st $sth 
             An executed DBI statement handle
Arg [2]    : (optional) Bio::EnsEMBL::Mapper $mapper 
             An mapper to be used to convert contig coordinates
             to assembly coordinates.
Arg [3]    : (optional) Bio::EnsEMBL::Slice $slice
             A slice to map the prediction transcript to.   
Example    : $p_transcripts = $self->_objs_from_sth($sth);
Description: Creates a list of Prediction transcripts from an executed DBI
             statement handle.  The columns retrieved via the statement 
             handle must be in the same order as the columns defined by the
             _columns method.  If the slice argument is provided then the
             the prediction transcripts will be in returned in the coordinate
             system of the $slice argument.  Otherwise the prediction 
             transcripts will be returned in the RawContig coordinate system.
Returntype : reference to a list of Bio::EnsEMBL::PredictionTranscripts
Exceptions : none
Caller     : superclass generic_fetch
Status     : Stable

store

Arg [1]    : list of Bio::EnsEMBL::PredictionTranscript @pre_transcripts 
Example    : $prediction_transcript_adaptor->store(@pre_transcripts);
Description: Stores a list of given prediction transcripts in database. 
             Puts dbID and Adaptor into each object stored object.
Returntype : none
Exceptions : on wrong argument type 
Caller     : general 
Status     : Stable

remove

Arg [1]    : Bio::EnsEMBL::PredictionTranscript $pt 
Example    : $prediction_transcript_adaptor->remove($pt);
Description: removes given prediction transcript $pt from database. 
Returntype : none
Exceptions : throws if argument not a  Bio::EnsEMBL::PredictionTranscript
Caller     : general
Status     : Stable

list_dbIDs

Arg [1]    : none
Example    : @feature_ids = @{$prediction_transcript_adaptor->list_dbIDs()};
Description: Gets an array of internal ids for all prediction transcript
             features in the current db
Arg[1]     : <optional> int. not 0 for the ids to be sorted by the seq_region.
Returntype : list of ints
Exceptions : none
Caller     : ?
Status     : Stable