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Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute
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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 : Stableget_all_DBLinks
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 : Stableget_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 : Stableget_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 : Stableget_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 : Stableadd_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 : Stableget_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 : Stableadd_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 : Stableflush_supporting_features
Example : $transcript->flush_supporting_features;
Description : Removes all supporting evidence from the transcript.
Return type : (Empty) listref
Exceptions : none
Caller : general
Status : Stableexternal_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 : Stableexternal_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 : Stableexternal_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 : Stablesource
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 : Stabledisplay_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 : Stableis_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 : Stabletranslation
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 : Stableget_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 : Stableadd_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 : Stablespliced_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 : Stabletranslateable_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 : Stablecdna_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 : Stablecdna_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 : Stablecoding_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 : Stablecoding_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 : Stableedits_enabled
Arg [1] : (optional) boolean $newval
Example : $transcript->edits_enabled(1);
Description: Enables/Disables the application of SeqEdits to this transcript.
Edits are enabled by default, and affect the cdna/mrna
sequences coordinates and the resultant translation.
Returntype : boolean - the current value of the edits
Exceptions : none
Caller : general, cdna_coding_start, cdna_coding_end, length
Status : Stableget_all_SeqEdits
Arg [1] : none
Example : my @seqeds = @{$transcript->get_all_SeqEdits()};
Description: Retrieves all post transcriptional sequence modifications for
this transcript.
Returntype : Bio::EnsEMBL::SeqEdit
Exceptions : none
Caller : spliced_seq()
Status : Stableget_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 : Stableadd_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 : Stableadd_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 : Stableget_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 : Stableget_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 : Stableget_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 : Stableget_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 : Noneadd_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 : Noneget_all_Introns
Arg [1] : none
Example : my @introns = @{$transcript->get_all_Introns()};
Description: Returns an listref of the introns in this transcript in order.
i.e. the first intron in the listref is the 5prime most exon in
the transcript.
Returntype : listref to Bio::EnsEMBL::Intron objects
Exceptions : none
Caller : general
Status : Stableget_all_CDS_Introns
Arg [1] : none
Example : my @introns = @{$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 : Stablelength
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 : Stableflush_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 : Stableflush_IntronSupportingEvidence
Example : $transcript->flush_IntronSupportingEvidence();
Description: Removes all IntronSupportingEvidence from this transcript
Returntype : none
Exceptions : none
Caller : general
Status : Stablefive_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 : Stablethree_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 : Stablefive_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 : nonethree_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 : noneget_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 : noneget_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 : noneget_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 : noneget_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 : Stabletranslate
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 : Stableseq
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 : Stablepep2genomic
Description: See Bio::EnsEMBL::TranscriptMapper::pep2genomicgenomic2pep
Description: See Bio::EnsEMBL::TranscriptMapper::genomic2pepcdna2genomic
Description: See Bio::EnsEMBL::TranscriptMapper::cdna2genomicgenomic2cdna
Description: See Bio::EnsEMBL::TranscriptMapper::genomic2cdnaget_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 : Stablestart_Exon
Title : start_Exon
Usage : $start_exon = $transcript->start_Exon;
Returntype : Bio::EnsEMBL::Exon
Description : The first exon in the transcript.
Args : NONE
Status : Stableend_Exon
Title : end_exon
Usage : $end_exon = $transcript->end_Exon;
Description : The last exon in the transcript.
Returntype : Bio::EnsEMBL::Exon
Args : NONE
Status : Stabledescription
Title : description
Usage : $obj->description($newval)
Function:
Returns : String
Args : newvalue (optional)
Status : Stableversion
Title : version
Usage : $obj->version()
Function:
Returns : String
Args :
Status : Stablestable_id
Title : stable_id
Usage : $obj->stable_id
Function:
Returns : String
Args :
Status : Stablestable_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 : Stableis_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 : Stablecreated_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 : Stablemodified_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 : Stableswap_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 : Stableexon_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 : Stableequals
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 timetransfer
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 : StableArgs : 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 : Stabledisplay_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 : Stableget_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 : Stableget_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 : Stableget_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 : Nonesummary_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 usegencode_basic
Example : $gencode_basic = $transcript->gencode_basic();
Description : Returns true if gencode_basic is set
Returns : booleangencode_primary
Example : $gencode_primary = $transcript->gencode_primary();
Description : Returns true if gencode_primary is set
Returns : booleantsl
Example : $tsl = $transcript->tsl();
Description : Returns the corresponding transcript support level
Returns : stringappris
Example : $appris = $transcript->appris();
Description : Returns the corresponding APPRIS tag
Returns : stringhavana_transcript
Example : $havana_transcript = $transcript->havana_transcript();
Description : Locates the corresponding havana transcript
Returns : Bio::EnsEMBL::DBEntryccds
Example : $ccds = $transcript->ccds();
Description : Locates the corresponding ccds xref
Returns : Bio::EnsEMBL::DBEntryget_Gene
Example : $gene = $transcript->get_Gene;
Description : Locates the parent Gene using a transcript dbID
Returns : Bio::EnsEMBL::Geneget_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 : noneset_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 providedbiotype Arg [1] : (optional) String - the biotype to set Example : $transcript->biotype("protein_coding"); Description: Getter/setter for the attribute biotype name. Recommended to use instead for a getter: $biotype = $transcript->get_Biotype; and for a setter: $biotype = $transcript->set_Biotype("protein_coding"); The String biotype name can then be retrieved by calling name on the Biotype object: $biotype_name = $biotype->name; Returntype : String Exceptions : none Caller : general Status : Stable
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
1 POD Error
The following errors were encountered while parsing the POD:
- Around line 2858:
Unknown directive: =head