Inheritance diagram for Bio::EnsEMBL::Gene:

Class Summary

Synopsis

  my $gene = Bio::EnsEMBL::Gene-\>new(
    -START  =\> 123,
    -END    =\> 1045,
    -STRAND =\> 1,
    -SLICE  =\> $slice
  );

  # print gene information
  print("gene start:end:strand is "
      . join( ":", map { $gene-\>$_ } qw(start end strand) )
      . "\n" );

  # set some additional attributes
  $gene-\>stable_id('ENSG000001');
  $gene-\>description('This is the gene description');

Description

A representation of a Gene within the Ensembl system. A gene is a set of one or
more alternative transcripts.

Definition at line 34 of file Gene.pm.

Available Methods
protected	_deprecated_transform ()
public Bio::EnsEMBL::DBSQL::BaseAdaptor	adaptor ()
public void	add_Attributes ()
public void	add_DBEntry ()
public DEPRECATED	add_DBLink ()
public	add_sub_SeqFeature ()
public void	add_Transcript ()
public void	add_unconventional_transcript_association ()
public Bio::EnsEMBL::Analysis	analysis ()
public String	biotype ()
public String	canonical_annotation ()
public Bio::EnsEMBL::Transcript	canonical_transcript ()
public	chr_name ()
public	confidence ()
public	contig ()
public String	coord_system_name ()
public String	created_date ()
public Int	dbID ()
public String	description ()
public String	display_id ()
public Bio::EnsEMBL::DBEntry	display_xref ()
public Int	end ()
public Boolean	equals ()
public String	external_db ()
public String	external_name ()
public String	external_status ()
public Bio::EnsEMBL::Slice	feature_Slice ()
public Listref	fetch_coded_for_regulatory_factors ()
public	flush_sub_SeqFeature ()
public Listref	get_all_alt_alleles ()
public Reference	get_all_alt_locations ()
public Listref	get_all_Attributes ()
public Hashref	get_all_DAS_Features ()
public	get_all_DASFactories ()
public Listref	get_all_DBEntries ()
public Listref	get_all_DBLinks ()
public Listref	get_all_Exons ()
public Listref	get_all_homologous_Genes ()
public Listref	get_all_object_xrefs ()
public Listref	get_all_Transcripts ()
public Listref	get_all_unconventional_transcript_associations ()
public Listref	get_all_xrefs ()
public Bio::EnsEMBL::Gene	get_nearest_Gene ()
public List	get_overlapping_Genes ()
public	id ()
public Int	is_current ()
public Boolean	is_known ()
public	is_reference ()
public Boolean	is_stored ()
public Int	length ()
public	load ()
public String	modified_date ()
public void	move ()
public Bio::EnsEMBL::Gene	new ()
public Bio::EnsEMBL::Feature	new_fast ()
public Boolean	overlaps ()
public List	project ()
public List	project_to_slice ()
public void	recalculate_coordinates ()
public Listref	remove_unconventional_transcript_associations ()
public Undef	seq ()
public Int	seq_region_end ()
public Unsigned	seq_region_length ()
public String	seq_region_name ()
public Int	seq_region_start ()
public Boolean	seq_region_strand ()
public String	seqname ()
public Bio::EnsEMBL::Slice	slice ()
public String	source ()
public String	species ()
public String	stable_id ()
public Int	start ()
public String	status ()
public Int	strand ()
public	sub_SeqFeature ()
public Hashref	summary_as_hash ()
public	temporary_id ()
public Bio::EnsEMBL::Gene	transfer ()
public Bio::EnsEMBL::Gene	transform ()
public	type ()
public Int	version ()

Method Documentation

protected Bio::EnsEMBL::Feature::_deprecated_transform ( ) [inherited]

Undocumented method

Code:

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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

Code:

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public void Bio::EnsEMBL::Gene::add_Attributes ( )

  Arg [1-N]  : list of Bio::EnsEMBL::Attribute's @attribs
               Attribute(s) to add
  Example    : my $attrib = Bio::EnsEMBL::Attribute->new(...);
               $gene->add_Attributes($attrib);
  Description: Adds an Attribute to the Gene. If you add an attribute before
               you retrieve any from database, lazy loading will be disabled.
  Returntype : none
  Exceptions : throw on incorrect arguments
  Caller     : general
  Status     : Stable

Code:

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public void Bio::EnsEMBL::Gene::add_DBEntry ( )

  Arg [1]    : Bio::EnsEMBL::DBEntry $dbe
               The dbEntry to be added
  Example    : my $dbe = Bio::EnsEMBL::DBEntery->new(...);
               $gene->add_DBEntry($dbe);
  Description: Associates a DBEntry with this gene. 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

Code:

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public DEPRECATED Bio::EnsEMBL::Gene::add_DBLink ( )

Description:

Deprecated:: This method has been deprecated in favour of the add_DBEntry method. Objects are responible for holding only xrefs directly associated with themselves now.

Code:

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public Bio::EnsEMBL::Feature::add_sub_SeqFeature ( ) [inherited]

Undocumented method

Code:

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public void Bio::EnsEMBL::Gene::add_Transcript ( )

  Arg [1]    : Bio::EnsEMBL::Transcript $trans
               The transcript to add to the gene
  Example    : my $transcript = Bio::EnsEMBL::Transcript->new(...);
               $gene->add_Transcript($transcript);
  Description: Adds another Transcript to the set of alternatively
               spliced Transcripts of this gene. If it shares exons 
               with another Transcript, these should be object-identical.
  Returntype : none
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public void Bio::EnsEMBL::Gene::add_unconventional_transcript_association ( )

  Arg [1]    : Bio::EnsEMBL::Transcript $trans
               The transcript to associate with the gene, in an unconventional manner.
  Arg [2]    : String $type
               The type of association between this gene and this transcript, e.g.
               "antisense","sense_intronic","sense_overlaping_exonic","chimeric_sense_exonic"
  Example    : my $transcript = Bio::EnsEMBL::Transcript->new(...);
               $gene->add_unconventional_transcript_association($transcript, "antisense");
  Description: Associate a transcript with this gene in a way that is
               non-conventional.
  Returntype : none
  Exceptions : none
  Caller     : general
  Status     : At Risk.

Code:

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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

Code:

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Reimplemented in Bio::EnsEMBL::DensityFeature.

public String Bio::EnsEMBL::Gene::biotype ( )

  Arg [1]    : (optional) String - the biotype to set
  Example    : $gene->biotype("protein_coding");
  Description: Getter/setter for the attribute biotype
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public String Bio::EnsEMBL::Gene::canonical_annotation ( )

  Arg [1]    : (optional) String - canonical_annotation
  Example    : $gene->canonical_annotation('This is the canonical_annotation');
  Description: Getter/setter for the canonical_annotation
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Bio::EnsEMBL::Transcript Bio::EnsEMBL::Gene::canonical_transcript ( )

  Arg [1]    : (optional) Bio::EnsEMBL::Transcipt - canonical_transcript object
  Example    : $gene->canonical_transcript($canonical_transcript);
  Description: Getter/setter for the canonical_transcript
  Returntype : Bio::EnsEMBL::Transcript
  Exceptions : Throws if argument is not a transcript object.
  Caller     : general
  Status     : Stable

Code:

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public Bio::EnsEMBL::Gene::chr_name ( )

Description:

Deprecated:: . Use project, tranform, or transfer to obtain this gene in another coord system. Use $gene->slice->seq_region_name to get the name of the underlying coord system. Or $gene->slice->name().

Code:

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public Bio::EnsEMBL::Gene::confidence ( )

  Description:
Deprecated:
. Use status() instead.

Code:

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public Bio::EnsEMBL::Feature::contig ( ) [inherited]

Undocumented method

Code:

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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

Code:

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public String Bio::EnsEMBL::Gene::created_date ( )

  Arg [1]    : (optional) String - created date to set (as a UNIX time int)
  Example    : $gene->created_date('1141948800');
  Description: Getter/setter for attribute created_date
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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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

Code:

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Reimplemented in Bio::EnsEMBL::Map::Ditag, and Bio::EnsEMBL::Map::DitagFeature.

public String Bio::EnsEMBL::Gene::description ( )

  Arg [1]    : (optional) String - the description to set
  Example    : $gene->description('This is the gene\'s description');
  Description: Getter/setter for gene description
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public String Bio::EnsEMBL::Gene::display_id ( )

  Example    : print $gene->display_id();
  Description: This method returns a string that is considered to be
               the 'display' identifier. For genes 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:

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Reimplemented from Bio::EnsEMBL::Feature.

public Bio::EnsEMBL::DBEntry Bio::EnsEMBL::Gene::display_xref ( )

  Arg [1]    : (optional) Bio::EnsEMBL::DBEntry - the display xref to set
  Example    : $gene->display_xref($db_entry);
  Description: Getter/setter display_xref for this gene.
  Returntype : Bio::EnsEMBL::DBEntry
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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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

Code:

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Reimplemented in Bio::EnsEMBL::Exon, Bio::EnsEMBL::Map::DitagFeature, Bio::EnsEMBL::SplicingEventFeature, and Bio::EnsEMBL::SplicingTranscriptPair.

public Boolean Bio::EnsEMBL::Gene::equals ( )

  Arg [1]       : Bio::EnsEMBL::Gene gene
  Example       : if ($geneA->equals($geneB)) { ... }
  Description   : Compares two genes 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 genes are *not* equal.
                  2. If the biotypes differ, then the genes are *not*
                     equal.
                  3. If both genes have stable IDs: if these are the
                     same, the genes are equal, otherwise not.
                  4. If both genes have the same number of transcripts
                     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-gene is passed as the argument.

Code:

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Reimplemented from Bio::EnsEMBL::Feature.

public String Bio::EnsEMBL::Gene::external_db ( )

  Arg [1]    : (optional) String - name of external db to set
  Example    : $gene->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

Code:

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public String Bio::EnsEMBL::Gene::external_name ( )

  Arg [1]    : (optional) String - the external name to set
  Example    : $gene->external_name('BRCA2');
  Description: Getter/setter for attribute external_name.
  Returntype : String or undef
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public String Bio::EnsEMBL::Gene::external_status ( )

  Arg [1]    : (optional) String - status of the external db
  Example    : $gene->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

Code:

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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

Code:

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public Listref Bio::EnsEMBL::Gene::fetch_coded_for_regulatory_factors ( )

Arg [1] : none Example : $gene->fetch_coded_for_regualtory_factors() Description:

Deprecated:: : Fetches any regulatory_factors that are coded for by this gene. Returntype : Listref of Bio::Ensembl::RegulatoryFactor Exceptions : Caller : ? Status : At Risk : under development

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public Bio::EnsEMBL::Feature::flush_sub_SeqFeature ( ) [inherited]

Undocumented method

Code:

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public Listref Bio::EnsEMBL::Gene::get_all_alt_alleles ( )

  Example    : my @alt_genes = @{ $gene->get_all_alt_alleles };
               foreach my $alt_gene (@alt_genes) {
                 print "Alternate allele: " . $alt_gene->stable_id() . "\\n";
               }
  Description: Returns a listref of Gene objects that represent this Gene on
               an alternative haplotype. Empty list if there is no such
               Gene (eg there is no overlapping haplotype).
  Returntype : listref of Bio::EnsEMBL::Gene objects
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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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

Code:

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sub get_all_alt_locations {
  my $self = shift;
  my $return_all = shift || 0;

  my $slice = $self->{'slice'} or return [];
  my $sa = $slice->adaptor() or return [];

  # get slice of entire region
  $slice = $sa->fetch_by_seq_region_id($slice->get_seq_region_id);

  my $axfa = $sa->db->get_AssemblyExceptionFeatureAdaptor();
  my $axfs = $axfa->fetch_all_by_Slice($slice);

  my (@haps, @alt);

  foreach my $axf (@$axfs) {
    if(uc($axf->type()) eq 'HAP') {
      push @haps, $axf;
    } elsif(uc($axf->type()) =~ 'PAR') {
      push @alt, $axf;
    } elsif( $axf->type() eq "PATCH_FIX"){
      push @haps, $axf;
    } elsif( $axf->type() eq "PATCH_FIX REF"){
      push @haps, $axf  if $return_all > 0 ;
    } elsif( $axf->type() eq "HAP REF" ) {
      push @haps, $axf if $return_all > 0 ;
      # do nothing when you are on REF
    } elsif( $axf->type() eq "PATCH_NOVEL"){
      push @haps, $axf;
    }elsif( $axf->type() eq "PATCH_NOVEL REF"){
      push @haps, $axf  if $return_all > 0 ;
    } else {
      warning("Unknown exception feature type ". $axf->type()."- ignoring.");
    }
  }

  # regions surrounding hap are those of interest, not hap itself
  # convert hap alt. exc. features to regions around haps instead
  foreach my $h (@haps) {
    my $haslice = $h->alternate_slice();
    my $hacs    = $haslice->coord_system();

    if($h->start() > 1 && $haslice->start() > 1) {
      my $aslice = $sa->fetch_by_region($hacs->name(),
                                        $haslice->seq_region_name(),
                                        1,
                                        $haslice->start()-1,
                                        $haslice->strand(),
                                        $hacs->version());

      push @alt, Bio::EnsEMBL::AssemblyExceptionFeature->new
        (-start  => 1,
         -end    => $h->start()-1,
         -alternate_slice => $aslice);
    }

    if($h->end() < $slice->seq_region_length() &&
       $haslice->end < $haslice->seq_region_length()) {
      my $aslice = $sa->fetch_by_region($hacs->name(),
                                        $haslice->seq_region_name(),
                                        $haslice->end()+1,
                                        $haslice->seq_region_length(),
                                        $haslice->strand(),
                                        $hacs->version());

      push @alt, Bio::EnsEMBL::AssemblyExceptionFeature->new
        (-start  => $h->end() + 1,
         -end    => $slice->seq_region_length(),
         -alternate_slice => $aslice);
    }
  }


  # check if exception regions contain our feature

  my @features;

  foreach my $axf (@alt) {
    # ignore other region if feature is not entirely on it
    next if($self->seq_region_start() < $axf->start() ||
            $self->seq_region_end()   > $axf->end());

    # quick shallow copy of the feature
    my $f;
    %$f = %$self;
    bless $f, ref($self);

    my $aslice = $axf->alternate_slice();

    # position feature on entire slice of other region
    $f->{'start'}  = $f->seq_region_start() - $axf->start() + $aslice->start();
    $f->{'end'}    = $f->seq_region_end()   - $axf->start() + $aslice->start();
    $f->{'strand'} *= $aslice->strand();

    $f->{'slice'} = $sa->fetch_by_seq_region_id($aslice->get_seq_region_id());

    push @features, $f;
  }

  return \@features;
}

public Listref Bio::EnsEMBL::Gene::get_all_Attributes ( )

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

Code:

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public Hashref Bio::EnsEMBL::Gene::get_all_DAS_Features ( )

  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 : none
  Caller     : webcode
  Status     : Stable

Code:

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Reimplemented from Bio::EnsEMBL::Storable.

public Bio::EnsEMBL::Gene::get_all_DASFactories ( )

  Example    : $dasref = $prot->get_all_DASFactories
  Description: Retrieves a listref of registered DAS objects
              TODO: Abstract to a DBLinkContainer obj
  Returntype : [ DAS_objects ]
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Listref Bio::EnsEMBL::Gene::get_all_DBEntries ( )

  Arg [1]    : (optional) String, external database name

  Arg [2]    : (optional) String, external_db type

  Example    : @dbentries = @{ $gene->get_all_DBEntries() };

  Description: Retrieves DBEntries (xrefs) for this gene.  This does
not* include DBEntries that are associated with the
               transcripts and corresponding translations of this
               gene (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 gene (i.e. they have not
               already been added or loaded).

  Return type: Listref of Bio::EnsEMBL::DBEntry objects
  Exceptions : none
  Caller     : get_all_DBLinks, GeneAdaptor::store
  Status     : Stable

Code:

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public Listref Bio::EnsEMBL::Gene::get_all_DBLinks ( )

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

  Example    : @dblinks = @{ $gene->get_all_DBLinks() };
               @dblinks = @{ $gene->get_all_DBLinks('Uniprot%') };

  Description: Retrieves *all* related DBEntries for this gene. This
               includes all DBEntries that are associated with the
               transcripts and corresponding translations of this
               gene.

               If you only want to retrieve the DBEntries
               associated with the gene (and not the transcript
               and translations) 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

Code:

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public Listref Bio::EnsEMBL::Gene::get_all_Exons ( )

  Example    : my @exons = @{ $gene->get_all_Exons };
  Description: Returns a set of all the exons associated with this gene.
  Returntype : Listref of Bio::EnsEMBL::Exon objects
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Listref Bio::EnsEMBL::Gene::get_all_homologous_Genes ( )

  Description: Queries the Ensembl Compara database and retrieves all
               Genes from other species that are orthologous.
               REQUIRES properly setup Registry conf file. Meaning that
               one of the aliases for each core db has to be "Genus species"
               e.g. "Homo sapiens" (as in the name column in genome_db table
               in the compara database).
  Returntype : listref [
                        Bio::EnsEMBL::Gene,
                        Bio::EnsEMBL::Compara::Homology,
                        string $species # needed as cannot get spp from Gene 
                       ]
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Listref Bio::EnsEMBL::Gene::get_all_object_xrefs ( )

  Arg [1]    : (optional) String, external database name

  Arg [2]    : (optional) String, external_db type

  Example    : @oxrefs = @{ $gene->get_all_object_xrefs() };

  Description: Retrieves xrefs for this gene.  This does *not*
               include xrefs that are associated with the
               transcripts or corresponding translations of this
               gene (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 gene (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

Code:

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public Listref Bio::EnsEMBL::Gene::get_all_Transcripts ( )

  Example    : my @transcripts = @{ $gene->get_all_Transcripts };
  Description: Returns the Transcripts in this gene.
  Returntype : Listref of Bio::EnsEMBL::Transcript objects
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Listref Bio::EnsEMBL::Gene::get_all_unconventional_transcript_associations ( )

  Arg [1]    : (optional) String - Only get transcripts where the association
               between this gene and the transcripts is of a certain type.
  Example    : my @transcripts = @{ $gene->get_all_unconventional_transcript_associations, "antisense" };
  Description: Returns the unconventional transcripts associated with this gene.
  Returntype : Listref of Bio::EnsEMBL::UnconventionalTranscriptAssociation objects
  Exceptions : none
  Caller     : general
  Status     : At risk.

Code:

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public Listref Bio::EnsEMBL::Gene::get_all_xrefs ( )

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

  Example    : @xrefs = @{ $gene->get_all_xrefs() };
               @xrefs = @{ $gene->get_all_xrefs('Uniprot%') };

  Description: Retrieves *all* related xrefs for this gene.  This
               includes all xrefs that are associated with the
               transcripts and corresponding translations of this
               gene.

               If you want to retrieve the xrefs associated
               with only the gene (and not the transcript
               or translations) 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

Code:

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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

Code:

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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

Code:

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public Bio::EnsEMBL::Feature::id ( ) [inherited]

Undocumented method

Code:

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public Int Bio::EnsEMBL::Gene::is_current ( )

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

Code:

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public Boolean Bio::EnsEMBL::Gene::is_known ( )

  Example    : print "Gene ".$gene->stable_id." is KNOWN\\n" if $gene->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

Code:

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public Bio::EnsEMBL::Gene::is_reference ( )

Undocumented method

Code:

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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

Code:

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public Int Bio::EnsEMBL::Feature::length ( ) [inherited]

  Arg [1]    : none
  Example    : $length = $feat->length();
  Description: Returns the length of this feature
  Returntype : Integer
  Exceptions : Throws if end < start and the feature is not on a
               circular slice
  Caller     : general
  Status     : Stable

Code:

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Reimplemented in Bio::EnsEMBL::Intron, Bio::EnsEMBL::Transcript, and Bio::EnsEMBL::Upstream.

public Bio::EnsEMBL::Gene::load ( )

  Arg [1]       : Boolean $load_xrefs
                  Load (or don't load) xrefs.  Default is to load xrefs.
  Example       : $gene->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 all the transcripts of the gene.
  Returns       :

Code:

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public String Bio::EnsEMBL::Gene::modified_date ( )

  Arg [1]    : (optional) String - modified date to set (as a UNIX time int)
  Example    : $gene->modified_date('1141948800');
  Description: Getter/setter for attribute modified_date
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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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

Code:

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Reimplemented in Bio::EnsEMBL::Exon, Bio::EnsEMBL::KaryotypeBand, and Bio::EnsEMBL::Map::QtlFeature.

public Bio::EnsEMBL::Gene Bio::EnsEMBL::Gene::new ( )

  Arg [-START]  : 
       int - start postion of the gene
  Arg [-END]    : 
       int - end position of the gene
  Arg [-STRAND] : 
       int - 1,-1 tehe strand the gene is on
  Arg [-SLICE]  : 
       Bio::EnsEMBL::Slice - the slice the gene is on
  Arg [-STABLE_ID] :
        string - the stable identifier of this gene
  Arg [-VERSION] :
        int - the version of the stable identifier of this gene
  Arg [-EXTERNAL_NAME] :
        string - the external database name associated with this gene
  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 gene when it is displayed.
  Arg [-TRANSCRIPTS]:
        Listref of Bio::EnsEMBL::Transcripts - this gene's transcripts
  Arg [-CREATED_DATE]:
        string - the date the gene was created
  Arg [-MODIFIED_DATE]:
        string - the date the gene was last modified
  Arg [-DESCRIPTION]:
        string - the genes description
  Arg [-BIOTYPE]:
        string - the biotype e.g. "protein_coding"
  Arg [-STATUS]:
        string - the gene status i.e. "KNOWN","NOVEL"
  Arg [-SOURCE]:
        string - the genes source, e.g. "ensembl"
  Arg [-IS_CURRENT]:
        Boolean - specifies if this is the current version of the gene
  Arg [-CANONICAL_TRANSCRIPT]:
        Bio::EnsEMBL::Transcript - the canonical transcript of this gene
  Arg [-CANONICAL_TRANSCRIPT_ID]:
        integer - the canonical transcript dbID of this gene, if the
        transcript object itself is not available.
  Arg [-CANONICAL_ANNOTATION]:
        string - canonical annotation

  Example    : $gene = Bio::EnsEMBL::Gene->new(...);
  Description: Creates a new gene object
  Returntype : Bio::EnsEMBL::Gene
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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sub new {
  my $caller = shift;

  my $class = ref($caller) || $caller;
  my $self = $class->SUPER::new(@_);
  my (
    $stable_id,               $version,
    $external_name,           $type,
    $external_db,             $external_status,
    $display_xref,            $description,
    $transcripts,             $created_date,
    $modified_date,           $confidence,
    $biotype,                 $source,
    $status,                  $is_current,
    $canonical_transcript_id, $canonical_transcript,
    $canonical_annotation
    )
    = rearrange( [
      'STABLE_ID',               'VERSION',
      'EXTERNAL_NAME',           'TYPE',
      'EXTERNAL_DB',             'EXTERNAL_STATUS',
      'DISPLAY_XREF',            'DESCRIPTION',
      'TRANSCRIPTS',             'CREATED_DATE',
      'MODIFIED_DATE',           'CONFIDENCE',
      'BIOTYPE',                 'SOURCE',
      'STATUS',                  'IS_CURRENT',
      'CANONICAL_TRANSCRIPT_ID', 'CANONICAL_TRANSCRIPT',
      'CANONICAL_ANNOTATION'
    ],
    @_
    );


  if ($transcripts) {
    $self->{'_transcript_array'} = $transcripts;
    $self->recalculate_coordinates();
  }

  $self->stable_id($stable_id);
  $self->version($version);
  $self->{'created_date'}  = $created_date;
  $self->{'modified_date'} = $modified_date;

  $self->external_name($external_name) if ( defined $external_name );
  $self->external_db($external_db)     if ( defined $external_db );
  $self->external_status($external_status)
    if ( defined $external_status );
  $self->display_xref($display_xref) if ( defined $display_xref );
  $self->biotype($type)              if ( defined $type );
  $self->biotype($biotype)           if ( defined $biotype );
  $self->description($description);
  $self->status($confidence);    # incase old naming is used.
      # kept to ensure routine is backwards compatible.
  $self->status($status);    # add new naming
  $self->source($source);

  # default to is_current
  $is_current = 1 unless (defined($is_current));
  $self->{'is_current'} = $is_current;

  # Add the canonical transcript if we were given one, otherwise add the
  # canonical transcript internal ID if we were given one.
  if ( defined($canonical_transcript) ) {
    $self->canonical_transcript($canonical_transcript);
  } elsif ( defined($canonical_transcript_id) ) {
    $self->{'canonical_transcript_id'} = $canonical_transcript_id;
  }

  $self->canonical_annotation($canonical_annotation)
    if ( defined $canonical_annotation );

  return $self;
}

Reimplemented from Bio::EnsEMBL::Feature.

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

Code:

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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

Code:

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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

Code:

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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

Code:

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public void Bio::EnsEMBL::Gene::recalculate_coordinates ( )

  Example    : $gene->recalculate_coordinates;
  Description: Called when transcript added to the gene, tries to adapt the
               coords for the gene.
  Returntype : none
  Exceptions : none
  Caller     : internal
  Status     : Stable

Code:

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public Listref Bio::EnsEMBL::Gene::remove_unconventional_transcript_associations ( )

  Args       : None
  Example    : $gene->remove_unconventional_transcript_associations();
  Description: Returns the unconventional transcripts associated with this gene.
  Returntype : Listref of Bio::EnsEMBL::UnconventionalTranscriptAssociation objects
  Exceptions : none
  Caller     : general
  Status     : At risk.

Code:

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public Undef Bio::EnsEMBL::Feature::seq ( ) [inherited]

  Args       : none
  Example    : my $dna_sequence = $simple_feature->seq();
  Description: Returns the dna sequence from the attached slice and 
               attached database that overlaps with this feature.
               Returns undef if there is no slice or no database.
               Returns undef if this feature is unstranded (i.e. strand=0).
  Returntype : undef or string
  Exceptions : warning if this feature is not stranded
  Caller     : general
  Status     : Stable

Code:

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Reimplemented in Bio::EnsEMBL::Exon, and Bio::EnsEMBL::Transcript.

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

Code:

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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

Code:

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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

Code:

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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

Code:

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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

Code:

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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

Code:

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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

Code:

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Reimplemented in Bio::EnsEMBL::Exon, and Bio::EnsEMBL::Map::DitagFeature.

public String Bio::EnsEMBL::Gene::source ( )

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

Code:

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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

Code:

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Reimplemented in Bio::EnsEMBL::FeaturePair.

public String Bio::EnsEMBL::Gene::stable_id ( )

  Arg [1]    : (optional) String - the stable ID to set
  Example    : $gene->stable_id("ENSG0000000001");
  Description: Getter/setter for stable id for this gene.
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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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

Code:

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Reimplemented in Bio::EnsEMBL::Exon, Bio::EnsEMBL::Map::DitagFeature, Bio::EnsEMBL::SplicingEventFeature, and Bio::EnsEMBL::SplicingTranscriptPair.

public String Bio::EnsEMBL::Gene::status ( )

  Arg [1]    : (optional) String - status to set
  Example    : $gene->status('KNOWN');
  Description: Getter/setter for attribute status
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Medium Risk

Code:

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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

Code:

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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

Code:

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public Hashref Bio::EnsEMBL::Gene::summary_as_hash ( )

  Example       : $gene_summary = $gene->summary_as_hash();
  Description   : Extends Feature::summary_as_hash
                  Retrieves a summary of this Gene object.

  Returns       : hashref of arrays of descriptive strings
  Status        : Intended for internal use

Code:

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Reimplemented from Bio::EnsEMBL::Feature.

public Bio::EnsEMBL::Gene::temporary_id ( )

Function:

Deprecated:: : Use dbID or stable_id or something else instead

Code:

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public Bio::EnsEMBL::Gene Bio::EnsEMBL::Gene::transfer ( )

  Arg [1]    : Bio::EnsEMBL::Slice $destination_slice
  Example    : my $new_gene = $gene->transfer($slice);
  Description: Moves this Gene to given target slice coordinates. If Transcripts
               are attached they are moved as well. Returns a new gene.
  Returntype : Bio::EnsEMBL::Gene
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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Reimplemented from Bio::EnsEMBL::Feature.

public Bio::EnsEMBL::Gene Bio::EnsEMBL::Gene::transform ( )

  Arg [1]    : String - coordinate system name to transform to
  Arg [2]    : String - coordinate system version
  Example    : my $new_gene = $gene->transform('supercontig');
  Description: Moves this gene to the given coordinate system. If this gene has
               Transcripts attached, they move as well.
  Returntype : Bio::EnsEMBL::Gene
  Exceptions : throw on wrong parameters
  Caller     : general
  Status     : Stable

Code:

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Reimplemented from Bio::EnsEMBL::Feature.

public Bio::EnsEMBL::Gene::type ( )

  Description:
Deprecated:
. Use biotype() instead.

Code:

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public Int Bio::EnsEMBL::Gene::version ( )

  Arg [1]    : (optional) Int
               A version number for the stable_id
  Example    : $gene->version(2);
  Description: Getter/setter for version number
  Returntype : Int
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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

Bio/EnsEMBL/Gene.pm

Class Summary

Synopsis

Description

Available Methods

Method Documentation