sub seq_region_start { my ($self) = @_; my $slice = $self->slice(); if ( defined($slice) ) { my $start; if ( $slice->strand() == 1 ) { if ( defined( $self->start() ) ) { if ($self->start < 0 && $slice->is_circular) { $start = $slice->seq_region_length + $self->start; } else { $start = $slice->start() + $self->start() - 1; } } } else { if ( defined( $self->end() ) ) { $start = $slice->end() - $self->end() + 1; } } if ( defined($start) && $slice->is_circular() && $start > $slice->seq_region_length() ) { $start -= $slice->seq_region_length(); } return $start; } return undef; } ## end sub seq_region_start

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

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

public void Bio::EnsEMBL::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

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

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.

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

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

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.

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

Reimplemented in Bio::EnsEMBL::DensityFeature.
public String Bio::EnsEMBL::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

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

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

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().

public Bio::EnsEMBL::Gene::confidence | ( | ) |
public Bio::EnsEMBL::Feature::contig | ( | ) | [inherited] |
Undocumented method

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

public 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

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

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

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

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

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

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

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

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

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

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

public 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

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

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

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

public 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

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

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

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

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

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

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

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

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

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.

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

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

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

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

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

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

public Bio::EnsEMBL::Gene::is_reference | ( | ) |
Undocumented method

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

public Int Bio::EnsEMBL::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

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 :

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

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

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

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

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

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

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

public 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

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.

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

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

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

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

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

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

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

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

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

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

Reimplemented in Bio::EnsEMBL::FeaturePair.
public 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

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

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

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

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

public Hashref Bio::EnsEMBL::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

Reimplemented from Bio::EnsEMBL::Feature.
public Bio::EnsEMBL::Gene::temporary_id | ( | ) |
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

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

Reimplemented from Bio::EnsEMBL::Feature.
public Bio::EnsEMBL::Gene::type | ( | ) |
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

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