/ 
Bio-EnsEMBL-112.0.0_57
River stage zero No dependents
/ Bio::EnsEMBL::Transcript

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

Please email comments or questions to the public Ensembl
developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.

Questions may also be sent to the Ensembl help desk at
<http://www.ensembl.org/Help/Contact>.

NAME

Bio::EnsEMBL::Transcript - object representing an Ensembl transcript

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.

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 transcripts description
Arg [-BIOTYPE]: 
      string - the biotype e.g. "protein_coding"
Arg [-IS_CURRENT]:
      Boolean - specifies if this is the current version of the transcript
Arg [-SOURCE]:
      string - the transcript source, e.g. "ensembl"

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
Arg [1]    : String database name (optional)
             SQL wildcard characters (_ and %) can be used to
             specify patterns.

Arg [2]    : (optional) String, external database type, can be one of
             ('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL'),
             SQL wildcard characters (_ and %) can be used to
             specify patterns.

Example    : my @dblinks = @{ $transcript->get_all_DBLinks() };
             @dblinks = @{ $transcript->get_all_DBLinks('Uniprot%') };}
             @dblinks = @{ $transcript->get_all_DBLinks('%', 'ENSEMBL') };

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

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

get_all_DBEntries

Arg [1]    : (optional) String, external database name,
             SQL wildcard characters (_ and %) can be used to
             specify patterns.

Arg [2]    : (optional) String, external database type, can be one of
             ('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL'),
             SQL wildcard characters (_ and %) can be used to
             specify patterns.

Example    : my @dbentries = @{ $transcript->get_all_DBEntries() };
             @dbentries = @{ $transcript->get_all_DBEntries('Uniprot%') };}
             @dbentries = @{ $transcript->get_all_DBEntries('%', 'ENSEMBL') };}

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

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

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

get_all_supporting_features

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

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

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

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

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

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

source

Arg [1]    : (optional) String - the source to set
Example    : $transcript->source('ensembl');
Description: Getter/setter for attribute source
Returntype : String
Exceptions : none
Caller     : general
Status     : Stable

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

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

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

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

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

spliced_seq

Args       : soft_mask (opt)
             if specified, will return a sequence where UTR regions are lowercased
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

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

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

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

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

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

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

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

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

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

add_Exon

Title   : add_Exon
Example : $trans->add_Exon($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

get_all_Exons

Arg [1]    : Boolean
             Only return constitutive exons if true (non-zero)

Example    : 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

get_all_ExonTranscripts

Example    : my @exon_transcripts = @{ $transcript->get_all_ExonTranscripts() };

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.

Returntype : listref to Bio::EnsEMBL::ExonTranscript objects
Exceptions : none
Caller     : general
Status     : Stable

get_all_constitutive_Exons

Arg        :  None

Example   :  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

get_all_IntronSupportingEvidence

Example     : $ise->get_all_IntronSupportingEvidence();
Description : Fetches all ISE instances linked to this Transript
Returntype  : ArrayRef[Bio::EnsEMBL::IntronSupportEvidence] retrieved from 
              the DB or from those added via C<add_IntronSupportingEvidence>
Exceptions  : None

add_IntronSupportingEvidence

Arg [1]     : Bio::EnsEMBL::IntronSupportEvidence Object to add
Example     : $ise->add_IntronSupportingEvidence($ise);
Description : Adds the IntronSupportEvidence instance to this Transcript. The
              code checks to see if it is a unique ISE instance
Returntype  : Boolean; true means it was added. False means it was not 
              as this ISE was already attached
Exceptions  : None

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

get_all_CDS_Introns

Arg [1]    : none
Example    : my @introns = @{$transcript->get_all_CDS_Introns()};
Description: Returns an listref of the introns between coding exons in this transcript in order.
Returntype : listref to Bio::EnsEMBL::Intron objects
Exceptions : none
Caller     : general
Status     : Stable

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

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

flush_IntronSupportingEvidence

Example    : $transcript->flush_IntronSupportingEvidence();
Description: Removes all IntronSupportingEvidence from this transcript
Returntype : none
Exceptions : none
Caller     : general
Status     : Stable

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

three_prime_utr

Arg [1]    : none
Example    : my $three_prime  = $transcrpt->three_prime_utr
               or warn "No three 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

five_prime_utr_Feature

Example    : my $five_prime  = $transcrpt->five_prime_utr_Feature
               or warn "No five prime UTR";
Description: Returns the genomic coordinates of the start and end of the
             5' UTR of this transcript. Note that if you want the sequence
             of the 5' UTR use C<five_prime_utr> as this will return the
             sequence from the spliced transcript. 
Returntype : Bio::EnsEMBL::Feature or undef if there is no UTR
Exceptions : none

three_prime_utr_Feature

Example    : my $five_prime  = $transcrpt->three_prime_utr_Feature
               or warn "No three prime UTR";
Description: Returns the genomic coordinates of the start and end of the
             3' UTR of this transcript. Note that if you want the sequence
             of the 3' UTR use C<three_prime_utr> as this will return the
             sequence from the spliced transcript. 
Returntype : Bio::EnsEMBL::Feature or undef if there is no UTR
Exceptions : none

get_all_five_prime_UTRs

Example    : my $five_primes  = $transcript->get_all_five_prime_UTRs
Description: Returns a list of features forming the 5' UTR of this transcript.
Returntype : listref of Bio::EnsEMBL::UTR
Exceptions : none

get_all_three_prime_UTRs

Example    : my $three_primes  = $transcript->get_all_three_prime_UTRs
Description: Returns a list of features forming the 3' UTR of this transcript.
Returntype : listref of Bio::EnsEMBL::UTR
Exceptions : none

get_all_CDS

Example    : my $cds  = $transcript->get_all_CDS
Description: Returns a list of features forming the coding regions of the transcript
Returntype : listref of Bio::EnsEMBL::CDS
Exceptions : none

get_all_translateable_Exons

Args       : 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

translate

Arg [1]    : Boolean, emulate the behavior of old bioperl versions where
             an incomplete final codon of 2 characters is padded and guessed
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

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 B<dna_seq> does.
Args       : none
Example    : none
Returntype : Bio::Seq
Exceptions : none
Caller     : general
Status     : Stable

pep2genomic

Description: See Bio::EnsEMBL::TranscriptMapper::pep2genomic

genomic2pep

Description: See Bio::EnsEMBL::TranscriptMapper::genomic2pep

cdna2genomic

Description: See Bio::EnsEMBL::TranscriptMapper::cdna2genomic

genomic2cdna

Description: See Bio::EnsEMBL::TranscriptMapper::genomic2cdna

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

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

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

description

Title   : description
Usage   : $obj->description($newval)
Function: 
Returns : String
Args    : newvalue (optional)
Status  : Stable

version

Title   : version
Usage   : $obj->version()
Function: 
Returns : String
Args    : 
Status  : Stable

stable_id

Title   : stable_id
Usage   : $obj->stable_id
Function: 
Returns : String
Args    : 
Status  : Stable

stable_id_version

Arg [1]    : (optional) String - the stable ID with version to set
Example    : $transcript->stable_id("ENST0000000001.3");
Description: Getter/setter for stable id with version for this transcript.
Returntype : String
Exceptions : none
Caller     : general
Status     : Stable

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

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

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

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

exon_rank

Arg [1]    : Bio::EnsEMBL::Exon $Exon
             Query exon
Example    : $rank = $transcript->exon_rank($exon);
Description: Returns the rank of an exon relative to the transcript
Returntype : none
Exceptions : Throws if the exon does not belong to the transcript
Caller     : General
Status     : Stable

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.

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

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

recalculate_coordinates

Args       : none
Example    : none
Description: called when exon coordinate change happened to recalculate the
             coords of the transcript.  This method should be called if one
             of the exons has been changed.
Returntype : none
Exceptions : none
Caller     : internal
Status     : Stable

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

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

get_all_DAS_Features

Arg [1]    : none
Example    : $features = $prot->get_all_DAS_Features;
Description: Retrieves 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

get_all_RNAProducts

Arg [1]    : optional string $type_code type of rnaproducts to retrieve
Example    : @transc_mirnas = @{$transcript->get_all_RNAProducts('miRNA')};
             @transc_rnaproducts = @{$transcript->get_all_RNAProducts()};
Description: Gets a list of RNAProducts of this transcript.
             Optionally just get RNAProducts for given type code.
Returntype : listref Bio::EnsEMBL::RNAProduct
Exceptions : none
Caller     : general
Status     : In Development

_compare_xrefs

Description: compare xrefs based on priority (descending), then
             name (ascending), then display_label (ascending)

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

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

gencode_basic

Example       : $gencode_basic = $transcript->tag();
Description   : Returns true if gencode_basic is set
Returns       : boolean

tsl

Example       : $tsl = $transcript->tsl();
Description   : Returns the corresponding transcript support level
Returns       : string

appris

Example       : $appris = $transcript->appris();
Description   : Returns the corresponding APPRIS tag
Returns       : string

havana_transcript

Example       : $havana_transcript = $transcript->havana_transcript();
Description   : Locates the corresponding havana transcript
Returns       : Bio::EnsEMBL::DBEntry

ccds

Example       : $ccds = $transcript->ccds();
Description   : Locates the corresponding ccds xref
Returns       : Bio::EnsEMBL::DBEntry

get_Gene

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

get_Biotype

Example    : my $biotype = $transcript->get_Biotype;
Description: Returns the Biotype object of this transcript.
             When no biotype exists, defaults to 'protein_coding'.
             When used to set to a biotype that does not exist in
             the biotype table, a biotype object is created with
             the provided argument as name and object_type transcript.
Returntype : Bio::EnsEMBL::Biotype
Exceptions : none

set_Biotype

Arg [1]    : Arg [1] : String - the biotype name to set
Example    : my $biotype = $transcript->set_Biotype('protin_coding');
Description: Sets the Biotype of this transcript to the provided biotype name.
             Returns the Biotype object of this transcript.
             When no biotype exists, defaults to 'protein_coding' name.
             When setting a biotype that does not exist in
             the biotype table, a biotype object is created with
             the provided argument as name and object_type transcript.
Returntype : Bio::EnsEMBL::Biotype
Exceptions : If no argument provided

mane_transcript Example : $mane = $transcript->mane_transcript(); Description: Retrieve the corresponding MANE transcript Returntype : Bio::EnsEMBL::MANE Exceptions : none Caller : general Status : Stable

is_mane Example : $boolean = $transcript->is_mane(); Description: Check if a transcript is part of MANE Returntype : boolean Exceptions : none Caller : general Status : Stable