Inheritance diagram for Bio::EnsEMBL::Slice:

Public Member Functions
public Bio::EnsEMBL::Slice	new ()

public Bio::EnsEMBL::Slice	new_fast ()

public Bio::EnsEMBL::DBSQL::SliceAdaptor	adaptor ()

public String	seq_region_name ()

public Int	seq_region_start ()

public Int	seq_region_end ()

public Int	seq_region_length ()

public Bio::EnsEMBL::CoordSystem	coord_system ()

public String	source ()

public String	coord_system_name ()

public Int	centrepoint ()

public Int	start ()

public Int	end ()

public Int	strand ()

public String	name ()

public Int	length ()

public Int	is_reference ()

public Int	is_toplevel ()

public Int	has_karyotype ()

public Int	karyotype_rank ()

public Int	is_circular ()

public Bio::EnsEMBL::Slice	invert ()

public String	seq ()

public Txt	subseq ()

public Bio::EnsEMBL::Utils::Iterator	sub_Slice_Iterator ()

public String	assembly_exception_type ()

public Boolean	is_chromosome ()

public Hashref	get_base_count ()

public List	project ()

protected	_constrain_to_region ()

public Bio::EnsEMBL::Slice	expand ()

public Bio::EnsEMBL::Slice	constrain_to_seq_region ()

public Bio::EnsEMBL::Slice	sub_Slice ()

public Bio::EnsEMBL::Slice	seq_region_Slice ()

public Int	get_seq_region_id ()

public Scalar	get_genome_component ()

public Listref	get_all_Attributes ()

public Listref	get_all_PredictionTranscripts ()

public Listref	get_all_DnaAlignFeatures ()

public Listref	get_all_ProteinAlignFeatures ()

protected	_get_AlignFeatures ()

public Listref	get_all_SimilarityFeatures ()

public Listref	get_all_SimpleFeatures ()

public Listref	get_all_RepeatFeatures ()

public Bio::EnsEMBL::Variation::LDFeatureContainer	get_all_LD_values ()

protected	_get_VariationFeatureAdaptor ()

protected	_get_StructuralVariationFeatureAdaptor ()

protected Bio::EnsEMBL::DBSQL::BaseAdaptor	_get_VariationAdaptor ()

protected Bio::EnsEMBL::DBSQL::BaseAdaptor	_get_CoreAdaptor ()

protected Bio::EnsEMBL::DBSQL::BaseAdaptor	_get_Adaptor ()

public Listref	get_all_VariationFeatures ()

public Listref	get_all_somatic_VariationFeatures ()

public Listref	get_all_somatic_VariationFeatures_by_source ()

public Listref	get_all_somatic_VariationFeatures_with_phenotype ()

public Listref	get_all_VariationFeatures_by_Population ()

public Listref	get_all_Genes ()

public Listref	get_all_Genes_by_type ()

public Listref	get_all_Genes_by_source ()

public Reference	get_all_Transcripts ()

public Listref	get_all_Transcripts_by_type ()

public Listref	get_all_Transcripts_by_source ()

public Reference	get_all_Exons ()

public Listref	get_all_KaryotypeBands ()

public Bio::EnsEMBL::RepeatMaskedSlice	get_repeatmasked_seq ()

protected void	_mask_features ()

public Listref	get_all_SearchFeatures ()

public Listref	get_all_AssemblyExceptionFeatures ()

public Listref	get_all_MiscFeatures ()

public Reference	get_all_MarkerFeatures ()

public Reference	get_MarkerFeatures_by_Name ()

public Reference	get_all_compara_DnaAlignFeatures ()

public Arrayref	get_all_compara_Syntenies ()

public Listref	get_all_Haplotypes ()

public	get_all_DASFactories ()

public	get_all_DASFeatures_dsn ()

public Hashref	get_all_DAS_Features ()

public	get_all_DASFeatures ()

public	old_get_all_DASFeatures ()

public Listref	get_all_ExternalFeatures ()

public Listref	get_all_DitagFeatures ()

public Hash	get_generic_features ()

public List	project_to_slice ()

public Reference	get_all_synonyms ()

public void	add_synonym ()

public String	feature_so_acc ()

public String	feature_so_term ()

public Hashref	summary_as_hash ()

public	slice ()

public	id ()

public	display_id ()

public	primary_id ()

public	desc ()

public	moltype ()

public	alphabet ()

public	accession_number ()

Detailed Description

Synopsis

$sa = $db->get_SliceAdaptor;
 
$slice =
  $sa->fetch_by_region( 'chromosome', 'X', 1_000_000, 2_000_000 );
 
# get some attributes of the slice
my $seqname = $slice->seq_region_name();
my $start   = $slice->start();
my $end     = $slice->end();
 
# get the sequence from the slice
my $seq = $slice->seq();
 
# get some features from the slice
foreach $gene ( @{ $slice->get_all_Genes } ) {
  # do something with a gene
}
 
foreach my $feature ( @{ $slice->get_all_DnaAlignFeatures } ) {
  # do something with dna-dna alignments
}

Description

A Slice object represents a region of a genome.  It can be used to retrieve
sequence or features from an area of interest.

NOTE: The Slice is defined by its Strand, but normal behaviour for get_all_*
methods is to return Features on both Strands.

Definition at line 50 of file Slice.pm.

Member Function Documentation

◆ _constrain_to_region()

protected Bio::EnsEMBL::Slice::_constrain_to_region ( )

Undocumented method

Code:

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◆ _get_Adaptor()

protected Bio::EnsEMBL::DBSQL::BaseAdaptor Bio::EnsEMBL::Slice::_get_Adaptor ( )

  Arg  [1]    : String object_type to retrieve an adaptor for
  Arg  [2]    : String dbtype to search for the given adaptor in
  Arg  [3]    : Boolean Turn off the checking of Registry->get_db() for your 
                adaptor.
  Description : Searches for the specified adaptor in the Registry and returns it. Otherwise
                it will return nothing if the adaptor was not found. We consult the 
                "special" adaptors held by Bio::EnsEMBL::Registry::get_db() method and then
                fall back to the normal methods of finding an adaptor.

                This method will warn when adaptors are missing but will never through an
                exception. It is up to the calling code to decide how to handle the unavailablity
                of an adaptor.
  ReturnType  : Bio::EnsEMBL::DBSQL::BaseAdaptor derrived instance. Otherwise it returns nothing
  Exceptions  : none

Code:

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◆ _get_AlignFeatures()

protected Bio::EnsEMBL::Slice::_get_AlignFeatures ( )

  Arg [1]    : (optional) string $logic_name
               The name of the analysis performed on the protein align features
               to obtain.
  Arg [2]    : (optional) float $score
               The mimimum score of the features to retrieve
  Arg [3]    : (optional) string $dbtype
               The name of an attached database to retrieve features from
               instead.
  Arg [4]    : (optional) float hcoverage
               The minimum hcoverage od the featurs to retrieve
  Arg [5]    : string $align_type
               The type of adaptor to retrieve alignments from. Must be an BaseAlignFeature derived
               class
  Description: Generic method which deals with the retrieval of either AlignFeature adaptor and allows
               you to switch the adaptor values are retrieved from.

Code:

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◆ _get_CoreAdaptor()

protected Bio::EnsEMBL::DBSQL::BaseAdaptor Bio::EnsEMBL::Slice::_get_CoreAdaptor ( )

  Arg  [1]    : String object_type to retrieve an adaptor for
  Arg  [2]    : String dbtype to search for the given adaptor in. Defaults to core
  Description : Searches for the specified adaptor in the Registry and returns it. Otherwise
                it will return nothing if the adaptor was not found
  ReturnType  : Bio::EnsEMBL::DBSQL::BaseAdaptor derrived instance (specific to core-like dbs)
  Exceptions  : none

Code:

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◆ _get_StructuralVariationFeatureAdaptor()

protected Bio::EnsEMBL::Slice::_get_StructuralVariationFeatureAdaptor ( )

Shortcut method here because StructuralVariationFeature is an often requested
adaptor type.

Code:

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◆ _get_VariationAdaptor()

protected Bio::EnsEMBL::DBSQL::BaseAdaptor Bio::EnsEMBL::Slice::_get_VariationAdaptor ( )

  Arg  [1]    : String object_type to retrieve an adaptor for
  Arg  [2]    : String dbtype to search for the given adaptor in. Defaults to variation
  Description : Searches for the specified adaptor in the Registry and returns it. Otherwise
                it will return nothing if the adaptor was not found
  ReturnType  : Bio::EnsEMBL::DBSQL::BaseAdaptor derrived instance (specific to variation)
  Exceptions  : none

Code:

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◆ _get_VariationFeatureAdaptor()

protected Bio::EnsEMBL::Slice::_get_VariationFeatureAdaptor ( )

Shortcut method here because VariationFeature is an often requested
adaptor type.

Code:

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◆ _mask_features()

protected void Bio::EnsEMBL::Slice::_mask_features ( )

◆ accession_number()

public Bio::EnsEMBL::Slice::accession_number ( )

  Description: Included for Bio::PrimarySeqI interface compliance (1.2)

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◆ adaptor()

public Bio::EnsEMBL::DBSQL::SliceAdaptor Bio::EnsEMBL::Slice::adaptor ( )

  Arg [1]    : (optional) Bio::EnsEMBL::DBSQL::SliceAdaptor $adaptor
  Example    :

$adaptor = $slice->adaptor();

  Description: Getter/Setter for the slice object adaptor used
               by this slice for database interaction.
  Returntype : Bio::EnsEMBL::DBSQL::SliceAdaptor
  Exceptions : thorws if argument passed is not a SliceAdaptor
  Caller     : general
  Status     : Stable

Code:

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◆ add_synonym()

public void Bio::EnsEMBL::Slice::add_synonym ( )

  Args[0]    : synonym.
  Example    :

$slice->add_synonym("alt_name");

  Description: add an alternative name for this slice
  Returntype : none
  Exception  : none
  Caller     : general
  Status     : At Risk

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◆ alphabet()

public Bio::EnsEMBL::Slice::alphabet ( )

  Description: Included for Bio::PrimarySeqI interface compliance (1.2)

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◆ assembly_exception_type()

public String Bio::EnsEMBL::Slice::assembly_exception_type ( )

  Example     :

$self->assembly_exception_type();

  Description : Returns the type of slice this is. If it is reference then you
                will get 'REF' back. Otherwise you will get the first
                element from get_all_AssemblyExceptionFeatures(). If no
                assembly exception exists you will get an empty string back.
  Returntype  : String
  Exceptions  : None
  Caller      : Public
  Status      : Beta

Code:

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◆ centrepoint()

public Int Bio::EnsEMBL::Slice::centrepoint ( )

  Arg [1]    : none
  Example    :

$cp = $slice->centrepoint();

  Description: Returns the mid position of this slice relative to the
               start of the sequence region that it was created on.
               Coordinates are inclusive and start at 1.
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ constrain_to_seq_region()

public Bio::EnsEMBL::Slice Bio::EnsEMBL::Slice::constrain_to_seq_region ( )

  Example    :

$new_slice = $slice->expand(1000,10000);

$new_slice = $new_slice->constrain_to_seq_region();

  Description: Used to prevent overly zealous expand calls going off the end of
               the sequence region. It contracts the start and end where needed
               and produces a slice copy with the tweaked coordinates.
  Returntype : Bio::EnsEMBL::Slice

Code:

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◆ coord_system()

public Bio::EnsEMBL::CoordSystem Bio::EnsEMBL::Slice::coord_system ( )

  Arg [1]    : none
  Example    :

print $slice->coord_system->name();

  Description: Returns the coordinate system that this slice is on.
  Returntype : Bio::EnsEMBL::CoordSystem
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ coord_system_name()

public String Bio::EnsEMBL::Slice::coord_system_name ( )

  Arg [1]    : none
  Example    :

print $slice->coord_system_name()

  Description: Convenience method.  Gets the name of the coord_system which
               this slice is on.
               Returns undef if this Slice does not have an attached
               CoordSystem.
  Returntype: string or undef
  Exceptions: none
  Caller    : general
  Status     : Stable

Code:

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◆ desc()

public Bio::EnsEMBL::Slice::desc ( )

Description: Included for Bio::PrimarySeqI interface compliance (1.2)

Code:

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◆ display_id()

public Bio::EnsEMBL::Slice::display_id ( )

  Description: Included for Bio::PrimarySeqI interface compliance (1.2)

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◆ end()

public Int Bio::EnsEMBL::Slice::end ( )

  Arg [1]    : none
  Example    :

$end = $slice->end();

  Description: Returns the end position of this slice relative to the
               start of the sequence region that it was created on.
               Coordinates are inclusive and start at 1.  Negative coordinates
               or coordinates exceeding the length of the sequence region are
               permitted.  End is always greater than or equal to start
               regardless of the orientation of the slice.
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ expand()

public Bio::EnsEMBL::Slice Bio::EnsEMBL::Slice::expand ( )

  Arg [1]    : (optional) int $five_prime_expand
               The number of basepairs to shift this slices five_prime
               coordinate by.  Positive values make the slice larger,
               negative make the slice smaller.
               coordinate left.
               Default = 0.
  Arg [2]    : (optional) int $three_prime_expand
               The number of basepairs to shift this slices three_prime
               coordinate by. Positive values make the slice larger,
               negative make the slice smaller.
               Default = 0.
  Arg [3]    : (optional) bool $force_expand
               if set to 1, then the slice will be contracted even in the case
               when shifts $five_prime_expand and $three_prime_expand overlap.
               In that case $five_prime_expand and $three_prime_expand will be set
               to a maximum possible number and that will result in the slice
               which would have only 2pbs.
               Default = 0.
  Arg [4]    : (optional) int* $fpref
               The reference to a number of basepairs to shift this slices five_prime
               coordinate by. Normally it would be set to $five_prime_expand.
               But in case when $five_prime_expand shift can not be applied and
               $force_expand is set to 1, then $$fpref will contain the maximum possible
               shift
  Arg [5]    : (optional) int* $tpref
               The reference to a number of basepairs to shift this slices three_prime
               coordinate by. Normally it would be set to $three_prime_expand.
               But in case when $five_prime_expand shift can not be applied and
               $force_expand is set to 1, then $$tpref will contain the maximum possible
               shift
  Example    :

my $expanded_slice      = $slice->expand( 1000, 1000);
              my $contracted_slice    = $slice->expand(-1000,-1000);
              my $shifted_right_slice = $slice->expand(-1000, 1000);
              my $shifted_left_slice  = $slice->expand( 1000,-1000);
              my $forced_contracted_slice    = $slice->expand(-1000,-1000, 1, \$five_prime_shift, \$three_prime_shift);

  Description: Returns a slice which is a resized copy of this slice.  The
               start and end are moved outwards from the center of the slice
               if positive values are provided and moved inwards if negative
               values are provided. This slice remains unchanged.  A slice
               may not be contracted below 1bp but may grow to be arbitrarily
               large.
  Returntype : Bio::EnsEMBL::Slice
  Exceptions : warning if an attempt is made to contract the slice below 1bp
  Caller     : general
  Status     : Stable

Code:

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sub expand {
  my $self              = shift;
  my $five_prime_shift  = shift || 0;
  my $three_prime_shift = shift || 0;
  my $force_expand      = shift || 0;
  my $fpref             = shift;
  my $tpref             = shift;
 
  if ( $self->{'seq'} ) {
    warning(
       "Cannot expand a slice which has a manually attached sequence ");
    return undef;
  }
 
  my $sshift = $five_prime_shift;
  my $eshift = $three_prime_shift;
 
  if ($sshift == 0 && $eshift == 0) { return $self; }
 
  if ( $self->{'strand'} != 1 ) {
    $eshift = $five_prime_shift;
    $sshift = $three_prime_shift;
  }
 
  my $new_start = $self->{'start'} - $sshift;
  my $new_end   = $self->{'end'} + $eshift;
 
  # Wrap around on circular slices
  if (( $new_start <= 0 || $new_start > $self->seq_region_length() || $new_end <= 0 
        || $new_end > $self->seq_region_length() ) && ( $self->is_circular() ) ) {
      
      if ( $new_start <= 0 ) {
        $new_start = $self->seq_region_length() + $new_start;
      }
      if ( $new_start > $self->seq_region_length() ) {
        $new_start -= $self->seq_region_length();
      }
  
      if ( $new_end <= 0 ) {
        $new_end = $self->seq_region_length() + $new_end;
      }
      if ( $new_end > $self->seq_region_length() ) {
        $new_end -= $self->seq_region_length();
      }      
      
  }
 
  if ( $new_start > $new_end  && (not $self->is_circular() ) ) {
   
      if ($force_expand) {
        # Apply max possible shift, if force_expand is set
        if ( $sshift < 0 ) {
          # if we are contracting the slice from the start - move the
          # start just before the end
          $new_start = $new_end - 1;
          $sshift    = $self->{start} - $new_start;
        }
 
        if ( $new_start > $new_end ) {
          # if the slice still has a negative length - try to move the
          # end
          if ( $eshift < 0 ) {
            $new_end = $new_start + 1;
            $eshift  = $new_end - $self->{end};
          }
        }
        # return the values by which the primes were actually shifted
        $$tpref = $self->{strand} == 1 ? $eshift : $sshift;
        $$fpref = $self->{strand} == 1 ? $sshift : $eshift;
      }
      if ( $new_start > $new_end ) {
        throw('Slice start cannot be greater than slice end');
      }
  }
 
  #fastest way to copy a slice is to do a shallow hash copy
  my %new_slice = %$self;
  $new_slice{'start'} = int($new_start);
  $new_slice{'end'}   = int($new_end);
 
  return bless \%new_slice, ref($self);
} ## end sub expand

◆ feature_so_acc()

public String Bio::EnsEMBL::Slice::feature_so_acc ( )

  Example     :

$slice_so_acc = $slice->feature_so_acc;

  Description : This method returns a string containing the SO accession number of the slice, based on the coordinate system name.
  Returns     : string (Sequence Ontology accession number)

Code:

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◆ feature_so_term()

public String Bio::EnsEMBL::Slice::feature_so_term ( )

  Description: This method returns a string containing the SO term of the slice, based on the coordinate system name
               Define constant SEQUENCE_ONTOLOGY in classes that require it, or override it for multiple possible values for a class.
  Returntype : String (Sequence Ontology term)
  Exceptions : Thrown if caller SEQUENCE_ONTOLOGY is undefined and is not a Bio::EnsEMBL::Slice

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◆ get_all_AssemblyExceptionFeatures()

public Listref Bio::EnsEMBL::Slice::get_all_AssemblyExceptionFeatures ( )

  Example    :

$slice->get_all_AssemblyExceptionFeatures();

  Description: Retrieves all misc features which overlap this slice. If
               a set code is provided only features which are members of
               the requested set are returned.
  Returntype : listref of Bio::EnsEMBL::AssemblyExceptionFeatures
  Exceptions : none
  Caller     : general
  Status     : Stable

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◆ get_all_Attributes()

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

  Arg [1]    : optional string $attrib_code
               The code of the attribute type to retrieve values for.
  Example    :

($htg_phase) = @{$slice->get_all_Attributes('htg_phase')};

@slice_attributes = @{$slice->get_all_Attributes()};

  Description: Gets a list of Attributes of this slice''s seq_region.
               Optionally just get Attrubutes for given code.
  Returntype : listref Bio::EnsEMBL::Attribute
  Exceptions : warning if slice does not have attached adaptor
  Caller     : general
  Status     : Stable

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◆ get_all_compara_DnaAlignFeatures()

public Reference Bio::EnsEMBL::Slice::get_all_compara_DnaAlignFeatures ( )

  Arg [1]    : string $qy_species
               The name of the species to retrieve similarity features from
  Arg [2]    : string $qy_assembly
               The name of the assembly to retrieve similarity features from
  Arg [3]    : string $type
               The type of the alignment to retrieve similarity features from
  Arg [4]    : <optional> compara dbadptor to use.
  Example    :

$fs = $slc->get_all_compara_DnaAlignFeatures('Mus musculus',
                               'MGSC3',
                               'WGA');

  Description: Retrieves a list of DNA-DNA Alignments to the species specified
               by the $qy_species argument.
               The compara database must be attached to the core database
               for this call to work correctly.  As well the compara database
               must have the core dbadaptors for both this species, and the
               query species added to function correctly.
  Returntype : reference to a list of Bio::EnsEMBL::DnaDnaAlignFeatures
  Exceptions : warning if compara database is not available
  Caller     : contigview
  Status     : Stable

Code:

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◆ get_all_compara_Syntenies()

public Arrayref Bio::EnsEMBL::Slice::get_all_compara_Syntenies ( )

  Arg [1]    : string $query_species e.g. "Mus_musculus" or "Mus musculus"
  Arg [2]    : string $method_link_type, default is "SYNTENY"
  Arg [3]    : <optional> compara dbadaptor to use.
  Description: gets all the compara syntenyies for a specfic species
  Returns    : arrayref of Bio::EnsEMBL::Compara::SyntenyRegion
  Status     : Stable

Code:

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◆ get_all_DAS_Features()

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

  Arg [1]    : none
  Example    :

$features = $slice->get_all_DASFeatures;

  Description: Retrieves 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 : ?
  Caller     : webcode
  Status     : Stable

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◆ get_all_DASFactories()

public Bio::EnsEMBL::Slice::get_all_DASFactories ( )

Undocumented method

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◆ get_all_DASFeatures()

public Bio::EnsEMBL::Slice::get_all_DASFeatures ( )

Undocumented method

Code:

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◆ get_all_DASFeatures_dsn()

public Bio::EnsEMBL::Slice::get_all_DASFeatures_dsn ( )

Undocumented method

Code:

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◆ get_all_DitagFeatures()

public Listref Bio::EnsEMBL::Slice::get_all_DitagFeatures ( )

  Arg [1]    : (optional) string ditag type
  Arg [1]    : (optional) string logic_name
  Example    :

@dna_dna_align_feats = @{$slice->get_all_DitagFeatures};

  Description: Retrieves the DitagFeatures of a specific type which overlap
               this slice. If type is not defined, all features are retrieved.
               Strandedness of the Slice is ignored.
  Returntype : listref of Bio::EnsEMBL::DitagFeatures
  Exceptions : warning if slice does not have attached adaptor
  Caller     : general
  Status     : Stable

Code:

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◆ get_all_DnaAlignFeatures()

public Listref Bio::EnsEMBL::Slice::get_all_DnaAlignFeatures ( )

  Arg [1]    : (optional) string $logic_name
               The name of the analysis performed on the dna align features
               to obtain.
  Arg [2]    : (optional) float $score
               The mimimum score of the features to retrieve
  Arg [3]    : (optional) string $dbtype
               The name of an attached database to retrieve the features from
               instead, e.g. 'otherfeatures'.
  Arg [4]    : (optional) float hcoverage
               The minimum hcoverage od the featurs to retrieve
  Example    :

@dna_dna_align_feats = @{$slice->get_all_DnaAlignFeatures};

  Description: Retrieves the DnaDnaAlignFeatures which overlap this slice with
               logic name $logic_name and with score above $score.  If
               $logic_name is not defined features of all logic names are
               retrieved.  If $score is not defined features of all scores are
               retrieved. Strand of the Slice is not considered.
  Returntype : listref of Bio::EnsEMBL::DnaDnaAlignFeatures
  Exceptions : warning if slice does not have attached adaptor
  Caller     : general
  Status     : Stable

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◆ get_all_Exons()

public Reference Bio::EnsEMBL::Slice::get_all_Exons ( )

  Arg [1]    : none
  Example    :

@exons = @{$slice->get_all_Exons};

  Description: Gets all exons which overlap this slice.  Note that these exons
               will not be associated with any transcripts, so this may not
               be terribly useful.
  Returntype : reference to a list of Bio::EnsEMBL::Exons
  Exceptions : none
  Caller     : general
  Status     : Stable

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◆ get_all_ExternalFeatures()

public Listref Bio::EnsEMBL::Slice::get_all_ExternalFeatures ( )

  Arg [1]    : (optional) string $track_name
               If specified only features from ExternalFeatureAdaptors with
               the track name $track_name are retrieved.
               If not set, all features from every ExternalFeatureAdaptor are
               retrieved.
  Example    :

@x_features = @{$slice->get_all_ExternalFeatures}

  Description: Retrieves features on this slice from external feature adaptors
  Returntype : listref of Bio::SeqFeatureI implementing objects in slice
               coordinates
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ get_all_Genes()

public Listref Bio::EnsEMBL::Slice::get_all_Genes ( )

  Arg [1]    : (optional) string $logic_name
               The name of the analysis used to generate the genes to retrieve
  Arg [2]    : (optional) string $dbtype
               The dbtype of genes to obtain.  This assumes that the db has
               been added to the DBAdaptor under this name (using the
               DBConnection::add_db_adaptor method).
  Arg [3]    : (optional) boolean $load_transcripts
               If set to true, transcripts will be loaded immediately rather
               than being lazy-loaded on request.  This will result in a
               significant speed up if the Transcripts and Exons are going to
               be used (but a slow down if they are not).
  Arg [4]    : (optional) string $source
               The source of the genes to retrieve.
  Arg [5]    : (optional) string $biotype
               The biotype of the genes to retrieve.
  Example    :

@genes = @{$slice->get_all_Genes};

  Description: Retrieves all genes that overlap this slice, including those on
               the reverse strand.
  Returntype : listref of Bio::EnsEMBL::Genes
  Exceptions : none
  Caller     : none
  Status     : Stable

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◆ get_all_Genes_by_source()

public Listref Bio::EnsEMBL::Slice::get_all_Genes_by_source ( )

  Arg [1]    : string source
  Arg [2]    : (optional) boolean $load_transcripts
               If set to true, transcripts will be loaded immediately rather
               than being lazy-loaded on request.  This will result in a
               significant speed up if the Transcripts and Exons are going to
               be used (but a slow down if they are not).
  Example    :

@genes = @{$slice->get_all_Genes_by_source('ensembl')};

  Description: Retrieves genes that overlap this slice of source $source.
               Strand of the Slice does not affect the result.
  Returntype : listref of Bio::EnsEMBL::Genes
  Exceptions : none
  Caller     : general
  Status     : Stable

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◆ get_all_Genes_by_type()

public Listref Bio::EnsEMBL::Slice::get_all_Genes_by_type ( )

  Arg [1]    : string $type
               The biotype of genes wanted.
  Arg [2]    : (optional) string $logic_name
  Arg [3]    : (optional) boolean $load_transcripts
               If set to true, transcripts will be loaded immediately rather
               than being lazy-loaded on request.  This will result in a
               significant speed up if the Transcripts and Exons are going to
               be used (but a slow down if they are not).
  Example    :

@genes = @{$slice->get_all_Genes_by_type('protein_coding',

'ensembl')};

  Description: Retrieves genes that overlap this slice of biotype $type.
               This is primarily used by the genebuilding code when several
               biotypes of genes are used.

               The logic name is the analysis of the genes that are retrieved.
               If not provided all genes will be retrieved instead. Both
               positive and negative strand Genes will be returned.

  Returntype : listref of Bio::EnsEMBL::Genes
  Exceptions : none
  Caller     : genebuilder, general
  Status     : Stable

Code:

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◆ get_all_Haplotypes()

public Listref Bio::EnsEMBL::Slice::get_all_Haplotypes ( )

  Arg [1]    : (optional) boolean $lite_flag
               if true lightweight haplotype objects are used
  Example    :

@haplotypes = $slice->get_all_Haplotypes;

  Description: Retrieves all of the haplotypes on this slice.  Only works
               if the haplotype adaptor has been attached to the core adaptor
               via $dba->add_db_adaptor('haplotype', $hdba);
  Returntype : listref of Bio::EnsEMBL::External::Haplotype::Haplotypes
  Exceptions : warning is Haplotype database is not available
  Caller     : contigview, general
  Status     : Stable

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◆ get_all_KaryotypeBands()

public Listref Bio::EnsEMBL::Slice::get_all_KaryotypeBands ( )

  Arg [1]    : none
  Example    :

@kary_bands = @{$slice->get_all_KaryotypeBands};

  Description: Retrieves the karyotype bands which this slice overlaps.
  Returntype : listref oif Bio::EnsEMBL::KaryotypeBands
  Exceptions : none
  Caller     : general, contigview
  Status     : Stable

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◆ get_all_LD_values()

public Bio::EnsEMBL::Variation::LDFeatureContainer Bio::EnsEMBL::Slice::get_all_LD_values ( )

    Arg [1]     : (optional) Bio::EnsEMBL::Variation::Population $population
    Description : returns all LD values on this slice. This function will only work correctly if the variation
                  database has been attached to the core database. If the argument is passed, will return the LD information
                  in that population
    ReturnType  : Bio::EnsEMBL::Variation::LDFeatureContainer
    Exceptions  : none
    Caller      : contigview, snpview
     Status     : Stable

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◆ get_all_MarkerFeatures()

public Reference Bio::EnsEMBL::Slice::get_all_MarkerFeatures ( )

  Arg [1]    : (optional) string logic_name
               The logic name of the marker features to retrieve
  Arg [2]    : (optional) int $priority
               Lower (exclusive) priority bound of the markers to retrieve
  Arg [3]    : (optional) int $map_weight
               Upper (exclusive) priority bound of the markers to retrieve
  Example    :

my @markers = @{$slice->get_all_MarkerFeatures(undef,50, 2)};

  Description: Retrieves all markers which lie on this slice fulfilling the
               specified map_weight and priority parameters (if supplied).
  Returntype : reference to a list of Bio::EnsEMBL::MarkerFeatures
  Exceptions : none
  Caller     : contigview, general
  Status     : Stable

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◆ get_all_MiscFeatures()

public Listref Bio::EnsEMBL::Slice::get_all_MiscFeatures ( )

  Arg [1]    : string $set (optional)
  Arg [2]    : string $database (optional)
  Example    :

$slice->get_all_MiscFeatures('cloneset');

  Description: Retrieves all misc features which overlap this slice. If
               a set code is provided only features which are members of
               the requested set are returned.
  Returntype : listref of Bio::EnsEMBL::MiscFeatures
  Exceptions : none
  Caller     : general
  Status     : Stable

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◆ get_all_PredictionTranscripts()

public Listref Bio::EnsEMBL::Slice::get_all_PredictionTranscripts ( )

  Arg [1]    : (optional) string $logic_name
               The name of the analysis used to generate the prediction
               transcripts obtained.
  Arg [2]    : (optional) boolean $load_exons
               If set to true will force loading of all PredictionExons
               immediately rather than loading them on demand later.  This
               is faster if there are a large number of PredictionTranscripts
               and the exons will be used.
  Example    :

@transcripts = @{$slice->get_all_PredictionTranscripts};

  Description: Retrieves the list of prediction transcripts which overlap
               this slice with logic_name $logic_name.  If logic_name is
               not defined then all prediction transcripts are retrieved.
  Returntype : listref of Bio::EnsEMBL::PredictionTranscript
  Exceptions : warning if slice does not have attached adaptor
  Caller     : none
  Status     : Stable

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◆ get_all_ProteinAlignFeatures()

public Listref Bio::EnsEMBL::Slice::get_all_ProteinAlignFeatures ( )

  Arg [1]    : (optional) string $logic_name
               The name of the analysis performed on the protein align features
               to obtain.
  Arg [2]    : (optional) float $score
               The mimimum score of the features to retrieve
  Arg [3]    : (optional) string $dbtype
               The name of an attached database to retrieve features from
               instead.
  Arg [4]    : (optional) float hcoverage
               The minimum hcoverage od the featurs to retrieve
  Example    :

@dna_pep_align_feats = @{$slice->get_all_ProteinAlignFeatures};

  Description: Retrieves the DnaPepAlignFeatures which overlap this slice with
               logic name $logic_name and with score above $score.  If
               $logic_name is not defined features of all logic names are
               retrieved.  If $score is not defined features of all scores are
               retrieved.
  Returntype : listref of Bio::EnsEMBL::DnaPepAlignFeatures
  Exceptions : warning if slice does not have attached adaptor
  Caller     : general
  Status     : Stable

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◆ get_all_RepeatFeatures()

public Listref Bio::EnsEMBL::Slice::get_all_RepeatFeatures ( )

  Arg [1]    : (optional) string $logic_name
               The name of the analysis performed on the repeat features
               to obtain.
  Arg [2]    : (optional) string/array $repeat_type
               Limits features returned to those of the specified 
               repeat_type. Can specify a single value or an array reference
               to limit by more than one
  Arg [3]    : (optional) string $db
               Key for database e.g. core/vega/cdna/....
  Example    :

@repeat_feats = @{$slice->get_all_RepeatFeatures(undef,'Type II Transposons')};

  Description: Retrieves the RepeatFeatures which overlap  with
               logic name $logic_name and with score above $score.  If
               $logic_name is not defined features of all logic names are
               retrieved.
  Returntype : listref of Bio::EnsEMBL::RepeatFeatures
  Exceptions : warning if slice does not have attached adaptor
  Caller     : general
  Status     : Stable

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◆ get_all_SearchFeatures()

public Listref Bio::EnsEMBL::Slice::get_all_SearchFeatures ( )

  Arg [1]    : scalar $ticket_ids
  Example    :

$slice->get_all_SearchFeatures('BLA_KpUwwWi5gY');

  Description: Retrieves all search features for stored blast
               results for the ticket that overlap this slice
  Returntype : listref of Bio::EnsEMBL::SeqFeatures
  Exceptions : none
  Caller     : general (webby!)
  Status     : Stable

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◆ get_all_SimilarityFeatures()

public Listref Bio::EnsEMBL::Slice::get_all_SimilarityFeatures ( )

  Arg [1]    : (optional) string $logic_name
               the name of the analysis performed on the features to retrieve
  Arg [2]    : (optional) float $score
               the lower bound of the score of the features to be retrieved
  Example    :

@feats = @{$slice->get_all_SimilarityFeatures};

  Description: Retrieves all dna_align_features and protein_align_features
               with analysis named $logic_name and with score above $score.
               It is probably faster to use get_all_ProteinAlignFeatures or
               get_all_DnaAlignFeatures if a sepcific feature type is desired.
               If $logic_name is not defined features of all logic names are
               retrieved.  If $score is not defined features of all scores are
               retrieved.
  Returntype : listref of Bio::EnsEMBL::BaseAlignFeatures
  Exceptions : warning if slice does not have attached adaptor
  Caller     : general
  Status     : Stable

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◆ get_all_SimpleFeatures()

public Listref Bio::EnsEMBL::Slice::get_all_SimpleFeatures ( )

  Arg [1]    : (optional) string $logic_name
               The name of the analysis performed on the simple features
               to obtain.
  Arg [2]    : (optional) float $score
               The mimimum score of the features to retrieve
  Example    :

@simple_feats = @{$slice->get_all_SimpleFeatures};

  Description: Retrieves the SimpleFeatures which overlap this slice with
               logic name $logic_name and with score above $score.  If
               $logic_name is not defined features of all logic names are
               retrieved.  If $score is not defined features of all scores are
               retrieved.
  Returntype : listref of Bio::EnsEMBL::SimpleFeatures
  Exceptions : warning if slice does not have attached adaptor
  Caller     : general
  Status     : Stable

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◆ get_all_somatic_VariationFeatures()

public Listref Bio::EnsEMBL::Slice::get_all_somatic_VariationFeatures ( )

    Args [1]    : (optional) ArrayRef $so_terms
                  SequenceOntology terms to limit the fetch to
    Args [2]    : (optional) boolean $without_children
                  Do not query using the children of the given SO terms 
                  i.e. query using the given terms directly
    Args [3]    : (optional) ArrayRef $included_so 
                  ArrayRef of SequenceOntology which should be queried for
                  without children. This argument allows you to combine SO terms with children
                  from argument 1 with extra non-child SO terms. e.g. you wish to query for
                  all protein_altering_variant (specified in argument 1) variations which 
                  would be defined by child SO terms but also wanted stop_retained_variant linked variations
                  defined by this argument
    Args [4]    : (optional) string $dbtype
                  The dbtype of variation to obtain (i.e. can be different from the "variation" type).
                  This assumes that the extra db has been added to the DBAdaptor under this name (using the
                  DBConnection::add_db_adaptor method).
    Description : Returns all somatic variation features on this slice. This function will only 
                  work correctly if the variation database has been attached to the core database.
    ReturnType  : listref of Bio::EnsEMBL::Variation::VariationFeature
    Exceptions  : none
    Status      : Stable

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◆ get_all_somatic_VariationFeatures_by_source()

public Listref Bio::EnsEMBL::Slice::get_all_somatic_VariationFeatures_by_source ( )

    Arg [1]     : string $source [optional]
                  The name of the source to query for
    Arg [2]     : string $dbtype [optional]
                  The dbtype of variation to obtain (i.e. can be different from the "variation" type).
                  This assumes that the extra db has been added to the DBAdaptor under this name (using the
                  DBConnection::add_db_adaptor method).
    Description : Returns all somatic variation features, from a defined source name (e.g.'COSMIC'), 
                  on this slice. This function will only work correctly if the variation database
                  has been attached to the core database.
    ReturnType  : listref of Bio::EnsEMBL::Variation::VariationFeature
    Exceptions  : none
    Status      : Stable

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◆ get_all_somatic_VariationFeatures_with_phenotype()

public Listref Bio::EnsEMBL::Slice::get_all_somatic_VariationFeatures_with_phenotype ( )

    Arg [1]     : $variation_feature_source [optional]
    Arg [2]     : $phenotype_source [optional]
    Arg [3]     : $phenotype_name [optional]
    Arg [4]     : string $dbtype [optional]
                  The dbtype of variation to obtain (i.e. can be different from the "variation" type).
                  This assumes that the extra db has been added to the DBAdaptor under this name (using the
                  DBConnection::add_db_adaptor method).
    Description : returns all somatic variation features on this slice associated with a phenotype.
                  (see get_all_VariationFeatures_with_phenotype for further documentation)
    ReturnType  : listref of Bio::EnsEMBL::Variation::VariationFeature
    Exceptions  : none
    Status      : Stable

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◆ get_all_synonyms()

public Reference Bio::EnsEMBL::Slice::get_all_synonyms ( )

  Args [1]   : String external_db_name The name of the database to retrieve 
               the synonym for
  Args [2]   : (optional) Integer external_db_version Optionally restrict
               results from external_db_name to a specific version of
               the the specified external database
  Example    :

my @alternative_names = @{$slice->get_all_synonyms()};

@alternative_names = @{$slice->get_all_synonyms('EMBL')};

  Description: get a list of alternative names for this slice
  Returntype : reference to list of SeqRegionSynonym objects.
  Exception  : none
  Caller     : general
  Status     : At Risk

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◆ get_all_Transcripts()

public Reference Bio::EnsEMBL::Slice::get_all_Transcripts ( )

  Arg [1]    : (optional) boolean $load_exons
               If set to true exons will not be lazy-loaded but will instead
               be loaded right away.  This is faster if the exons are
               actually going to be used right away.
  Arg [2]    : (optional) string $logic_name
               the logic name of the type of features to obtain
  Arg [3]    : (optional) string $db_type
  Example    :

@transcripts = @{$slice->get_all_Transcripts)_};

  Description: Gets all transcripts which overlap this slice.  If you want to
               specify a particular analysis or type, then you are better off
               using get_all_Genes or get_all_Genes_by_type and iterating
               through the transcripts of each gene. Strand of the Slice is
               ignored.
  Returntype : reference to a list of Bio::EnsEMBL::Transcripts
  Exceptions : none
  Caller     : general
  Status     : Stable

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◆ get_all_Transcripts_by_source()

public Listref Bio::EnsEMBL::Slice::get_all_Transcripts_by_source ( )

  Arg [1]    : string source
  Arg [2]    : (optional) boolean $load_exons
               If set to true exons will not be lazy-loaded but will instead
               be loaded right away.  This is faster if the exons are
               actually going to be used right away.
  Example    :

@transcripts = @{$slice->get_all_Transcripts_by_source('ensembl')};

  Description: Retrieves transcripts that overlap this slice of source $source.
               Strand of the Slice does not affect the result.
  Returntype : listref of Bio::EnsEMBL::Transcripts
  Exceptions : none
  Caller     : general
  Status     : Stable

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◆ get_all_Transcripts_by_type()

public Listref Bio::EnsEMBL::Slice::get_all_Transcripts_by_type ( )

  Arg [1]    : string $type
               The biotype of transcripts wanted.
  Arg [2]    : (optional) string $logic_name
  Arg [3]    : (optional) boolean $load_exons
               If set to true exons will not be lazy-loaded but will instead
               be loaded right away.  This is faster if the exons are
               actually going to be used right away.

  Example    :

@transcripts = @{$slice->get_all_Transcripts_by_type('protein_coding',

'ensembl')};

  Description: Retrieves transcripts that overlap this slice of biotype $type.
               This is primarily used by the genebuilding code when several
               biotypes of transcripts are used.

               The logic name is the analysis of the transcripts that are retrieved.
               If not provided all transcripts will be retrieved instead. Both
               positive and negative strand transcripts will be returned.

  Returntype : listref of Bio::EnsEMBL::Transcripts
  Exceptions : none
  Caller     : genebuilder, general
  Status     : Stable

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◆ get_all_VariationFeatures()

public Listref Bio::EnsEMBL::Slice::get_all_VariationFeatures ( )

Args [1] : (optional) ArrayRef $so_terms
SequenceOntology terms to limit the fetch to
Args [2] : (optional) boolean $without_children
Do not query using the children of the given SO terms
i.e. query using the given terms directly
Args [3] : (optional) ArrayRef $included_so
ArrayRef of SequenceOntology which should be queried for
without children. This argument allows you to combine SO terms with children
from argument 1 with extra non-child SO terms. e.g. you wish to query for
all protein_altering_variant (specified in argument 1) variations which
would be defined by child SO terms but also wanted stop_retained_variant linked variations
defined by this argument
Args [4] : (optional) string $dbtype
The dbtype of variation to obtain (i.e. can be different from the "variation" type).
This assumes that the extra db has been added to the DBAdaptor under this name (using the
DBConnection::add_db_adaptor method).
Description : Returns all germline variation features on this slice. This function will
only work correctly if the variation database has been attached to the core
database.
If $so_terms is specified, only variation features with a consequence type
that matches or is an ontological child of any of the supplied terms will
be returned
ReturnType : listref of Bio::EnsEMBL::Variation::VariationFeature
Exceptions : none
Caller : contigview, snpview
Status : Stable

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◆ get_all_VariationFeatures_by_Population()

public Listref Bio::EnsEMBL::Slice::get_all_VariationFeatures_by_Population ( )

    Arg [1]     : Bio::EnsEMBL::Variation::Population
    Arg [2]     : $minimum_frequency [optional]
    Arg [3]     : string $dbtype [optional]
                  The dbtype of variation to obtain (i.e. can be different from the "variation" type).
                  This assumes that the extra db has been added to the DBAdaptor under this name (using the
                  DBConnection::add_db_adaptor method).
    Example     :

$pop = $pop_adaptor->fetch_by_dbID(659);

@vfs = @{$slice->get_all_VariationFeatures_by_Population($pop,$slice)};

    Description : Retrieves all variation features in a slice which are stored for
                  a specified population. If $minimum_frequency is supplied, only
                  variations with a minor allele frequency (MAF) greater than
                  $minimum_frequency will be returned.
    Returntype  : listref of Bio::EnsEMBL::Variation::VariationFeature
    Exceptions  : throw on incorrect argument
    Caller      : general
    Status      : At Risk

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◆ get_base_count()

public Hashref Bio::EnsEMBL::Slice::get_base_count ( )

  Arg [1]    : none
  Example    :

$c_count = $slice->get_base_count->{'c'};

  Description: Retrieves a hashref containing the counts of each bases in the
               sequence spanned by this slice.  The format of the hash is :
               { 'a' => num,
                 'c' => num,
                 't' => num,
                 'g' => num,
                 'n' => num,
                 'gc' => num }

               All bases which are not in the set [A,a,C,c,T,t,G,g] are
               included in the 'n' count.  The 'n' count could therefore be
               inclusive of ambiguity codes such as 'y'.
               The gc is the ratio of GC to AT content as in:
               total(GC)/total(ACTG) * 100
               This function is conservative in its memory usage and scales to
               work for entire chromosomes.
  Returntype : hashref
  Exceptions : none
  Caller     : general
  Status     : Stable

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◆ get_generic_features()

public Hash Bio::EnsEMBL::Slice::get_generic_features ( )

  Arg [1]    : (optional) List of names of generic feature types to return.
               If no feature names are given, all generic features are
               returned.
  Example    :

my %features = %{$slice->get_generic_features()};

  Description: Gets generic features via the generic feature adaptors that
               have been added via DBAdaptor->add_GenricFeatureAdaptor (if
               any)
  Returntype : Hash of named features.
  Exceptions : none
  Caller     : none
  Status     : Stable

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◆ get_genome_component()

public Scalar Bio::EnsEMBL::Slice::get_genome_component ( )

  Arg []     : none
  Example    :

my $genome_component = $slice->get_genome_component();

  Description: Returns the genome component of the slice
  Returntype : Scalar; the identifier of the genome component of the slice
  Exceptions : none
  Caller     : general
  Status     : Stable

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◆ get_MarkerFeatures_by_Name()

public Reference Bio::EnsEMBL::Slice::get_MarkerFeatures_by_Name ( )

  Arg [1]    : string marker Name
               The name (synonym) of the marker feature(s) to retrieve
  Example    :

my @markers = @{$slice->get_MarkerFeatures_by_Name('z1705')};

  Description: Retrieves all markers with this ID
  Returntype : reference to a list of Bio::EnsEMBL::MarkerFeatures
  Exceptions : none
  Caller     : contigview, general
  Status     : Stable

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◆ get_repeatmasked_seq()

public Bio::EnsEMBL::RepeatMaskedSlice Bio::EnsEMBL::Slice::get_repeatmasked_seq ( )

  Arg [1]    : listref of strings $logic_names (optional)
  Arg [2]    : int $soft_masking_enable (optional)
  Arg [3]    : hash reference $not_default_masking_cases (optional, default is {})
               The values are 0 or 1 for hard and soft masking respectively
               The keys of the hash should be of 2 forms
               "repeat_class_" . $repeat_consensus->repeat_class,
                e.g. "repeat_class_SINE/MIR"
               "repeat_name_" . $repeat_consensus->name
                e.g. "repeat_name_MIR"
               depending on which base you want to apply the not default
               masking either the repeat_class or repeat_name. Both can be
               specified in the same hash at the same time, but in that case,
               repeat_name setting has priority over repeat_class. For example,
               you may have hard masking as default, and you may want soft
               masking of all repeat_class SINE/MIR, but repeat_name AluSp
               (which are also from repeat_class SINE/MIR).
               Your hash will be something like {"repeat_class_SINE/MIR" => 1,
                                                 "repeat_name_AluSp" => 0}
  Example    :

$rm_slice = $slice->get_repeatmasked_seq();

$softrm_slice = $slice->get_repeatmasked_seq(['RepeatMask'],1);

  Description: Returns Bio::EnsEMBL::Slice that can be used to create repeat
               masked sequence instead of the regular sequence.
               Sequence returned by this new slice will have repeat regions
               hardmasked by default (sequence replaced by N) or
               or soft-masked when arg[2] = 1 (sequence in lowercase)
               Will only work with database connection to get repeat features.
  Returntype : Bio::EnsEMBL::RepeatMaskedSlice
  Exceptions : none
  Caller     : general
  Status     : Stable

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◆ get_seq_region_id()

public Int Bio::EnsEMBL::Slice::get_seq_region_id ( )

  Arg [1]    : none
  Example    :

my $seq_region_id = $slice->get_seq_region_id();

  Description: Gets the internal identifier of the seq_region that this slice
               is on. Note that this function will not work correctly if this
               slice does not have an attached adaptor. Also note that it may
               be better to go through the SliceAdaptor::get_seq_region_id
               method if you are working with multiple databases since is
               possible to work with slices from databases with different
               internal seq_region identifiers.
  Returntype : int or undef if slices does not have attached adaptor
  Exceptions : warning if slice is not associated with a SliceAdaptor
  Caller     : assembly loading scripts, general
  Status     : Stable

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◆ has_karyotype()

public Int Bio::EnsEMBL::Slice::has_karyotype ( )

  Arg        : none
  Example    :

my $top = $slice->has_karyotype()

  Description: Returns 1 if slice is part of the karyotype else 0
  Returntype : int
  Caller     : general
  Status     : At Risk

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◆ id()

public Bio::EnsEMBL::Slice::id ( )

  Description: Included for Bio::PrimarySeqI interface compliance (0.7)

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◆ invert()

public Bio::EnsEMBL::Slice Bio::EnsEMBL::Slice::invert ( )

  Arg [1]    : none
  Example    :

$inverted_slice = $slice->invert;

  Description: Creates a copy of this slice on the opposite strand and
               returns it.
  Returntype : Bio::EnsEMBL::Slice
  Exceptions : none
  Caller     : general
  Status     : Stable

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◆ is_chromosome()

public Boolean Bio::EnsEMBL::Slice::is_chromosome ( )

  Example           :

print ($slice->is_chromosome()) ? 'I am a chromosome' : 'Not one';

  Description : A chromosome is a slice with a karyotype rank assigned to it.
  Returntype    : Boolean indicates if the current object is a chromosome
  Exceptions    : None

Code:

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◆ is_circular()

public Int Bio::EnsEMBL::Slice::is_circular ( )

  Arg        : none
  Example    :

my $circ = $slice->is_circular()

  Description: Returns 1 if slice is a circular slice else 0
  Returntype : int
  Caller     : general
  Status     : Stable

Code:

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◆ is_reference()

public Int Bio::EnsEMBL::Slice::is_reference ( )

  Arg        : none
  Example    :

my $reference = $slice->is_reference()

  Description: Returns 1 if slice is a reference  slice else 0
  Returntype : int
  Caller     : general
  Status     : At Risk

Code:

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◆ is_toplevel()

public Int Bio::EnsEMBL::Slice::is_toplevel ( )

  Arg        : none
  Example    :

my $top = $slice->is_toplevel()

  Description: Returns 1 if slice is a toplevel slice else 0
  Returntype : int
  Caller     : general
  Status     : At Risk

Code:

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◆ karyotype_rank()

public Int Bio::EnsEMBL::Slice::karyotype_rank ( )

  Arg        : none
  Example    :

my $rank = $slice->karyotype_rank()

  Description: Returns the numeric ranking in the karyotype. Otherwise 0 is returned
  Returntype : int
  Caller     : general
  Status     : At Risk

Code:

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◆ length()

public Int Bio::EnsEMBL::Slice::length ( )

  Arg [1]    : none
  Example    :

$length = $slice->length();

  Description: Returns the length of this slice in basepairs
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ moltype()

public Bio::EnsEMBL::Slice::moltype ( )

Description: Included for Bio::PrimarySeqI interface compliance (0.7)

Code:

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◆ name()

public String Bio::EnsEMBL::Slice::name ( )

  Arg [1]    : none
  Example    :

my $results = $cache{$slice->name()};

  Description: Returns the name of this slice. The name is formatted as a colon
               delimited string with the following attributes:
               coord_system:version:seq_region_name:start:end:strand

               Slices with the same name are equivalent and thus the name can
               act as a hash key.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ new()

public Bio::EnsEMBL::Slice Bio::EnsEMBL::Slice::new ( )

  Arg [...]  : List of named arguments
               Bio::EnsEMBL::CoordSystem COORD_SYSTEM
               string SEQ_REGION_NAME,
               int    START,
               int    END,
               int    SEQ_REGION_LENGTH, (optional)
               string SEQ (optional)
               int    STRAND, (optional, defaults to 1)
               Bio::EnsEMBL::DBSQL::SliceAdaptor ADAPTOR (optional)
  Example    :

$slice = Bio::EnsEMBL::Slice->new(-coord_system => $cs,
                                                -start => 1,
                                                -end => 10000,
                                                -strand => 1,
                                                -seq_region_name => 'X',
                                                -seq_region_length => 12e6,
                                                -adaptor => $slice_adaptor);

  Description: Creates a new slice object.  A slice represents a region
               of sequence in a particular coordinate system.  Slices can be
               used to retrieve sequence and features from an area of
               interest in a genome.

               Coordinates start at 1 and are inclusive.  Negative
               coordinates or coordinates exceeding the length of the
               seq_region are permitted.  Start must be less than or equal.
               to end regardless of the strand.

               Slice objects are immutable. Once instantiated their attributes
               (with the exception of the adaptor) may not be altered.  To
               change the attributes a new slice must be created.
  Returntype : Bio::EnsEMBL::Slice
  Exceptions : throws if start, end, coordsystem or seq_region_name not specified or not of the correct type
  Caller     : general, Bio::EnsEMBL::SliceAdaptor
  Status     : Stable

Code:

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sub new {
  my $caller = shift;
 
  #new can be called as a class or object method
  my $class = ref($caller) || $caller;
 
  my ($seq, $coord_system, $seq_region_name, $seq_region_length,
      $start, $end, $strand, $adaptor, $empty) =
        rearrange([qw(SEQ COORD_SYSTEM SEQ_REGION_NAME SEQ_REGION_LENGTH
                      START END STRAND ADAPTOR EMPTY)], @_);
 
  if ( !defined($seq_region_name) ) {
    throw('SEQ_REGION_NAME argument is required');
  }
  if ( !defined($start) ) { throw('START argument is required') }
  if ( !defined($end) )   { throw('END argument is required') }
 
  ## if ( $start > $end + 1 ) {
  ##   throw('start must be less than or equal to end+1');
  ## }
 
  if ( !defined($seq_region_length) ) { $seq_region_length = $end }
 
  if ( $seq_region_length <= 0 ) {
    throw('SEQ_REGION_LENGTH must be > 0');
  }
 
  if ( defined($seq) && CORE::length($seq) != ( $end - $start + 1 ) ) {
    throw('SEQ must be the same length as the defined LENGTH not '
        . CORE::length($seq)
        . ' compared to '
        . ( $end - $start + 1 ) );
  }
 
  if(defined($coord_system)) {
   if(!ref($coord_system) || !$coord_system->isa('Bio::EnsEMBL::CoordSystem')){
     throw('COORD_SYSTEM argument must be a Bio::EnsEMBL::CoordSystem');
   }
   if($coord_system->is_top_level()) {
     throw('Cannot create slice on toplevel CoordSystem.');
   }
  } else {
   warning("Slice without coordinate system");
  }
 
  $strand ||= 1;
 
  if($strand != 1 && $strand != -1) {
    throw('STRAND argument must be -1 or 1');
  }
 
  if(defined($adaptor)) {
    if(!ref($adaptor) || !$adaptor->isa('Bio::EnsEMBL::DBSQL::SliceAdaptor')) {
      throw('ADAPTOR argument must be a Bio::EnsEMBL::DBSQL::SliceAdaptor');
    }
  }
 
  my $self = bless {'coord_system'      => $coord_system,
                'seq'               => $seq,
                'seq_region_name'   => $seq_region_name,
                'seq_region_length' => $seq_region_length,
                'start'             => int($start),
                'end'               => int($end),
                'strand'            => $strand}, $class;
 
  $self->adaptor($adaptor);
 
  return $self;
 
}

◆ new_fast()

public Bio::EnsEMBL::Slice Bio::EnsEMBL::Slice::new_fast ( )

  Arg [1]    : hashref to be blessed
  Description: Construct a new Bio::EnsEMBL::Slice using the hashref.
  Exceptions : none
  Returntype : Bio::EnsEMBL::Slice
  Caller     : general
  Status     : Stable

Code:

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◆ old_get_all_DASFeatures()

public Bio::EnsEMBL::Slice::old_get_all_DASFeatures ( )

Undocumented method

Code:

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◆ primary_id()

public Bio::EnsEMBL::Slice::primary_id ( )

  Description: Included for Bio::PrimarySeqI interface compliance (1.2)

Code:

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◆ project()

public List Bio::EnsEMBL::Slice::project ( )

  Arg [1]    : string $name
               The name of the coordinate system to project this slice onto
  Arg [2]    : string $version
               The version of the coordinate system (such as 'NCBI34') to
               project this slice onto
  Example    :

my $clone_projection = $slice->project('clone');
 
foreach my $segment (@$clone_projection) {
  my $clone = $segment->to_Slice();
  print $slice->seq_region_name(), ':', $segment->from_start(), '-',
        $segment->from_end(), ' -> ',
        $clone->seq_region_name(), ':', $clone->start(), '-',$clone->end(),
        ':', $clone->strand(), "\n";
}

  Description: Returns the results of 'projecting' this slice onto another
               coordinate system.  Projecting to a coordinate system that
               the slice is assembled from is analagous to retrieving a tiling
               path.  This method may also be used to 'project up' to a higher
               level coordinate system, however.

               This method returns a listref of triplets [start,end,slice]
               which represents the projection.  The start and end defined the
               region of this slice which is made up of the third value of
               the triplet: a slice in the requested coordinate system.
  Returntype : list reference of Bio::EnsEMBL::ProjectionSegment objects which
               can also be used as [$start,$end,$slice] triplets
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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sub project {
  my $self = shift;
  my $cs_name = shift;
  my $cs_version = shift;
 
  throw('Coord_system name argument is required') if(!$cs_name);
 
  my $slice_adaptor = $self->adaptor();
 
  if(!$slice_adaptor) {
    warning("Cannot project without attached adaptor.");
    return [];
  }
 
  if(!$self->coord_system()) {
    warning("Cannot project without attached coord system.");
    return [];
  }
 
 
  my $db = $slice_adaptor->db();
  my $csa = $db->get_CoordSystemAdaptor();
  my $cs = $csa->fetch_by_name($cs_name, $cs_version);
  my $slice_cs = $self->coord_system();
 
  if(!$cs) {
    throw("Cannot project to unknown coordinate system " .
          "[$cs_name $cs_version]");
  }
 
  # no mapping is needed if the requested coord system is the one we are in
  # but we do need to check if some of the slice is outside of defined regions
  if($slice_cs->equals($cs)) {
    return $self->_constrain_to_region();
  }
 
  my @projection;
 
  # decompose this slice into its symlinked components.
  # this allows us to handle haplotypes and PARs
  my $normal_slice_proj =
    $slice_adaptor->fetch_normalized_slice_projection($self);
  foreach my $segment (@$normal_slice_proj) {
    my $normal_slice = $segment->[2];
 
    $slice_cs = $normal_slice->coord_system();
 
    my $asma = $db->get_AssemblyMapperAdaptor();
    my $asm_mapper = $asma->fetch_by_CoordSystems($slice_cs, $cs);
    next unless defined $asm_mapper;
    
    # perform the mapping between this slice and the requested system
    my @coords = $asm_mapper->map($normal_slice->seq_region_name(),
                  $normal_slice->start(),
                  $normal_slice->end(),
                  $normal_slice->strand(),
                  $slice_cs, undef, undef, 1);
 
    # construct a projection from the mapping results and return it
    foreach my $coord (@coords) {
      my $original = $coord->{original};
      my $mapped = $coord->{mapped};
 
      # skip gaps
      next unless $mapped->isa('Bio::EnsEMBL::Mapper::Coordinate');
 
      my $mapped_start = $mapped->start();
      my $mapped_end = $mapped->end();
      my ($current_start, $current_end);
      if ($self->strand == 1) {
    $current_start = $original->start() - $self->start + 1;
    $current_end = $original->end() - $self->start + 1;
      } else {
    $current_start = $self->end() - $original->end + 1;
    $current_end = $self->end - $original->start + 1;
      }
      
      my $coord_cs = $mapped->coord_system();
 
      # If the normalised projection just ended up mapping to the
      # same coordinate system we were already in then we should just
      # return the original region.  This can happen for example, if we
      # were on a PAR region on Y which refered to X and a projection to
      # 'toplevel' was requested.
      if($coord_cs->equals($slice_cs)) {
    # trim off regions which are not defined
    return $self->_constrain_to_region();
      }
      #create slices for the mapped-to coord system
      my $slice = $slice_adaptor->fetch_by_seq_region_id($mapped->id(),
                             $mapped_start,
                             $mapped_end,
                             $mapped->strand());
 
      if ($current_end > $slice->seq_region_length() && $slice->is_circular ) {
    $current_end -= $slice->seq_region_length();
      }
      
      push @projection, bless([$current_start, $current_end, $slice],
                  "Bio::EnsEMBL::ProjectionSegment");
      
    }
  }
 
  return \@projection;
}

◆ project_to_slice()

public List Bio::EnsEMBL::Slice::project_to_slice ( )

  Arg [1]    : Slice to project to.
  Example    :

my $chr_projection = $clone_slice->project_to_slice($chrom_slice);
               foreach my $segment ( @$chr_projection ){
                 $chr_slice = $segment->to_Slice();
                 print $clone_slice->seq_region_name(). ':'. $segment->from_start(). '-'.
                       $segment->from_end(). ' -> '.$chr_slice->seq_region_name(). ':'. $chr_slice->start().
                   '-'.$chr_slice->end().

                         $chr_slice->strand(). " length: ".($chr_slice->end()-$chr_slice->start()+1). "\n";
                }
  Description: Projection of slice to another specific slice. Needed for where we have multiple mappings
               and we want to state which one to project to.
  Returntype : list reference of Bio::EnsEMBL::ProjectionSegment objects which
               can also be used as [$start,$end,$slice] triplets.
  Exceptions : none
  Caller     : none
  Status     : At Risk

Code:

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sub project_to_slice {
  my $self = shift;
  my $to_slice = shift;
 
  throw('Slice argument is required') if(!$to_slice);
 
  my $slice_adaptor = $self->adaptor();
 
  if(!$slice_adaptor) {
    warning("Cannot project without attached adaptor.");
    return [];
  }
 
 
  my $mapper_aptr = $slice_adaptor->db->get_AssemblyMapperAdaptor();
 
  my $cs = $to_slice->coord_system();
  my $slice_cs = $self->coord_system();
  my $to_slice_id = $to_slice->get_seq_region_id;
 
  my @projection;
 
  # decompose this slice into its symlinked components.
  # this allows us to handle haplotypes and PARs
  my $normal_slice_proj =
    $slice_adaptor->fetch_normalized_slice_projection($self);
  foreach my $segment (@$normal_slice_proj) {
    my $normal_slice = $segment->[2];
 
    $slice_cs = $normal_slice->coord_system();
 
    my $asma = $self->adaptor->db->get_AssemblyMapperAdaptor();
    my $asm_mapper = $asma->fetch_by_CoordSystems($slice_cs, $cs);
    next unless defined $asm_mapper;
    
    # perform the mapping between this slice and the requested system
    my @coords = $asm_mapper->map($normal_slice->seq_region_name(),
                  $normal_slice->start(),
                  $normal_slice->end(),
                  $normal_slice->strand(),
                  $slice_cs, undef, $to_slice, 1);
 
    #construct a projection from the mapping results and return it
    foreach my $coord (@coords) {
      my $original = $coord->{original};
      my $mapped = $coord->{mapped};
 
      # skip gaps
      next unless $mapped->isa('Bio::EnsEMBL::Mapper::Coordinate');
 
      my $mapped_start = $mapped->start();
      my $mapped_end = $mapped->end();
      my ($current_start, $current_end);
      if ($self->strand == 1) {
    $current_start = $original->start() - $self->start + 1;
    $current_end = $original->end() - $self->start + 1;
      } else {
    $current_start = $self->end() - $original->end + 1;
    $current_end = $self->end - $original->start + 1;
      }
            
      # for multiple mappings only get the correct one
      next unless $mapped->id == $to_slice_id;
    
      my $coord_cs = $mapped->coord_system();
 
      # If the normalised projection just ended up mapping to the
      # same coordinate system we were already in then we should just
      # return the original region.  This can happen for example, if we
      # were on a PAR region on Y which refered to X and a projection to
      # 'toplevel' was requested.
      #        if($coord_cs->equals($slice_cs)) {
      #          # trim off regions which are not defined
      #          return $self->_constrain_to_region();
      #        }
 
      # create slices for the mapped-to coord system
      my $slice = $slice_adaptor->fetch_by_seq_region_id($mapped->id(),
                             $mapped_start,
                             $mapped_end,
                             $mapped->strand());
      
      push @projection, bless([$current_start, $current_end, $slice],
                  "Bio::EnsEMBL::ProjectionSegment");
    }
  }
 
 
  # delete the cache as we may want to map to different set next time and old
  # results will be cached.
  $mapper_aptr->delete_cache;
 
  return \@projection;
}

◆ seq()

public String Bio::EnsEMBL::Slice::seq ( )

  Arg [1]    : none
  Example    :

print "SEQUENCE = ", $slice->seq();

  Description: Returns the sequence of the region represented by this
               slice formatted as a string.
               Only available for the default coord_system
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ seq_region_end()

public Int Bio::EnsEMBL::Slice::seq_region_end ( )

  Example    :

$seq_region_end = $slice->seq_region_end();

  Description: Returns the end position of this slice relative to the
               start of the sequence region that it was created on.
               Since slices are always in genomic coordinates this is
               an alias to end()
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ seq_region_length()

public Int Bio::EnsEMBL::Slice::seq_region_length ( )

  Arg [1]    : none
  Example    :

$seq_region_length = $slice->seq_region_length();

  Description: Returns the length of the entire seq_region that this slice is
               on. For example if this slice is on a chromosome this will be
               the length (in basepairs) of the entire chromosome.
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ seq_region_name()

public String Bio::EnsEMBL::Slice::seq_region_name ( )

  Arg [1]    : none
  Example    :

$seq_region = $slice->seq_region_name();

  Description: Returns the name of the seq_region that this slice is on. For
               example if this slice is in chromosomal coordinates the
               seq_region_name might be 'X' or '10'.

               This function was formerly named chr_name, but since slices can
               now be on coordinate systems other than chromosomal it has been
               changed.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ seq_region_Slice()

public Bio::EnsEMBL::Slice Bio::EnsEMBL::Slice::seq_region_Slice ( )

  Arg [1]    : none
  Example    :

$slice = $slice->seq_region_Slice();

  Description: Returns a slice which spans the whole seq_region which this slice
               is on.  For example if this is a slice which spans a small region
               of chromosome X, this method will return a slice which covers the
               entire chromosome X. The returned slice will always have strand
               of 1 and start of 1.  This method cannot be used if the sequence
               of the slice has been set manually.
  Returntype : Bio::EnsEMBL::Slice
  Exceptions : warning if called when sequence of Slice has been set manually.
  Caller     : general
  Status     : Stable

Code:

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◆ seq_region_start()

public Int Bio::EnsEMBL::Slice::seq_region_start ( )

  Example    :

$seq_region_start = $slice->seq_region_start();

  Description: Returns the start position of this slice relative to the
               start of the sequence region that it was created on.
               Since slices are always in genomic coordinates this is
               an alias to start()
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ slice()

public Bio::EnsEMBL::Slice::slice ( )

Undocumented method

Code:

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◆ source()

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

  Arg [1]    : (optional) String $value
  Example    :

print $slice->source();

  Description: Returns the source this slice is coming from
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ start()

public Int Bio::EnsEMBL::Slice::start ( )

  Arg [1]    : none
  Example    :

$start = $slice->start();

  Description: Returns the start position of this slice relative to the
               start of the sequence region that it was created on.
               Coordinates are inclusive and start at 1.  Negative coordinates
               or coordinates exceeding the length of the sequence region are
               permitted.  Start is always less than or equal to end
               regardless of the orientation of the slice.
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ strand()

public Int Bio::EnsEMBL::Slice::strand ( )

  Arg [1]    : none
  Example    :

$strand = $slice->strand();

  Description: Returns the orientation of this slice on the seq_region it has
               been created on
  Returntype : int (either 1 or -1)
  Exceptions : none
  Caller     : general, invert
  Status     : Stable

Code:

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◆ sub_Slice()

public Bio::EnsEMBL::Slice Bio::EnsEMBL::Slice::sub_Slice ( )

  Arg   1    : int $start, refers to the start of the subslice relative to the input slice
  Arg   2    : int $end, refers to the end of the subslice relative to the input slice
  Arge [3]   : int $strand
  Example    :

none

  Description: Makes another Slice that covers only part of this Slice
               If a Slice is requested which lies outside of the boundaries
               of this function will return undef.  This means that
               behaviour will be consistant whether or not the slice is
               attached to the database (i.e. if there is attached sequence
               to the slice).  Alternatively the expand() method or the
               SliceAdaptor::fetch_by_region method can be used instead.
  Returntype : Bio::EnsEMBL::Slice or undef if arguments are wrong
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ sub_Slice_Iterator()

public Bio::EnsEMBL::Utils::Iterator Bio::EnsEMBL::Slice::sub_Slice_Iterator ( )

  Arg[1]      : int The chunk size to request
  Example     :

my $i = $slice->sub_Slice_Iterator(60000);

while($i->has_next()) { warn $i->next()->name(); }

  Description : Returns an iterator which batches subslices of this Slice 
                in the requested chunk size
  Returntype  : Bio::EnsEMBL::Utils::Iterator next() will return the next
                 chunk of Slice
  Exceptions  : None

Code:

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◆ subseq()

public Txt Bio::EnsEMBL::Slice::subseq ( )

  Arg  [1]   : int $startBasePair
               relative to start of slice, which is 1.
  Arg  [2]   : int $endBasePair
               relative to start of slice.
  Arg  [3]   : (optional) int $strand
               The strand of the slice to obtain sequence from. Default
               value is 1.
  Description: returns string of dna sequence
  Returntype : txt
  Exceptions : end should be at least as big as start
               strand must be set
  Caller     : general
  Status     : Stable

Code:

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◆ summary_as_hash()

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

  Example       :

$slice_summary = $slice->summary_as_hash();

  Description   : Retrieves a textual summary of this slice.
  Returns       : hashref of descriptive strings

Code:

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

ensembl/modules/Bio/EnsEMBL/Slice.pm

Public Member Functions

Detailed Description

Synopsis

Description

Member Function Documentation

◆ _constrain_to_region()

◆ _get_Adaptor()

◆ _get_AlignFeatures()

◆ _get_CoreAdaptor()

◆ _get_StructuralVariationFeatureAdaptor()

◆ _get_VariationAdaptor()

◆ _get_VariationFeatureAdaptor()

◆ _mask_features()

◆ accession_number()

◆ adaptor()

◆ add_synonym()

◆ alphabet()

◆ assembly_exception_type()

◆ centrepoint()

◆ constrain_to_seq_region()

◆ coord_system()

◆ coord_system_name()

◆ desc()

◆ display_id()

◆ end()

◆ expand()

◆ feature_so_acc()

◆ feature_so_term()

◆ get_all_AssemblyExceptionFeatures()

◆ get_all_Attributes()

◆ get_all_compara_DnaAlignFeatures()

◆ get_all_compara_Syntenies()

◆ get_all_DAS_Features()

◆ get_all_DASFactories()

◆ get_all_DASFeatures()

◆ get_all_DASFeatures_dsn()

◆ get_all_DitagFeatures()

◆ get_all_DnaAlignFeatures()

◆ get_all_Exons()

◆ get_all_ExternalFeatures()

◆ get_all_Genes()

◆ get_all_Genes_by_source()

◆ get_all_Genes_by_type()

◆ get_all_Haplotypes()

◆ get_all_KaryotypeBands()

◆ get_all_LD_values()

◆ get_all_MarkerFeatures()

◆ get_all_MiscFeatures()

◆ get_all_PredictionTranscripts()

◆ get_all_ProteinAlignFeatures()

◆ get_all_RepeatFeatures()

◆ get_all_SearchFeatures()

◆ get_all_SimilarityFeatures()

◆ get_all_SimpleFeatures()

◆ get_all_somatic_VariationFeatures()

◆ get_all_somatic_VariationFeatures_by_source()

◆ get_all_somatic_VariationFeatures_with_phenotype()

◆ get_all_synonyms()

◆ get_all_Transcripts()

◆ get_all_Transcripts_by_source()

◆ get_all_Transcripts_by_type()

◆ get_all_VariationFeatures()

◆ get_all_VariationFeatures_by_Population()

◆ get_base_count()

◆ get_generic_features()

◆ get_genome_component()

◆ get_MarkerFeatures_by_Name()

◆ get_repeatmasked_seq()

◆ get_seq_region_id()

◆ has_karyotype()

◆ id()

◆ invert()

◆ is_chromosome()

◆ is_circular()

◆ is_reference()

◆ is_toplevel()

◆ karyotype_rank()

◆ length()

◆ moltype()

◆ name()