Bio::EnsEMBL::PredictionTranscript Class Reference

Inheritance diagram for Bio::EnsEMBL::PredictionTranscript:

Public Member Functions
public Bio::EnsEMBL::PredictionTranscript	new ()
public Int	coding_region_start ()
public Int	coding_region_end ()
public Listref	get_all_translateable_Exons ()
public String	display_label ()
public Hashref	summary_as_hash ()
public String	stable_id ()
public	get_all_DBEntries ()
public	get_all_DBLinks ()
public	add_DBEntry ()
public	external_db ()
public	external_status ()
public	external_name ()
public	is_known ()
public Int	translation ()
public A	translate ()
public Int	cdna_coding_start ()
public Int	cdna_coding_end ()
public Bio::EnsEMBL::PredictionTranscript	transform ()
public Bio::EnsEMBL::PredictionTranscript	transfer ()
public A	get_all_Exons ()
public String	display_id ()
public EMPTY	get_all_Attributes ()
Public Member Functions inherited from Bio::EnsEMBL::Transcript
public Bio::EnsEMBL::Transcript	new ()
public Listref	get_all_DBLinks ()
public Listref	get_all_xrefs ()
public Listref	get_all_DBEntries ()
public Listref	get_all_object_xrefs ()
public void	add_DBEntry ()
public Listref	get_all_supporting_features ()
public void	add_supporting_features ()
public	flush_supporting_features ()
public String	external_db ()
public String	external_status ()
public String	external_name ()
public String	source ()
public Bio::EnsEMBL::DBEntry	display_xref ()
public Boolean	is_canonical ()
public Bio::EnsEMBL::Translation	translation ()
public Arrayref	get_all_alternative_translations ()
public void	add_alternative_translation ()
public Text	spliced_seq ()
public Text	translateable_seq ()
public Int	cdna_coding_start ()
public Int	cdna_coding_end ()
public Int	coding_region_start ()
public Int	coding_region_end ()
public Boolean	edits_enabled ()
public Bio::EnsEMBL::SeqEdit	get_all_SeqEdits ()
public Listref	get_all_Attributes ()
public void	add_Attributes ()
public void	add_Exon ()
public Listref	get_all_Exons ()
public Listref	get_all_ExonTranscripts ()
public Listref	get_all_constitutive_Exons ()
public ArrayRef	get_all_IntronSupportingEvidence ()
public Boolean	add_IntronSupportingEvidence ()
public Listref	get_all_Introns ()
public Listref	get_all_CDS_Introns ()
public Int	length ()
public void	flush_Exons ()
public void	flush_IntronSupportingEvidence ()
public Bio::Seq	five_prime_utr ()
public Bio::Seq	three_prime_utr ()
public Bio::EnsEMBL::Feature	five_prime_utr_Feature ()
public Bio::EnsEMBL::Feature	three_prime_utr_Feature ()
public Listref	get_all_five_prime_UTRs ()
public Listref	get_all_three_prime_UTRs ()
public Listref	get_all_CDS ()
public Listref	get_all_translateable_Exons ()
public Bio::Seq	translate ()
public Bio::Seq	seq ()
public	pep2genomic ()
public	genomic2pep ()
public	cdna2genomic ()
public	genomic2cdna ()
public Bio::EnsEMBL::TranscriptMapper	get_TranscriptMapper ()
public Bio::EnsEMBL::Exon	start_Exon ()
public Bio::EnsEMBL::Exon	end_Exon ()
public String	description ()
public String	version ()
public String	stable_id ()
public String	stable_id_version ()
public Int	is_current ()
public String	created_date ()
public String	modified_date ()
public void	swap_exons ()
public void	exon_rank ()
public Boolean	equals ()
public Bio::EnsEMBL::Transcript	transform ()
public Bio::EnsEMBL::Transcript	transfer ()
public	recalculate_coordinates ()
public String	display_id ()
public	get_all_DASFactories ()
public Hashref	get_all_DAS_Features ()
public Listref	get_all_RNAProducts ()
protected	_compare_xrefs ()
public void	load ()
public Hashref	summary_as_hash ()
public Boolean	gencode_basic ()
public String	tsl ()
public String	appris ()
public Bio::EnsEMBL::DBEntry	havana_transcript ()
public Bio::EnsEMBL::DBEntry	ccds ()
public Bio::EnsEMBL::Gene	get_Gene ()
public Bio::EnsEMBL::Biotype	get_Biotype ()
public Bio::EnsEMBL::Biotype	set_Biotype ()
public String	biotype ()
public Bio::EnsEMBL::MANE	mane_transcript ()
public Boolean	is_mane ()
Public Member Functions inherited from Bio::EnsEMBL::Feature
public Bio::EnsEMBL::Feature	new ()
public Int	start ()
public Int	end ()
public Int	strand ()
public void	move ()
public Int	length ()
public Bio::EnsEMBL::Analysis	analysis ()
public Bio::EnsEMBL::Slice	slice ()
public Boolean Or Undef	equals ()
public Bio::EnsEMBL::Feature	transform ()
public Bio::EnsEMBL::Feature	transfer ()
public Listref	project_to_slice ()
public Listref	project ()
public String	seqname ()
public String	display_id ()
public String	version ()
public Bio::EnsEMBL::Slice	feature_Slice ()
public String	seq_region_name ()
public Int	seq_region_length ()
public Boolean	seq_region_strand ()
public Int	seq_region_start ()
public Int	seq_region_end ()
public String	coord_system_name ()
public String	seq ()
public Listref	get_all_alt_locations ()
public Boolean	overlaps ()
public Boolean	overlaps_local ()
public List	get_overlapping_Genes ()
public Bio::EnsEMBL::Gene	get_nearest_Gene ()
public String	feature_so_acc ()
public String	feature_so_term ()
public Hashref	summary_as_hash ()
public String	species ()
public	sub_SeqFeature ()
public	add_sub_SeqFeature ()
public	flush_sub_SeqFeature ()
Public Member Functions inherited from Bio::EnsEMBL::Storable
public Bio::EnsEMBL::Storable	new ()
public Instance	new_fast ()
public Int	dbID ()
public Bio::EnsEMBL::DBSQL::BaseAdaptor	adaptor ()
public Boolean	is_stored ()
public	get_all_DAS_Features ()

Detailed Description

Synopsis

Description

Container for single transcript ab initio gene prediction such as
GenScan or SNAP. Is directly storable/retrievable in Ensembl using
PredictionTranscriptAdaptor.

Creation:

  my $tran = new Bio::EnsEMBL::PredictionTranscript();
  $tran->add_Exon($pred_exon);

  my $tran =
    new Bio::EnsEMBL::PredictionTranscript( -EXONS => \@pred_exons );

Manipulation:

  # Returns an array of PredictionExon objects
  my \@pred_exons = \@{ $tran->get_all_Exons };

  # Returns the peptide translation as string
  my $pep = $tran->translate()->seq();

  # Get the exon cdna sequence.
  my $cdna = $trans->spliced_seq();

Definition at line 39 of file PredictionTranscript.pm.

Member Function Documentation

add_DBEntry()

public Bio::EnsEMBL::PredictionTranscript::add_DBEntry

(

)

Undocumented method

Code:

cdna_coding_end()

public Int Bio::EnsEMBL::PredictionTranscript::cdna_coding_end

(

)

  Arg [1]    : none
  Example    :

$relative_coding_start = $transcript->cdna_coding_end();

  Description: Retrieves the position of the coding end of this transcript
               in cdna coordinates (relative to the start of the 5prime end of
               the transcript, excluding introns, including utrs). This is
               always te length of the cdna for prediction transcripts because
               they have no UTRs.
  Returntype : int
  Exceptions : none
  Caller     : five_prime_utr, get_all_snps, general
  Status     : Stable

Code:

cdna_coding_start()

public Int Bio::EnsEMBL::PredictionTranscript::cdna_coding_start

(

)

  Arg [1]    : none
  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 is
               always 1 for prediction transcripts because they have no UTRs.
  Returntype : int
  Exceptions : none
  Caller     : five_prime_utr, get_all_snps, general
  Status     : Stable

Code:

coding_region_end()

public Int Bio::EnsEMBL::PredictionTranscript::coding_region_end

(

)

  Arg [1]    : none
  Example    :

$coding_region_end = $transcript->coding_region_end

  Description: Retrieves the start of the coding region of this prediction
               transcript. For prediction transcripts this is always the same
               as the end since no UTRs are stored.
               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 start since on the reverse strand the biological coding
               end would be the lower genomic value.
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

coding_region_start()

public Int Bio::EnsEMBL::PredictionTranscript::coding_region_start

(

)

  Arg [1]    : none
  Example    :

$coding_region_start = $pt->coding_region_start

  Description: Retrieves the start of the coding region of this transcript in
               slice coordinates.  For prediction transcripts this
               is always the start of the transcript (i.e. there is no UTR).
               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.
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

display_id()

public String Bio::EnsEMBL::PredictionTranscript::display_id

(

)

  Arg [1]    : none
  Example    :

print $rf->display_id();

  Description: This method returns a string that is considered to be
               the 'display' identifier. For prediction 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

Code:

display_label()

public String Bio::EnsEMBL::PredictionTranscript::display_label

(

)

  Arg [1]    : string $newval (optional)
               The new value to set the display_label attribute to
  Example    :

$display_label = $pt->display_label()

  Description: Getter/Setter for a displayable identifier for this
               prediction transcript.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

external_db()

public Bio::EnsEMBL::PredictionTranscript::external_db

(

)

Undocumented method

Code:

external_name()

public Bio::EnsEMBL::PredictionTranscript::external_name

(

)

Undocumented method

Code:

external_status()

public Bio::EnsEMBL::PredictionTranscript::external_status

(

)

Undocumented method

Code:

get_all_Attributes()

public EMPTY Bio::EnsEMBL::PredictionTranscript::get_all_Attributes

(

)

  Arg [1]    : none
  Example    :

  Description: DOES NOTHING, Returns empty listref. Provided here to prevent
               Transcript attributes being returned for PredictionTranscripts.
  Returntype : EMPTY listref Bio::EnsEMBL::Attribute
  Exceptions : none
  Caller     : general
  Status     : At risk

Code:

get_all_DBEntries()

public Bio::EnsEMBL::PredictionTranscript::get_all_DBEntries

(

)

Undocumented method

Code:

get_all_DBLinks()

public Bio::EnsEMBL::PredictionTranscript::get_all_DBLinks

(

)

Undocumented method

Code:

get_all_Exons()

public A Bio::EnsEMBL::PredictionTranscript::get_all_Exons

(

)

  Arg [1]    : none
  Example    :

my @exons = @{$transcript->get_all_Exons()};

  Description: Returns an listref of the exons in this transcipr in order.
               i.e. the first exon in the listref is the 5prime most exon in 
               the transcript.
  Returntype : a list reference to Bio::EnsEMBL::Exon objects
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

get_all_translateable_Exons()

public Listref Bio::EnsEMBL::PredictionTranscript::get_all_translateable_Exons

(

)

  Arg [1]    : none
  Example    :

$exons = $self->get_all_translateable_Exons

  Description: Retrieves the translateable portion of all exons in this
               transcript.  For prediction transcripts this means all exons
               since no UTRs are stored for them.
  Returntype : listref of Bio::EnsEMBL::PredictionExons
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

is_known()

public Bio::EnsEMBL::PredictionTranscript::is_known

(

)

Undocumented method

Code:

new()

public Bio::EnsEMBL::PredictionTranscript Bio::EnsEMBL::PredictionTranscript::new

(

)

  Arg [-DISPLAY_LABEL]
    string - a displayable identifier for this prediction
  Arg [...]  : See Bio::EnsEMBL::Transcript superclass constructor
  Example    :

$pt = Bio::EnsEMBL::PredictionTranscript->new
                 ( '-start'         =>  $seq_region_start,
                   '-end'           =>  $seq_region_end,
                   '-strand'        =>  $seq_region_strand,
                   '-adaptor'       =>  $self,
                   '-slice'         =>  $slice,
                   '-analysis'      =>  $analysis,
                   '-dbID'          =>  $prediction_transcript_id,
                   '-display_label' =>  $display_label);

  Description: Constructor. Creates a new Bio::EnsEMBL::PredictionTranscript
               object
  Returntype : Bio::EnsEMBL::PredictionTranscript
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

stable_id()

public String Bio::EnsEMBL::PredictionTranscript::stable_id

(

)

  Arg [1]    : none
  Example    :

print $pt->stable_id();

  Description: Gets a 'stable' identifier for this prediction transcript.  Note
               that prediction transcripts do not have true *stable*
               identifiers (i.e. identifiers maintained between releases).
               This method chains to the display_label method and is intended
               to provide polymorphism with the Transcript class.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

summary_as_hash()

public Hashref Bio::EnsEMBL::PredictionTranscript::summary_as_hash

(

)

  Example    :

my $hash = $misc_feature->summary_as_hash();

  Description: Retrieves a textual summary of this prediction.
               Not inherited from Features.
  Returntype : Hashref of arrays of descriptive strings
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

transfer()

public Bio::EnsEMBL::PredictionTranscript Bio::EnsEMBL::PredictionTranscript::transfer

(

)

  Arg  1     : Bio::EnsEMBL::Slice $destination_slice
  Example    :

$ptrans = $ptrans->transfer($slice);

  Description: Moves this PredictionTranscript to the given slice.
               If this Transcripts has Exons attached, they move as well.
               If this transcript cannot be moved then undef is returned
               instead.
  Returntype : Bio::EnsEMBL::PredictionTranscript
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

transform()

public Bio::EnsEMBL::PredictionTranscript Bio::EnsEMBL::PredictionTranscript::transform

(

)

  Arg  1     : String $coordinate_system_name
  Arg [2]    : String $coordinate_system_version
  Example    :

$ptrans = $ptrans->transform('chromosome', 'NCBI33');
              $ptrans = $ptrans->transform('clone');

  Description: Moves this PredictionTranscript to the given coordinate system.
               If this Transcript has Exons attached, they move as well.
               A new Transcript is returned or undefined if this PT is not
               defined in the new coordinate system.
  Returntype : Bio::EnsEMBL::PredictionTranscript
  Exceptions : wrong parameters
  Caller     : general
  Status     : Stable

Code:

translate()

public A Bio::EnsEMBL::PredictionTranscript::translate

(

)

  Arg [1]   : Boolean, emulate the behavior of old bioperl versions where
              an incomplete final codon of 2 characters is padded and guessed
  Function  : Give a peptide translation of all exons currently in
              the PT. Gives empty string when none is in.
  Returntype: a Bio::Seq as in transcript->translate()
  Exceptions: none
  Caller    : general
  Status     : Stable

Code:

translation()

public Int Bio::EnsEMBL::PredictionTranscript::translation

(

)

  Arg [1]    : none
  Example    :

$translation = $pt->translation();

  Description: Retrieves a Bio::EnsEMBL::Translation object for this prediction
               transcript.  Note that this translation is generated on the fly
               and is not stored in the database.  The translation always
               spans the entire transcript (no UTRs; all CDS) and does not
               have an associated dbID, stable_id or adaptor.
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

---

The documentation for this class was generated from the following file:

• ensembl/modules/Bio/EnsEMBL/PredictionTranscript.pm