Inheritance diagram for Bio::EnsEMBL::Upstream:

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

Code:

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

Undocumented method

Code:

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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

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sub _derive_coords {
  my ($self, $direction) = @_;

  # Check direction
  throw("Must specify either \'up\' of \'down\'-stream direction to derive coords.")
    unless (($direction eq 'up')||($direction eq 'down'));

  # Put things in easily accessible places.
  my $core_db_slice_adaptor = $self->transcript->slice->adaptor;
  my $region_length = $self->length;

  # Whatever coord system the gene is currently is, transform to the toplevel.
  my $transcript = $self->transcript->transform('toplevel');

  # Use our transformed transcript to determine the upstream region coords.
  # End should always be just before the coding start (like ATG), including 3' UTR.
  # Start is the outer limit of the region upstream (furthest from ATG).

  my $region_start;
  my $region_end;

  if ($transcript->strand == 1){
    if ($direction eq 'up'){
      $region_end = $transcript->coding_region_start - 1;
      $region_start = $region_end - $region_length;
    } elsif ($direction eq 'down'){
      $region_end = $self->_first_coding_Exon->end + 1;
      $region_start = $region_end + $region_length;
    }
  } elsif ($transcript->strand == -1) {
    if ($direction eq 'up'){
      $region_end = $transcript->coding_region_end + 1;
      $region_start = $region_end + $region_length;

    } elsif ($direction eq 'down'){
      $region_end = $self->_first_coding_Exon->start - 1;
      $region_start = $region_end - $region_length;
    }
  }

  # Trim the upstream/downstream region to remove extraneous coding sequences 
  # from other genes and/or transcripts.
    
  my ($slice_low_coord, $slice_high_coord) = sort {$a <=> $b} ($region_start, $region_end);

  my $region_slice 
      = $core_db_slice_adaptor->fetch_by_region($transcript->slice->coord_system->name,
                        $transcript->slice->seq_region_name, 
                        $slice_low_coord, 
                        $slice_high_coord);

  if ($transcript->strand == 1) {
    if ($direction eq 'up') {
      $region_start += $self->_bases_to_trim('left_end', $region_slice);
    } elsif ($direction eq 'down') {
      $region_start -= $self->_bases_to_trim('right_end', $region_slice);
    }
  } elsif ($transcript->strand == -1) {
    if ($direction eq 'up') {
      $region_start -= $self->_bases_to_trim('right_end', $region_slice);
    } elsif ($direction eq 'down') {
      $region_start += $self->_bases_to_trim('left_end', $region_slice);
    }
  }

  # Always return start < end

  ($region_start, $region_end) = sort {$a <=> $b} ($region_start, $region_end);

  if ($direction eq 'up') {
    $self->upstart($region_start);
    $self->upend($region_end);
  } elsif ($direction eq 'down') {
    $self->downstart($region_start);
    $self->downend($region_end);
  }
}

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

Code:

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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

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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

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

Undocumented method

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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

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Reimplemented in Bio::EnsEMBL::DensityFeature.

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

Undocumented method

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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 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 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

Code:

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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

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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

Code:

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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

Code:

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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

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 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.

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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

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

Undocumented method

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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 Bio::EnsEMBL::Storable::get_all_DAS_Features ( ) [inherited]

Undocumented method

Code:

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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

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

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

Undocumented method

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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

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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

Code:

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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

Code:

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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

Code:

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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 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::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 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 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::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

Code:

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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

Code:

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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

Code:

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sub transfer {
  my $self = shift;
  my $slice = shift;

  if(!$slice || !ref($slice) || (!$slice->isa('Bio::EnsEMBL::Slice') && !$slice->isa('Bio::EnsEMBL::LRGSlice'))) {
    throw('Slice argument is required');
  }

  #make a shallow copy of the feature to be transfered
  my $feature;
  %{$feature} = %{$self};
  bless $feature, ref($self);

  my $current_slice = $self->{'slice'};

  if(!$current_slice) {
    warning("Feature cannot be transfered without attached slice.");
    return undef;
  }

  my $cur_cs = $current_slice->coord_system();
  my $dest_cs = $slice->coord_system();

  #if we are not in the same coord system a transformation step is needed first
  if(!$dest_cs->equals($cur_cs)) {
    $feature = $feature->transform($dest_cs->name, $dest_cs->version, $slice);
    return undef if(!defined($feature));
    $current_slice = $feature->{'slice'};
  }

  # feature went to entirely different seq_region
  if($current_slice->seq_region_name() ne $slice->seq_region_name()) {
    return undef;
  }

  #if the current feature positions are not relative to the start of the
  #seq region, convert them so they are
  my $cur_slice_start  = $current_slice->start();
  my $cur_slice_strand = $current_slice->strand();
  if($cur_slice_start != 1 || $cur_slice_strand != 1) {
    my $fstart = $feature->{'start'};
    my $fend   = $feature->{'end'};

    if($cur_slice_strand == 1) {
      $feature->{'start'} = $fstart + $cur_slice_start - 1;
      $feature->{'end'}   = $fend   + $cur_slice_start - 1;
    } else {
      my $cur_slice_end = $current_slice->end();
      $feature->{'start'}  = $cur_slice_end - $fend   + 1;
      $feature->{'end'}    = $cur_slice_end - $fstart + 1;
      $feature->{'strand'} *= -1;
    }
  }

  my $fstart = $feature->{'start'};
  my $fend   = $feature->{'end'};

  #convert to destination slice coords
  if($slice->strand == 1) {
    $feature->{'start'} = $fstart - $slice->start() + 1;
    $feature->{'end'}   = $fend   - $slice->start() + 1;
  } else {
    $feature->{'start'} = $slice->end() - $fend   + 1;
    $feature->{'end'}   = $slice->end() - $fstart + 1;
    $feature->{'strand'} *= -1;
  }

  $feature->{'slice'} = $slice;

  return $feature;
}

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

Code:

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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

Code:

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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

Code:

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

Bio/EnsEMBL/Upstream.pm

Class Summary

Synopsis

Description

Available Methods

Method Documentation