sub downstart { my $self = shift; if (@_) { $self->{_downstart} = shift @_; return } if (! defined $self->{_downstart}) { $self->_derive_coords('down'); } return $self->{_downstart} }

Class Summary
Synopsis
use Bio::EnsEMBL::Upstream; my $upstream = Bio::EnsEMBL::Upstream-\>new( -transcript =\> $transcript, -length =\> 2000 # bp ); # Retrieve coordinates of upstream region my $upstream_region_start = $upstream-\>upstart; my $upstream_region_end = $upstream-\>upend; # Retrieve coordinates in 'downstream' first intron my $intron_region_start = $upstream-\>downstart; my $intron_region_end = $upstream-\>downend; # Coordinates are returned in the same scheme as the input transcript. # However, the coordinates of an upstream region can be transformed to # any other scheme using a slice $upstream-\>transform($slice); # Coordinates can be retrieved in scheme in the same manner as the # above.
Description
An object that determines the upstream region of a transcript. Such a region is non-coding and ensures that other genes or transcripts are not present. Ultimately, these objects can be used to looking for promoter elements. To this end, it is also possible to derive a region downstream of the first exon, within the first intron and where promoter elements sometimes are found.
Definition at line 45 of file Upstream.pm.
Available Methods | |
protected In | _bases_to_trim () |
protected | _deprecated_transform () |
protected void | _derive_coords () |
protected Bio::EnsEMBL::Exon | _first_coding_Exon () |
protected void | _flush_cache () |
public Bio::EnsEMBL::DBSQL::BaseAdaptor | adaptor () |
public | add_sub_SeqFeature () |
public Bio::EnsEMBL::Analysis | analysis () |
public | contig () |
public String | coord_system_name () |
public Int | dbID () |
public Arrayref | derive_downstream_coords () |
public Arrayref | derive_upstream_coords () |
public String | display_id () |
public Int | downend () |
public Int | downstart () |
public Int | end () |
public Boolean Or Undef | equals () |
public Bio::EnsEMBL::Slice | feature_Slice () |
public | flush_sub_SeqFeature () |
public Reference | get_all_alt_locations () |
public | get_all_DAS_Features () |
public Bio::EnsEMBL::Gene | get_nearest_Gene () |
public List | get_overlapping_Genes () |
public | id () |
public Boolean | is_stored () |
public Int | length () |
public void | move () |
public Bio::EnsEMBL::Upstream | new () |
public Bio::EnsEMBL::Feature | new_fast () |
public Boolean | overlaps () |
public List | project () |
public List | project_to_slice () |
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 | species () |
public Int | start () |
public Int | strand () |
public | sub_SeqFeature () |
public Hashref | summary_as_hash () |
public Bio::EnsEMBL::Transcript | transcript () |
public Bio::EnsEMBL::Feature | transfer () |
public | transform () |
public Int | upend () |
public Int | upstart () |
Method Documentation
protected In Bio::EnsEMBL::Upstream::_bases_to_trim | ( | ) |
Arg : string $end_to_trim (either 'right_end' or 'left_end'). Arg : Bio::EnsEMBL::Slice Example : $self->_derive_coords('right_end', $slice); Description: Finds exons from other genes/transcripts that invade our upstream/downstream slice and returns the number of bases that should be truncated from the appropriate end of the upstream/downstream region. Returntype : in Exceptions : Throws if argument is not either 'right_end' or 'left_end' Caller : $self->_derive_coords Status : Stable

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

protected void Bio::EnsEMBL::Upstream::_derive_coords | ( | ) |
Arg : string $direction (either 'up' or 'down'). Example : $self->_derive_coords('up'); Description: Determines the coordinates of either upstream or downstream region. Returntype : none Exceptions : Throws if argument is not either 'up' or 'down' Caller : $self->upstart, $self->upend, $self->downstart, $self->downend Status : Stable

protected Bio::EnsEMBL::Exon Bio::EnsEMBL::Upstream::_first_coding_Exon | ( | ) |
Arg : none Example : $self->_first_coding_Exon; Description: Finds the first exon of our transcript that contains coding bases. Returntype : Bio::EnsEMBL::Exon Exceptions : none Caller : $self->_derive_coords, $self->_bases_to_trim Status : Stable

protected void Bio::EnsEMBL::Upstream::_flush_cache | ( | ) |
Arg : none Example : $self->_flush_cache; Description: Empties cached coordinates (called when coordinate scheme or region length has changed). Returntype : none Exceptions : none Caller : $self->length, $self->transform Status : Stable

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

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 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 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 Arrayref Bio::EnsEMBL::Upstream::derive_downstream_coords | ( | ) |
Arg : none Example : my ($downstart, $downend) = $self->derive_downstream_coords; Description: Derives downstream coordinates (for compatability with older scripts). Returntype : arrayref Exceptions : none Caller : general Status : Stable

public Arrayref Bio::EnsEMBL::Upstream::derive_upstream_coords | ( | ) |
Arg : none Example : my ($upstart, $upend) = $self->derive_upstream_coords; Description: Derives upstream coordinates (for compatability with older scripts). Returntype : arrayref Exceptions : none Caller : general Status : Stable

public String Bio::EnsEMBL::Feature::display_id | ( | ) | [inherited] |
Arg [1] : none Example : print $f->display_id(); Description: This method returns a string that is considered to be the 'display' identifier. It is overridden by subclasses to return an appropriate value for objects of that particular class. If no appropriate display id is available an empty string is returned instead. Returntype : string Exceptions : none Caller : web drawing code Status : Stable

Reimplemented in Bio::EnsEMBL::AssemblyExceptionFeature, Bio::EnsEMBL::Exon, Bio::EnsEMBL::FeaturePair, Bio::EnsEMBL::Gene, Bio::EnsEMBL::KaryotypeBand, Bio::EnsEMBL::Map::MarkerFeature, Bio::EnsEMBL::MiscFeature, Bio::EnsEMBL::PredictionTranscript, Bio::EnsEMBL::RepeatFeature, Bio::EnsEMBL::SimpleFeature, and Bio::EnsEMBL::Transcript.
public Int Bio::EnsEMBL::Upstream::downend | ( | ) |
Arg : none Example : $self->downend; Description: Returns the end coordinate of the region in the first intron of the transcript. This coordinate is always furthest from the first exon (irregardless of strand). Returntype : int Exceptions : none Caller : general Status : Stable

public Int Bio::EnsEMBL::Upstream::downstart | ( | ) |
Arg : none Example : $self->downstart; Description: Returns the start coordinate of the region in the first intron of the transcript. This coordinate is always closest to the first exon (irregardless of strand). Returntype : int 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 Or Undef Bio::EnsEMBL::Feature::equals | ( | ) | [inherited] |
Arg [1] : Bio::EnsEMBL::Feature object Example : if ($featureA->equals($featureB)) { ... } Description : Compares two features using various criteria. The test for eqality goes through the following list and terminates at the first true match:
1. If the two features are the same object, they are equal. 2. If they are of different types (e.g., transcript and gene), they are *not* equal. 3. If they both have dbIDs: if these are the same, then they are equal, otherwise not. 4. If they both have slices and analysis objects: if the analysis dbIDs are the same and the seq_region_id are the same, along with seq_region_start and seq_region_end, then they are equal, otherwise not.
If none of the above is able to determine equality, undef is returned.
Return type : tri-Boolean (0, 1, undef = "unknown")
Exceptions : Thrown if a non-feature is passed as the argument.

Reimplemented in Bio::EnsEMBL::Exon, Bio::EnsEMBL::Gene, and Bio::EnsEMBL::Transcript.
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 Bio::EnsEMBL::Feature::flush_sub_SeqFeature | ( | ) | [inherited] |
Undocumented method

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 Bio::EnsEMBL::Storable::get_all_DAS_Features | ( | ) | [inherited] |
Undocumented method

Reimplemented in Bio::EnsEMBL::Gene, Bio::EnsEMBL::Transcript, and Bio::EnsEMBL::Translation.
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 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::Upstream::length | ( | ) |
Arg : (optional) int $length Example : $self->length(2000); # bp Description: Getter/setter for upstream region length. Returntype : int Exceptions : Throws if length is requested before it has been set. Caller : $self->new, $self->_derive_coords Status : Stable

Reimplemented from Bio::EnsEMBL::Feature.
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::Upstream Bio::EnsEMBL::Upstream::new | ( | ) |
Arg [transcript] : (optional) Bio::EnsEMBL::Transcript Arg [length] : (optional) int $length Example : $upstream = Bio::EnsEMBL::Upstream->new(-transcript => $transcript, -length => 2000); Description: Creates a new upstream object Returntype : Bio::EnsEMBL::Upstream Exceptions : none Caller : Bio::EnsEMBL::Transcript, 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 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::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 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 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::Feature::summary_as_hash | ( | ) | [inherited] |
Example : $feature_summary = $feature->summary_as_hash(); Description : Retrieves a textual summary of this Feature. Should be overidden by subclasses for specific tweaking Returns : hashref of arrays of descriptive strings Status : Intended for internal use

Reimplemented in Bio::EnsEMBL::Gene, and Bio::EnsEMBL::Transcript.
public Bio::EnsEMBL::Transcript Bio::EnsEMBL::Upstream::transcript | ( | ) |
Arg : (optional) Bio::EnsEMBL::Transcript Example : $self->transcript($transcript); Description: Getter/setter for transcript object Returntype : Bio::EnsEMBL::Transcript Exceptions : Throws if argument is not undefined or a Bio::EnsEMBL::Transcript Caller : $self->new, $self->_derive_coords, $self->_first_coding_Exon Status : Stable

public Bio::EnsEMBL::Feature Bio::EnsEMBL::Feature::transfer | ( | ) | [inherited] |
Arg [1] : Bio::EnsEMBL::Slice $slice The slice to transfer this feature to Example : $feature = $feature->transfer($slice); next if(!defined($feature)); Description: Returns a copy of this feature which has been shifted onto another slice.
If the new slice is in a different coordinate system the feature is transformed first and then placed on the slice. If the feature would be split across a coordinate system boundary or mapped to a gap undef is returned instead.
If the feature cannot be placed on the provided slice because it maps to an entirely different location, undef is returned instead.
Returntype : Bio::EnsEMBL::Feature (or undef) Exceptions : throw on incorrect argument throw if feature does not have attached slice Caller : general, transform() Status : Stable

Reimplemented in Bio::EnsEMBL::Exon, Bio::EnsEMBL::Gene, Bio::EnsEMBL::PredictionExon, Bio::EnsEMBL::PredictionTranscript, and Bio::EnsEMBL::Transcript.
public Bio::EnsEMBL::Upstream::transform | ( | ) |
Arg : Example : Description: Not yet implemented Returntype : Exceptions : Caller : Status : At Risk

Reimplemented from Bio::EnsEMBL::Feature.
public Int Bio::EnsEMBL::Upstream::upend | ( | ) |
Arg : none Example : $self->upend; Description: Returns the end coordinate of the region upstream of the transcript. This coordinate always always abutts the translation initiation codon, whereas upstart always returns the coorindate furthest from the translation initiation codon. Returntype : int Exceptions : none Caller : general Status : Stable

public Int Bio::EnsEMBL::Upstream::upstart | ( | ) |
Arg : none Example : $self->upstart; Description: Returns the start coordinate of the region upstream of the transcript. This coordinate is always the furthest from the translation initiation codon, whereas upend always abutts the translation initiation codon. Returntype : int Exceptions : none Caller : general Status : Stable

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