sub cdna_coding_start { my $self = shift; if( @_ ) { $self->{'cdna_coding_start'} = shift; } if(!defined $self->{'cdna_coding_start'} && defined $self->translation){ # calc coding start relative from the start of translation (in cdna coords) my $start = 0; my @exons = @{$self->get_all_Exons}; my $exon; while($exon = shift @exons) { if($exon == $self->translation->start_Exon) { #add the utr portion of the start exon $start += $self->translation->start; last; } else { #add the entire length of this non-coding exon $start += $exon->length; } } # adjust cdna coords if sequence edits are enabled if($self->edits_enabled()) { my @seqeds = @{$self->get_all_SeqEdits()}; # sort in reverse order to avoid adjustment of downstream edits @seqeds = sort {$b->start() <=> $a->start()} @seqeds; foreach my $se (@seqeds) { # use less than start so that start of CDS can be extended if($se->start() < $start) { $start += $se->length_diff(); } } } $self->{'cdna_coding_start'} = $start; } return $self->{'cdna_coding_start'}; }

Class Summary
Synopsis
Creation: my $tran = new Bio::EnsEMBL::Transcript(); my $tran = new Bio::EnsEMBL::Transcript( -EXONS =\> \@exons ); Manipulation: # Returns an array of Exon objects my @exons = @{ $tran-\>get_all_Exons() }; # Returns the peptide translation of the exons as a Bio::Seq if ( $tran-\>translation() ) { my $pep = $tran-\>translate(); } else { print "Transcript ", $tran-\>stable_id(), " is non-coding\n"; }
Description
A representation of a transcript within the Ensembl system. A transcript consists of a set of Exons and (possibly) a Translation which defines the coding and non-coding regions of the exons.
Definition at line 39 of file Transcript.pm.
Method Documentation
protected Bio::EnsEMBL::Transcript::_compare_xrefs | ( | ) |
Description: compare xrefs based on priority (descending), then name (ascending), then display_label (ascending)

protected Bio::EnsEMBL::Feature::_deprecated_transform | ( | ) | [inherited] |
Undocumented method

protected Bio::EnsEMBL::Transcript::_translation_id | ( | ) |
Undocumented method

public Bio::EnsEMBL::DBSQL::BaseAdaptor Bio::EnsEMBL::Storable::adaptor | ( | ) | [inherited] |
Arg [1] : Bio::EnsEMBL::DBSQL::BaseAdaptor $adaptor Example : none Description: get/set for this objects Adaptor Returntype : Bio::EnsEMBL::DBSQL::BaseAdaptor Exceptions : none Caller : general, set from adaptor on store Status : Stable

public void Bio::EnsEMBL::Transcript::add_alternative_translation | ( | ) |
Args : Bio::EnsEMBL::Translation $translation Example :
$transcript->add_alternative_translation($translation);
Description: Adds an alternative translation to this transcript. Returntype : None Exceptions : None Caller : General Status : Stable

public void Bio::EnsEMBL::Transcript::add_Attributes | ( | ) |
Arg [1...] : Bio::EnsEMBL::Attribute $attribute You can have more Attributes as arguments, all will be added. Example : $transcript->add_Attributes($rna_edit_attribute); Description: Adds an Attribute to the Transcript. Usefull to do _rna_edits. If you add an attribute before you retrieve any from database, lazy load will be disabled. Returntype : none Exceptions : throw on incorrect arguments Caller : general Status : Stable

public void Bio::EnsEMBL::Transcript::add_DBEntry | ( | ) |
Arg [1] : Bio::EnsEMBL::DBEntry $dbe The dbEntry to be added Example : my $dbe = Bio::EnsEMBL::DBEntery->new(...); $transcript->add_DBEntry($dbe); Description: Associates a DBEntry with this transcript. Note that adding DBEntries will prevent future lazy-loading of DBEntries for this gene (see get_all_DBEntries). Returntype : none Exceptions : thrown on incorrect argument type Caller : general Status : Stable

Reimplemented in Bio::EnsEMBL::PredictionTranscript.
public void Bio::EnsEMBL::Transcript::add_Exon | ( | ) |
Title : add_Exon Usage : $trans->add_Exon($exon) Returns : None Args [1]: Bio::EnsEMBL::Exon object to add Args [2]: rank Exceptions: throws if not a valid Bio::EnsEMBL::Exon : or exon clashes with another one Status : Stable

public Bio::EnsEMBL::Feature::add_sub_SeqFeature | ( | ) | [inherited] |
Undocumented method

public void Bio::EnsEMBL::Transcript::add_supporting_features | ( | ) |
Arg [1-N] : Bio::EnsEMBL::FeaturePair $feature The supporting features to add Example : $transcript->add_supporting_features(@features); Description: Adds a list of supporting features to this Transcript. The added features can be retieved by get_all_supporting_features(). Returntype : none Exceptions : throw if any of the features are not FeaturePairs throw if any of the features are not in the same coordinate system as the Transcript Caller : general Status : Stable

public Bio::EnsEMBL::Analysis Bio::EnsEMBL::Feature::analysis | ( | ) | [inherited] |
Arg [1] : (optional) Bio::EnsEMBL::Analysis $analysis Example : $feature->analysis(new Bio::EnsEMBL::Analysis(...)) Description: Getter/Setter for the analysis that is associated with this feature. The analysis describes how this feature was derived. Returntype : Bio::EnsEMBL::Analysis Exceptions : thrown if an invalid argument is passed Caller : general Status : Stable

Reimplemented in Bio::EnsEMBL::DensityFeature.
public String Bio::EnsEMBL::Transcript::biotype | ( | ) |
Arg [1] : string $biotype Example : none Description: get/set for attribute biotype Returntype : string Exceptions : none Caller : general Status : Stable

public Bio::EnsEMBL::Transcript::cdna2genomic | ( | ) |
public Int Bio::EnsEMBL::Transcript::cdna_coding_end | ( | ) |
Arg [1] : (optional) $value Example : $cdna_coding_end = $transcript->cdna_coding_end; Description: Retrieves the end of the coding region of this transcript in cdna coordinates (relative to the five prime end of the transcript, excluding introns, including utrs).
This will return undef if this transcript is a pseudogene (i.e. a transcript with no translation and therefor no CDS). Returntype : int Exceptions : none Caller : general Status : Stable

Reimplemented in Bio::EnsEMBL::PredictionTranscript.
public Int Bio::EnsEMBL::Transcript::cdna_coding_start | ( | ) |
Arg [1] : (optional) $value Example : $relative_coding_start = $transcript->cdna_coding_start; Description: Retrieves the position of the coding start of this transcript in cdna coordinates (relative to the start of the 5prime end of the transcript, excluding introns, including utrs).
This will return undef if this is a pseudogene (i.e. a transcript with no translation). Returntype : int Exceptions : none Caller : five_prime_utr, get_all_snps, general Status : Stable

Reimplemented in Bio::EnsEMBL::PredictionTranscript.
public Int Bio::EnsEMBL::Transcript::coding_region_end | ( | ) |
Arg [1] : (optional) $value Example : $coding_region_end = $transcript->coding_region_end Description: Retrieves the end of the coding region of this transcript in genomic coordinates (i.e. in either slice or contig coords). By convention, the coding_region_end is always higher than the value returned by the coding_region_start method. The value returned by this function is NOT the biological coding end since on the reverse strand the biological coding end would be the lower genomic value.
This function will return undef if this is a pseudogene (a non-translated transcript). Returntype : int Exceptions : none Caller : general Status : Stable

Reimplemented in Bio::EnsEMBL::PredictionTranscript.
public Int Bio::EnsEMBL::Transcript::coding_region_start | ( | ) |
Arg [1] : (optional) $value Example : $coding_region_start = $transcript->coding_region_start Description: Retrieves the start of the coding region of this transcript in genomic coordinates (i.e. in either slice or contig coords). By convention, the coding_region_start is always lower than the value returned by the coding_end method. The value returned by this function is NOT the biological coding start since on the reverse strand the biological coding start would be the higher genomic value.
This function will return undef if this is a pseudogene (a non-translated transcript). Returntype : int Exceptions : none Caller : general Status : Stable

Reimplemented in Bio::EnsEMBL::PredictionTranscript.
public Bio::EnsEMBL::Transcript::confidence | ( | ) |
public Bio::EnsEMBL::Feature::contig | ( | ) | [inherited] |
Undocumented method

public String Bio::EnsEMBL::Feature::coord_system_name | ( | ) | [inherited] |
Arg [1] : none Example : print $feature->coord_system_name() Description: Gets the name of the coord_system which this feature is on. Returns undef if this Feature is not on a slice. Returntype : string or undef Exceptions : none Caller : general Status : Stable

public Bio::EnsEMBL::Transcript::created | ( | ) |
public String Bio::EnsEMBL::Transcript::created_date | ( | ) |
Arg [1] : (optional) string to be used for the created date Example : none Description: get/set for attribute created date Returntype : string Exceptions : none Caller : general Status : Stable

public Int Bio::EnsEMBL::Storable::dbID | ( | ) | [inherited] |
Arg [1] : int $dbID Example : none Description: getter/setter for the database internal id Returntype : int Exceptions : none Caller : general, set from adaptor on store Status : Stable

Reimplemented in Bio::EnsEMBL::Map::Ditag, and Bio::EnsEMBL::Map::DitagFeature.
public String Bio::EnsEMBL::Transcript::description | ( | ) |
Title : description Usage : $obj->description($newval) Function: Returns : String Args : newvalue (optional) Status : Stable

public String Bio::EnsEMBL::Transcript::display_id | ( | ) |
Arg [1] : none Example : print $transcript->display_id(); Description: This method returns a string that is considered to be the 'display' identifier. For transcripts this is (depending on availability and in this order) the stable Id, the dbID or an empty string. Returntype : string Exceptions : none Caller : web drawing code Status : Stable

Reimplemented from Bio::EnsEMBL::Feature.
Reimplemented in Bio::EnsEMBL::PredictionTranscript.
public Bio::EnsEMBL::DBEntry Bio::EnsEMBL::Transcript::display_xref | ( | ) |
Arg [1] : (optional) Bio::EnsEMBL::DBEntry - the display xref to set Example : $transcript->display_xref($db_entry); Description: Getter/setter for display_xref for this transcript. Returntype : Bio::EnsEMBL::DBEntry Exceptions : none Caller : general Status : Stable

public Boolean Bio::EnsEMBL::Transcript::edits_enabled | ( | ) |
Arg [1] : (optional) boolean $newval Example : $transcript->edits_enabled(1); Description: Enables/Disables the application of SeqEdits to this transcript. Edits are enabled by default, and affect the cdna/mrna sequences coordinates and the resultant translation. Returntype : boolean - the current value of the edits Exceptions : none Caller : general, cdna_coding_start, cdna_coding_end, length Status : Stable

public Int Bio::EnsEMBL::Feature::end | ( | ) | [inherited] |
Arg [1] : (optional) int $end Example : $end = $feat->end(); Description: Getter/Setter for the end of this feature relative to the start of the slice that it is on. Note that negative values, of values exceeding the length of the slice are permitted. End must be greater than or equal to start regardless of the strand. Coordinate values start at 1 and are inclusive. Returntype : int Exceptions : none Caller : general Status : Stable

Reimplemented in Bio::EnsEMBL::Exon, Bio::EnsEMBL::Map::DitagFeature, Bio::EnsEMBL::SplicingEventFeature, and Bio::EnsEMBL::SplicingTranscriptPair.
public Bio::EnsEMBL::Exon Bio::EnsEMBL::Transcript::end_Exon | ( | ) |
Title : end_exon Usage : $end_exon = $transcript->end_Exon; Description : The last exon in the transcript. Returntype : Bio::EnsEMBL::Exon Args : NONE Status : Stable

public Boolean Bio::EnsEMBL::Transcript::equals | ( | ) |
Arg [1] : Bio::EnsEMBL::Transcript transcript Example : if ($transcriptA->equals($transcriptB)) { ... } Description : Compares two transcripts for equality. The test for eqality goes through the following list and terminates at the first true match:
1. If Bio::EnsEMBL::Feature::equals() returns false, then the transcripts are *not* equal. 2. If the biotypes differ, then the transcripts are not* equal. 3. If both transcripts have stable IDs: if these are the same, the transcripts are equal, otherwise not. 4. If both transcripts have the same number of exons and if these are (when compared pair-wise sorted by start-position and length) the same, then they are equal, otherwise not.
Return type : Boolean (0, 1)
Exceptions : Thrown if a non-transcript is passed as the argument.

Reimplemented from Bio::EnsEMBL::Feature.
public String Bio::EnsEMBL::Transcript::external_db | ( | ) |
Arg [1] : (optional) String - name of external db to set Example : $transcript->external_db('HGNC'); Description: Getter/setter for attribute external_db. The db is the one that belongs to the external_name. Returntype : String Exceptions : none Caller : general Status : Stable

Reimplemented in Bio::EnsEMBL::PredictionTranscript.
public String Bio::EnsEMBL::Transcript::external_name | ( | ) |
Arg [1] : (optional) String - the external name to set Example : $transcript->external_name('BRCA2-001'); Description: Getter/setter for attribute external_name. Returntype : String or undef Exceptions : none Caller : general Status : Stable

Reimplemented in Bio::EnsEMBL::PredictionTranscript.
public String Bio::EnsEMBL::Transcript::external_status | ( | ) |
Arg [1] : (optional) String - status of the external db Example : $transcript->external_status('KNOWNXREF'); Description: Getter/setter for attribute external_status. The status of the external db of the one that belongs to the external_name. Returntype : String Exceptions : none Caller : general Status : Stable

Reimplemented in Bio::EnsEMBL::PredictionTranscript.
public Bio::EnsEMBL::Slice Bio::EnsEMBL::Feature::feature_Slice | ( | ) | [inherited] |
Args : none Example : $slice = $feature->feature_Slice() Description: This is a convenience method to return a slice that covers the Area of this feature. The feature start will be at 1 on it, and it will have the length of this feature. Returntype : Bio::EnsEMBL::Slice or undef if this feature has no attached Slice. Exceptions : warning if Feature does not have attached slice. Caller : web drawing code Status : Stable

public Bio::Seq Bio::EnsEMBL::Transcript::five_prime_utr | ( | ) |
Arg [1] : none Example : my $five_prime = $transcrpt->five_prime_utr or warn "No five prime UTR"; Description: Obtains a Bio::Seq object of the five prime UTR of this transcript. If this transcript is a pseudogene (i.e. non-translating) or has no five prime UTR undef is returned instead. Returntype : Bio::Seq or undef Exceptions : none Caller : general Status : Stable

public void Bio::EnsEMBL::Transcript::flush_Exons | ( | ) |
Arg [1] : none Example : $transcript->flush_Exons(); Description: Removes all Exons from this transcript and flushes related internal caches. Returntype : none Exceptions : none Caller : general Status : Stable

public Bio::EnsEMBL::Feature::flush_sub_SeqFeature | ( | ) | [inherited] |
Undocumented method

public Bio::EnsEMBL::Transcript::flush_supporting_features | ( | ) |
Example : $transcript->flush_supporting_features; Description : Removes all supporting evidence from the transcript. Return type : (Empty) listref Exceptions : none Caller : general Status : Stable

public Bio::EnsEMBL::Transcript::genomic2cdna | ( | ) |
public Bio::EnsEMBL::Transcript::genomic2pep | ( | ) |
public Reference Bio::EnsEMBL::Feature::get_all_alt_locations | ( | ) | [inherited] |
Arg [1] : none Example : @features = @{$feature->get_all_alt_locations()}; foreach $f (@features) { print $f->slice->seq_region_name,' ',$f->start, $f->end,"\\n"; }
Description: Retrieves shallow copies of this feature in its alternate locations. A feature can be considered to have multiple locations when it sits on a alternative structural haplotype or when it is on a pseudo autosomal region. Most features will just return a reference to an empty list though. The features returned by this method will be on a slice which covers the entire alternate region.
Currently this method does not take into account alternate locations on the alternate locations (e.g. a reference sequence may have multiple alternate haplotypes. Asking for alternate locations of a feature on one of the alternate haplotypes will give you back the reference location, but not locations on the other alternate haplotypes).
Returntype : reference to list of features of the same type of this feature. Exceptions : none Caller : general Status : Stable

public Arrayref Bio::EnsEMBL::Transcript::get_all_alternative_translations | ( | ) |
Args : None Example :
my @alt_translations = @{ $transcript->get_all_alternative_translations() };
Description: Fetches all alternative translations defined for this transcript. The canonical translation is not returned.
Returntype : Arrayref to Bio::EnsEMBL::Translation Exceptions : None Caller : General Status : Stable

public Listref Bio::EnsEMBL::Transcript::get_all_Attributes | ( | ) |
Arg [1] : optional string $attrib_code The code of the attribute type to retrieve values for. Example : ($rna_edits) = @{$transcript->get_all_Attributes('_rna_edit')}; @transc_attributes = @{$transcript->get_all_Attributes()}; Description: Gets a list of Attributes of this transcript. Optionally just get Attrubutes for given code. Returntype : listref Bio::EnsEMBL::Attribute Exceptions : warning if transcript does not have attached adaptor and attempts lazy load. Caller : general Status : Stable

Reimplemented in Bio::EnsEMBL::PredictionTranscript.
public Bio::EnsEMBL::Transcript::get_all_cdna_SNPs | ( | ) |
Description: See Bio::EnsEMBL::Utils::TranscriptSNPs::get_all_cdna_SNPs
Status : At Risk : Will be replaced with modules from the ensembl-variation package

public Listref Bio::EnsEMBL::Transcript::get_all_constitutive_Exons | ( | ) |
Arg : None
Examples : my @exons = @{ $transcript->get_all_constitutive_Exons() };
Description: Returns an listref of the constitutive exons in this transcript in order, i.e. the first exon in the listref is the 5prime most exon in the transcript.
Returntype : listref to Bio::EnsEMBL::Exon objects Exceptions : none Caller : general Status : Stable

public Hashref Bio::EnsEMBL::Transcript::get_all_DAS_Features | ( | ) |
Arg [1] : none Example : $features = $prot->get_all_DAS_Features; Description: Retreives a hash reference to a hash of DAS feature sets, keyed by the DNS, NOTE the values of this hash are an anonymous array containing: (1) a pointer to an array of features; (2) a pointer to the DAS stylesheet Returntype : hashref of Bio::SeqFeatures Exceptions : ? Caller : webcode Status : Stable

Reimplemented from Bio::EnsEMBL::Storable.
public Bio::EnsEMBL::Transcript::get_all_DASFactories | ( | ) |
Arg [1] : none Function : Retrieves a listref of registered DAS objects Returntype: [ DAS_objects ] Exceptions: Caller : Example : $dasref = $prot->get_all_DASFactories Status : Stable

public Listref Bio::EnsEMBL::Transcript::get_all_DBEntries | ( | ) |
Arg [1] : (optional) String, external database name
Arg [2] : (optional) String, external database type
Example : my @dbentries = @{ $transcript->get_all_DBEntries() };
Description: Retrieves DBEntries (xrefs) for this transcript. This does *not* include the corresponding translations DBEntries (see get_all_DBLinks()).
This method will attempt to lazy-load DBEntries from a database if an adaptor is available and no DBEntries are present on the transcript (i.e. they have not already been added or loaded).
Returntype : Listref of Bio::EnsEMBL::DBEntry objects Exceptions : none Caller : get_all_DBLinks, TranscriptAdaptor::store Status : Stable

Reimplemented in Bio::EnsEMBL::PredictionTranscript.
public Listref Bio::EnsEMBL::Transcript::get_all_DBLinks | ( | ) |
Arg [1] : String database name (optional) SQL wildcard characters (_ and %) can be used to specify patterns.
Example : my @dblinks = @{ $transcript->get_all_DBLinks() }; my @dblinks = @{ $transcript->get_all_DBLinks('Uniprot%') };
Description: Retrieves *all* related DBEntries for this transcript. This includes all DBEntries that are associated with the corresponding translation.
If you only want to retrieve the DBEntries associated with the transcript (and not the translation) then you should use the get_all_DBEntries() call instead.
Note: Each entry may be listed more than once. No uniqueness checks are done. Also if you put in an incorrect external database name no checks are done to see if this exists, you will just get an empty list.
Return type: Listref of Bio::EnsEMBL::DBEntry objects Exceptions : none Caller : general Status : Stable

Reimplemented in Bio::EnsEMBL::PredictionTranscript.
public Listref Bio::EnsEMBL::Transcript::get_all_Exons | ( | ) |
Arg [CONSTITUTIVE] : Boolean Only return constitutive exons if true (non-zero)
Examples : my @exons = @{ $transcript->get_all_Exons() };
my @exons = @{ $transcript->get_all_Exons( -constitutive => 1 ) };
Description: Returns an listref of the exons in this transcript in order, i.e. the first exon in the listref is the 5prime most exon in the transcript. Only returns constitutive exons if the CONSTITUTIVE argument is true.
Returntype : listref to Bio::EnsEMBL::Exon objects Exceptions : none Caller : general Status : Stable

Reimplemented in Bio::EnsEMBL::PredictionTranscript.
public Listref Bio::EnsEMBL::Transcript::get_all_Introns | ( | ) |
Arg [1] : none Example : my @introns = @{$transcript->get_all_Introns()}; Description: Returns an listref of the introns in this transcript in order. i.e. the first intron in the listref is the 5prime most exon in the transcript. Returntype : listref to Bio::EnsEMBL::Intron objects Exceptions : none Caller : general Status : Stable

public Listref Bio::EnsEMBL::Transcript::get_all_object_xrefs | ( | ) |
Arg [1] : (optional) String, external database name
Arg [2] : (optional) String, external_db type
Example : @oxrefs = @{ $transcript->get_all_object_xrefs() };
Description: Retrieves xrefs for this transcript. This does not* include xrefs that are associated with the corresponding translations of this transcript (see get_all_xrefs()).
This method will attempt to lazy-load xrefs from a database if an adaptor is available and no xrefs are present on the transcript (i.e. they have not already been added or loaded).
NB: This method is an alias for the get_all_DBentries() method.
Return type: Listref of Bio::EnsEMBL::DBEntry objects
Status : Stable

public Bio::EnsEMBL::Transcript::get_all_peptide_variations | ( | ) |
Description: See Bio::EnsEMBL::Utils::TranscriptSNPs::get_all_peptide_variations Status : At Risk : Will be replaced with modules from the ensembl-variation package

public Bio::EnsEMBL::SeqEdit Bio::EnsEMBL::Transcript::get_all_SeqEdits | ( | ) |
Arg [1] : none Example : my @seqeds = @{$transcript->get_all_SeqEdits()}; Description: Retrieves all post transcriptional sequence modifications for this transcript. Returntype : Bio::EnsEMBL::SeqEdit Exceptions : none Caller : spliced_seq() Status : Stable

public Bio::EnsEMBL::Transcript::get_all_SNPs | ( | ) |
Description: See Bio::EnsEMBL::Utils::TranscriptSNPs::get_all_SNPs
Status : At Risk : Will be replaced with modules from the ensembl-variation package

public Listref Bio::EnsEMBL::Transcript::get_all_supporting_features | ( | ) |
Example : my @evidence = @{ $transcript->get_all_supporting_features }; Description: Retreives any supporting features added manually by calls to add_supporting_features. Returntype : Listref of Bio::EnsEMBL::FeaturePair objects Exceptions : none Caller : general Status : Stable

public Listref Bio::EnsEMBL::Transcript::get_all_translateable_Exons | ( | ) |
Args : none Example : none Description: Returns a list of exons that translate with the start and end exons truncated to the CDS regions. This function does not take into account any SeqEdits (post transcriptional RNA modifictions) when constructing the the 'translateable' exons, and it does not update the phase information of the created 'translateable' exons.
If this transcript is a pseudogene (i.e. non-translateable) a reference to an empty list is returned.
Returntype : listref Bio::EnsEMBL::Exon Exceptions : throw if translation has invalid information Caller : Genebuild Status : Stable

Reimplemented in Bio::EnsEMBL::PredictionTranscript.
public Listref Bio::EnsEMBL::Transcript::get_all_xrefs | ( | ) |
Arg [1] : String database name (optional) SQL wildcard characters (_ and %) can be used to specify patterns.
Example : @xrefs = @{ $transcript->get_all_xrefs() }; @xrefs = @{ $transcript->get_all_xrefs('Uniprot%') };
Description: Retrieves *all* related xrefs for this transcript. This includes all xrefs that are associated with the corresponding translation of this transcript.
If you want to retrieve the xrefs associated with only the transcript (and not the translation) then you should use the get_all_object_xrefs() method instead.
Note: Each entry may be listed more than once. No uniqueness checks are done. Also if you put in an incorrect external database name no checks are done to see if this exists, you will just get an empty list.
NB: This method is an alias for the get_all_DBLinks() method.
Return type: Listref of Bio::EnsEMBL::DBEntry objects
Status : Stable

public Bio::EnsEMBL::Gene Bio::EnsEMBL::Transcript::get_Gene | ( | ) |
Example : $gene = $transcript->get_Gene; Description : Locates the parent Gene using a transcript dbID Returns : Bio::EnsEMBL::Gene

public Bio::EnsEMBL::Gene Bio::EnsEMBL::Feature::get_nearest_Gene | ( | ) | [inherited] |
Description: Get all the nearest gene to the feature Returntype : Bio::EnsEMBL::Gene Caller : general Status : UnStable

public List Bio::EnsEMBL::Feature::get_overlapping_Genes | ( | ) | [inherited] |
Description: Get all the genes that overlap this feature. Returntype : list ref of Bio::EnsEMBL::Gene Caller : general Status : UnStable

public Bio::EnsEMBL::TranscriptMapper Bio::EnsEMBL::Transcript::get_TranscriptMapper | ( | ) |
Args : none Example : my $trans_mapper = $transcript->get_TranscriptMapper(); Description: Gets a TranscriptMapper object which can be used to perform a variety of coordinate conversions relating this transcript, genomic sequence and peptide resulting from this transcripts translation. Returntype : Bio::EnsEMBL::TranscriptMapper Exceptions : none Caller : cdna2genomic, pep2genomic, genomic2cdna, cdna2genomic Status : Stable

public Bio::EnsEMBL::Feature::id | ( | ) | [inherited] |
Undocumented method

public Boolean Bio::EnsEMBL::Transcript::is_canonical | ( | ) |
Args [1] : (optional) Boolean is_canonical
Example : if ($transcript->is_canonical()) { ... }
Description : Returns true (non-zero) if the transcript is the canonical transcript of its gene, false (0) if not. If the code returns an undefined it is because its state is not currently known. Internally the code will consult the database for this value if it is unknown and the transcript has a dbID and an attached adaptor
Return type : Boolean
Status : Stable

public Int Bio::EnsEMBL::Transcript::is_current | ( | ) |
Arg [1] : Boolean $is_current Example : $transcript->is_current(1) Description: Getter/setter for is_current state of this transcript. Returntype : Int Exceptions : none Caller : general Status : Stable

public Boolean Bio::EnsEMBL::Transcript::is_known | ( | ) |
Example : print "Transcript ".$transcript->stable_id." is KNOWN\\n" if $transcript->is_known; Description: Returns TRUE if this gene has a status of 'KNOWN' Returntype : TRUE if known, FALSE otherwise Exceptions : none Caller : general Status : Stable

Reimplemented in Bio::EnsEMBL::PredictionTranscript.
public Boolean Bio::EnsEMBL::Storable::is_stored | ( | ) | [inherited] |
Arg [1] : Bio::EnsEMBL::DBSQL::DBConnection : or Bio::EnsEMBL::DBSQL::DBAdaptor Example : do_something if($object->is_stored($db)); Description: Returns true if this object is stored in the provided database. This works under the assumption that if the adaptor and dbID are set and the database of the adaptor shares the port, dbname and hostname with the provided database, this object is stored in that database. Returntype : 1 or 0 Exceptions : throw if dbID is set but adaptor is not throw if adaptor is set but dbID is not throw if incorrect argument is passed Caller : store methods Status : Stable

public Int Bio::EnsEMBL::Transcript::length | ( | ) |
Args : none Example : my $t_length = $transcript->length Description: Returns the sum of the length of all the exons in the transcript. Returntype : int Exceptions : none Caller : general Status : Stable

Reimplemented from Bio::EnsEMBL::Feature.
public void Bio::EnsEMBL::Transcript::load | ( | ) |
Arg [1] : Boolean $load_xrefs Load (or don't load) xrefs. Default is to load xrefs. Example : $transcript->load(); Description : The Ensembl API makes extensive use of lazy-loading. Under some circumstances (e.g., when copying genes between databases), all data of an object needs to be fully loaded. This method loads the parts of the object that are usually lazy-loaded. It will also call the equivalent method on any translation and on all exons of the transcript. Returntype : None

public Bio::EnsEMBL::Transcript::modified | ( | ) |
public String Bio::EnsEMBL::Transcript::modified_date | ( | ) |
Arg [1] : (optional) string to be used for the modified date Example : none Description: get/set for attribute modified date Returntype : string Exceptions : none Caller : general Status : Stable

public void Bio::EnsEMBL::Feature::move | ( | ) | [inherited] |
Arg [1] : int start Arg [2] : int end Arg [3] : (optional) int strand Example : None Description: Sets the start, end and strand in one call rather than in 3 seperate calls to the start(), end() and strand() methods. This is for convenience and for speed when this needs to be done within a tight loop. Returntype : none Exceptions : Thrown is invalid arguments are provided Caller : general Status : Stable

Reimplemented in Bio::EnsEMBL::Exon, Bio::EnsEMBL::KaryotypeBand, and Bio::EnsEMBL::Map::QtlFeature.
public Bio::EnsEMBL::Transcript Bio::EnsEMBL::Transcript::new | ( | ) |
Arg [-EXONS] : reference to list of Bio::EnsEMBL::Exon objects - exons which make up this transcript Arg [-STABLE_ID] : string - the stable identifier of this transcript Arg [-VERSION] : int - the version of the stable identifier of this transcript Arg [-EXTERNAL_NAME] : string - the external database name associated with this transcript Arg [-EXTERNAL_DB] : string - the name of the database the external name is from Arg [-EXTERNAL_STATUS]: string - the status of the external identifier Arg [-DISPLAY_XREF]: Bio::EnsEMBL::DBEntry - The external database entry that is used to label this transcript when it is displayed. Arg [-CREATED_DATE]: string - the date the transcript was created Arg [-MODIFIED_DATE]: string - the date the transcript was last modified Arg [-DESCRIPTION]: string - the transcipts description Arg [-BIOTYPE]: string - the biotype e.g. "protein_coding" Arg [-STATUS]: string - the transcripts status i.e. "KNOWN","NOVEL" Arg [-IS_CURRENT]: Boolean - specifies if this is the current version of the transcript Example : $tran = new Bio::EnsEMBL::Transcript(-EXONS => \@exons); Description: Constructor. Instantiates a Transcript object. Returntype : Bio::EnsEMBL::Transcript Exceptions : throw on bad arguments Caller : general Status : Stable

Reimplemented from Bio::EnsEMBL::Feature.
Reimplemented in Bio::EnsEMBL::PredictionTranscript.
public Bio::EnsEMBL::Feature Bio::EnsEMBL::Feature::new_fast | ( | ) | [inherited] |
Arg [1] : hashref to be blessed Description: Construct a new Bio::EnsEMBL::Feature using the hashref. Exceptions : none Returntype : Bio::EnsEMBL::Feature Caller : general, subclass constructors Status : Stable

Reimplemented in Bio::EnsEMBL::AssemblyExceptionFeature, Bio::EnsEMBL::BaseAlignFeature, Bio::EnsEMBL::DensityFeature, Bio::EnsEMBL::DnaPepAlignFeature, Bio::EnsEMBL::MiscFeature, Bio::EnsEMBL::RepeatFeature, and Bio::EnsEMBL::SimpleFeature.
public Boolean Bio::EnsEMBL::Feature::overlaps | ( | ) | [inherited] |
Arg [1] : Bio::EnsEMBL::Feature $f The other feature you want to check overlap with this feature for. Description: This method does a range comparison of this features start and end and compares it with another features start and end. It will return true if these ranges overlap and the features are on the same seq_region. Returntype : TRUE if features overlap, FALSE if they don't Exceptions : warning if features are on different seq_regions Caller : general Status : Stable

public Bio::EnsEMBL::Transcript::pep2genomic | ( | ) |
public List Bio::EnsEMBL::Feature::project | ( | ) | [inherited] |
Arg [1] : string $name The name of the coordinate system to project this feature onto Arg [2] : string $version (optional) The version of the coordinate system (such as 'NCBI34') to project this feature onto Example : my $clone_projection = $feature->project('clone');
foreach my $seg (@$clone_projection) { my $clone = $seg->to_Slice(); print "Features current coords ", $seg->from_start, '-', $seg->from_end, " project onto clone coords " . $clone->seq_region_name, ':', $clone->start, '-', $clone->end, $clone->strand, "\\n"; } Description: Returns the results of 'projecting' this feature onto another coordinate system. This is useful to see where a feature would lie in a coordinate system in which it crosses a boundary.
This method returns a reference to a list of Bio::EnsEMBL::ProjectionSegment objects. ProjectionSegments are blessed arrays and can also be used as triplets [from_start,from_end,to_Slice]. The from_start and from_end are the coordinates relative to the feature start. For example, if a feature is current 100-200bp on a slice then the triplets returned might be: [1,50,$slice1], [51,101,$slice2]
The to_Slice is a slice spanning the region on the requested coordinate system that this feature projected to.
If the feature projects entirely into a gap then a reference to an empty list is returned.
Returntype : list reference of Bio::EnsEMBL::ProjectionSegments which can also be used as [$start,$end,$slice] triplets Exceptions : slice does not have an adaptor Caller : general Status : Stable

public List Bio::EnsEMBL::Feature::project_to_slice | ( | ) | [inherited] |
Arg [1] : slice to project to
Example : my $clone_projection = $feature->project_to_slice($slice);
foreach my $seg (@$clone_projection) { my $clone = $seg->to_Slice(); print "Features current coords ", $seg->from_start, '-', $seg->from_end, " project onto clone coords " . $clone->seq_region_name, ':', $clone->start, '-', $clone->end, $clone->strand, "\\n"; } Description: Returns the results of 'projecting' this feature onto another slcie . This is useful to see where a feature would lie in a coordinate system in which it crosses a boundary.
This method returns a reference to a list of Bio::EnsEMBL::ProjectionSegment objects. ProjectionSegments are blessed arrays and can also be used as triplets [from_start,from_end,to_Slice]. The from_start and from_end are the coordinates relative to the feature start. For example, if a feature is current 100-200bp on a slice then the triplets returned might be: [1,50,$slice1], [51,101,$slice2]
The to_Slice is a slice spanning the region on the requested coordinate system that this feature projected to.
If the feature projects entirely into a gap then a reference to an empty list is returned.
Returntype : list reference of Bio::EnsEMBL::ProjectionSegments which can also be used as [$start,$end,$slice] triplets Exceptions : slice does not have an adaptor Caller : general Status : At Risk

public Bio::EnsEMBL::Transcript::recalculate_coordinates | ( | ) |
Undocumented method

public Bio::Seq Bio::EnsEMBL::Transcript::seq | ( | ) |
Description: Returns a Bio::Seq object which consists of just : the sequence of the exons concatenated together, : without messing about with padding with N\'s from : Exon phases like dna_seq does. Args : none Example : none Returntype : Bio::Seq Exceptions : none Caller : general Status : Stable

Reimplemented from Bio::EnsEMBL::Feature.
public Int Bio::EnsEMBL::Feature::seq_region_end | ( | ) | [inherited] |
Arg [1] : none Example : print $feature->seq_region_end(); Description: Convenience method which returns the absolute end of this feature on the seq_region, as opposed to the relative (slice) position.
Returns undef if this feature is not on a slice. Returntype : int or undef Exceptions : none Caller : general Status : Stable

public Unsigned Bio::EnsEMBL::Feature::seq_region_length | ( | ) | [inherited] |
Arg [1] : none Example : print $feature->seq_region_length(); Description: Returns the length of the seq_region which this feature is on Returns undef if this Feature is not on a slice. Returntype : unsigned int or undef Exceptions : none Caller : general Status : Stable

public String Bio::EnsEMBL::Feature::seq_region_name | ( | ) | [inherited] |
Arg [1] : none Example : print $feature->seq_region_name(); Description: Gets the name of the seq_region which this feature is on. Returns undef if this Feature is not on a slice. Returntype : string or undef Exceptions : none Caller : general Status : Stable

public Int Bio::EnsEMBL::Feature::seq_region_start | ( | ) | [inherited] |
Arg [1] : none Example : print $feature->seq_region_start(); Description: Convenience method which returns the absolute start of this feature on the seq_region, as opposed to the relative (slice) position.
Returns undef if this feature is not on a slice. Returntype : int or undef Exceptions : none Caller : general Status : Stable

public Boolean Bio::EnsEMBL::Feature::seq_region_strand | ( | ) | [inherited] |
Arg [1] : none Example : print $feature->seq_region_strand(); Description: Returns the strand of the seq_region which this feature is on (i.e. feature_strand * slice_strand) Returns undef if this Feature is not on a slice. Returntype : 1,0,-1 or undef Exceptions : none Caller : general Status : Stable

public String Bio::EnsEMBL::Feature::seqname | ( | ) | [inherited] |
Arg [1] : (optional) $seqname Example : $seqname = $feat->seqname(); Description: Getter/Setter for the name of the sequence that this feature is on. Normally you can get away with not setting this value and it will default to the name of the slice on which this feature is on. It is useful to set this value on features which do not ordinarily sit on features such as ProteinFeatures which sit on peptides. Returntype : string Exceptions : none Caller : general Status : Stable

public Bio::EnsEMBL::Slice Bio::EnsEMBL::Feature::slice | ( | ) | [inherited] |
Arg [1] : (optional) Bio::EnsEMBL::Slice $slice Example : $seqname = $feature->slice()->name(); Description: Getter/Setter for the Slice that is associated with this feature. The slice represents the underlying sequence that this feature is on. Note that this method call is analagous to the old SeqFeature methods contig(), entire_seq(), attach_seq(), etc. Returntype : Bio::EnsEMBL::Slice Exceptions : thrown if an invalid argument is passed Caller : general Status : Stable

Reimplemented in Bio::EnsEMBL::Exon, and Bio::EnsEMBL::Map::DitagFeature.
public Bio::EnsEMBL::Transcript::sort | ( | ) |
Description:
- Deprecated:
- . This method is no longer needed. Exons are sorted automatically when added to the transcript.

public String Bio::EnsEMBL::Feature::species | ( | ) | [inherited] |
Example : $feature->species(); Description : Shortcut to the feature's DBAdaptor and returns its species name Returntype : String the species name Exceptions : Thrown if there is no attached adaptor Caller : Webcode

Reimplemented in Bio::EnsEMBL::FeaturePair.
public Text Bio::EnsEMBL::Transcript::spliced_seq | ( | ) |
Args : none Example : none Description: Retrieves all Exon sequences and concats them together. No phase padding magic is done, even if phases do not align. Returntype : Text Exceptions : none Caller : general Status : Stable

public String Bio::EnsEMBL::Transcript::stable_id | ( | ) |
Title : stable_id Usage : $obj->stable_id Function: Returns : String Args : Status : Stable

Reimplemented in Bio::EnsEMBL::PredictionTranscript.
public Int Bio::EnsEMBL::Feature::start | ( | ) | [inherited] |
Arg [1] : (optional) int $start The start of this feature relative to the start of the slice that it is on. Example : $start = $feat->start() Description: Getter/Setter for the start of this feature relative to the start of the slice it is on. Note that negative values, or values exceeding the length of the slice are permitted. Start must be less than or equal to the end regardless of the strand. Coordinate values start at 1 and are inclusive. Returntype : int Exceptions : none Caller : general Status : Stable

Reimplemented in Bio::EnsEMBL::Exon, Bio::EnsEMBL::Map::DitagFeature, Bio::EnsEMBL::SplicingEventFeature, and Bio::EnsEMBL::SplicingTranscriptPair.
public Bio::EnsEMBL::Exon Bio::EnsEMBL::Transcript::start_Exon | ( | ) |
Title : start_Exon Usage : $start_exon = $transcript->start_Exon; Returntype : Bio::EnsEMBL::Exon Description : The first exon in the transcript. Args : NONE Status : Stable

public String Bio::EnsEMBL::Transcript::status | ( | ) |
Arg [1] : string $status Example : none Description: get/set for attribute status Returntype : string Exceptions : none Caller : general Status : Medium Risk

public Int Bio::EnsEMBL::Feature::strand | ( | ) | [inherited] |
Arg [1] : (optional) int $strand Example : $feat->strand(-1); Description: Getter/Setter for the strand of this feature relative to the slice it is on. 0 is an unknown or non-applicable strand. -1 is the reverse (negative) strand and 1 is the forward (positive) strand. No other values are permitted. Returntype : int Exceptions : thrown if an invalid strand argument is passed Caller : general Status : Stable

Reimplemented in Bio::EnsEMBL::DensityFeature, Bio::EnsEMBL::Exon, Bio::EnsEMBL::KaryotypeBand, Bio::EnsEMBL::Map::DitagFeature, Bio::EnsEMBL::Map::QtlFeature, and Bio::EnsEMBL::ProteinFeature.
public Bio::EnsEMBL::Feature::sub_SeqFeature | ( | ) | [inherited] |
Undocumented method

public Hashref Bio::EnsEMBL::Transcript::summary_as_hash | ( | ) |
Example : $transcript_summary = $transcript->summary_as_hash(); Description : Extends Feature::summary_as_hash Retrieves a summary of this Transcript. Returns : hashref of descriptive strings Status : Intended for internal use

Reimplemented from Bio::EnsEMBL::Feature.
public void Bio::EnsEMBL::Transcript::swap_exons | ( | ) |
Arg [1] : Bio::EnsEMBL::Exon $old_Exon An exon that should be replaced Arg [2] : Bio::EnsEMBL::Exon $new_Exon The replacement Exon Example : none Description: exchange an exon in the current Exon list with a given one. Usually done before storing of Gene, so the Exons can be shared between Transcripts. Returntype : none Exceptions : none Caller : GeneAdaptor->store() Status : Stable

public Bio::EnsEMBL::Transcript::temporary_id | ( | ) |
public Bio::Seq Bio::EnsEMBL::Transcript::three_prime_utr | ( | ) |
Arg [1] : none Example : my $three_prime = $transcrpt->three_prime_utr or warn "No five prime UTR"; Description: Obtains a Bio::Seq object of the three prime UTR of this transcript. If this transcript is a pseudogene (i.e. non-translating) or has no three prime UTR, undef is returned instead. Returntype : Bio::Seq or undef Exceptions : none Caller : general Status : Stable

public Bio::EnsEMBL::Transcript Bio::EnsEMBL::Transcript::transfer | ( | ) |
Arg 1 : Bio::EnsEMBL::Slice $destination_slice Example : $transcript = $transcript->transfer($slice); Description: Moves this transcript to the given slice. If this Transcripts has Exons attached, they move as well. Returntype : Bio::EnsEMBL::Transcript Exceptions : none Caller : general Status : Stable

Reimplemented from Bio::EnsEMBL::Feature.
Reimplemented in Bio::EnsEMBL::PredictionTranscript.
public Bio::EnsEMBL::Transcript Bio::EnsEMBL::Transcript::transform | ( | ) |
Arg 1 : String $coordinate_system_name Arg [2] : String $coordinate_system_version Example : $transcript = $transcript->transform('contig'); $transcript = $transcript->transform('chromosome', 'NCBI33'); Description: Moves this Transcript to the given coordinate system. If this Transcript has Exons attached, they move as well. A new Transcript is returned. If the transcript cannot be transformed to the destination coordinate system undef is returned instead. Returntype : Bio::EnsEMBL::Transcript Exceptions : wrong parameters Caller : general Status : Medium Risk : deprecation needs to be removed at some time

Reimplemented from Bio::EnsEMBL::Feature.
Reimplemented in Bio::EnsEMBL::PredictionTranscript.
public Bio::Seq Bio::EnsEMBL::Transcript::translate | ( | ) |
Args : none Example : none Description: Return the peptide (plus eventual stop codon) for this transcript. Does N-padding of non-phase matching exons. It uses translateable_seq internally. Returns undef if this Transcript does not have a translation (i.e. pseudogene). Returntype : Bio::Seq or undef Exceptions : none Caller : general Status : Stable

Reimplemented in Bio::EnsEMBL::PredictionTranscript.
public Text Bio::EnsEMBL::Transcript::translateable_seq | ( | ) |
Args : none Example : print $transcript->translateable_seq(), "\\n"; Description: Returns a sequence string which is the the translateable part of the transcripts sequence. This is formed by splicing all Exon sequences together and apply all defined RNA edits. Then the coding part of the sequence is extracted and returned. The code will not support monkey exons any more. If you want to have non phase matching exons, defined appropriate _rna_edit attributes!
An empty string is returned if this transcript is a pseudogene (i.e. is non-translateable). Returntype : Text Exceptions : none Caller : general Status : Stable

public Bio::EnsEMBL::Translation Bio::EnsEMBL::Transcript::translation | ( | ) |
Args : None Example : if ( $transcript->translation() ) { print( $transcript->translation()->stable_id(), "\\n" ); } else { print("Pseudogene\\n"); } Description: Getter/setter for the Translation object which defines the CDS (and as a result the peptide encoded by) this transcript. This function will return undef if this transcript is a pseudogene, i.e. a non-translating transcript such as an ncRNA. This is the accepted method of determining whether a transcript is a pseudogene or not. Returntype : Bio::EnsEMBL::Translation Exceptions : none Caller : general Status : Stable

Reimplemented in Bio::EnsEMBL::PredictionTranscript.
public Bio::EnsEMBL::Transcript::type | ( | ) |
public String Bio::EnsEMBL::Transcript::version | ( | ) |
Title : version Usage : $obj->version() Function: Returns : String Args : Status : Stable

The documentation for this class was generated from the following file:
- Bio/EnsEMBL/Transcript.pm