Inheritance diagram for Bio::EnsEMBL::CircularSlice:

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

public Int	centrepoint ()

public Int	length ()

protected	_split ()

public String	seq ()

public Txt	subseq ()

public Bio::EnsEMBL::Slice	expand ()

public Listref	get_all_VariationFeatures ()

public Listref	get_all_genotyped_VariationFeatures ()

public Hashref	get_all_DASFeatures ()

public List	project_to_slice ()

public	id ()

public	display_id ()

public	primary_id ()

public	desc ()

public	moltype ()

public	alphabet ()

public	accession_number ()

public	is_circular ()

Public Member Functions inherited from Bio::EnsEMBL::Slice
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.

Definition at line 48 of file CircularSlice.pm.

Member Function Documentation

◆ _split()

protected Bio::EnsEMBL::CircularSlice::_split ( )

Undocumented method

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◆ accession_number()

public Bio::EnsEMBL::CircularSlice::accession_number ( )

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

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◆ alphabet()

public Bio::EnsEMBL::CircularSlice::alphabet ( )

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

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◆ centrepoint()

public Int Bio::EnsEMBL::CircularSlice::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

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◆ desc()

public Bio::EnsEMBL::CircularSlice::desc ( )

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

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◆ display_id()

public Bio::EnsEMBL::CircularSlice::display_id ( )

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

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◆ expand()

public Bio::EnsEMBL::Slice Bio::EnsEMBL::CircularSlice::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

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◆ get_all_DASFeatures()

public Hashref Bio::EnsEMBL::CircularSlice::get_all_DASFeatures ( )

  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_genotyped_VariationFeatures()

public Listref Bio::EnsEMBL::CircularSlice::get_all_genotyped_VariationFeatures ( )

    Args       : none
    Description: returns all variation features on this slice that have been genotyped.
                 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
    Caller     : contigview, snpview, ldview
    Status     : At Risk
               : Variation database is under development.

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◆ get_all_VariationFeatures()

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

    Args       : $filter [optional]
    Description:returns all variation features on this slice. This function will only work 
                correctly if the variation database has been attached to the core database.
                If $filter is "genotyped" return genotyped Snps only... (nice likkle hack);
    ReturnType : listref of Bio::EnsEMBL::Variation::VariationFeature
    Exceptions : none
    Caller     : contigview, snpview
    Status     : At Risk
               : Variation database is under development.

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◆ id()

public Bio::EnsEMBL::CircularSlice::id ( )

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

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◆ is_circular()

public Bio::EnsEMBL::CircularSlice::is_circular ( )

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

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◆ length()

public Int Bio::EnsEMBL::CircularSlice::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

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◆ moltype()

public Bio::EnsEMBL::CircularSlice::moltype ( )

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

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◆ new()

public Bio::EnsEMBL::CircularSlice Bio::EnsEMBL::CircularSlice::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::CircularSlice->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::CircularSlice
  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

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◆ primary_id()

public Bio::EnsEMBL::CircularSlice::primary_id ( )

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

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◆ project_to_slice()

public List Bio::EnsEMBL::CircularSlice::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

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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 @projection;
  my $current_start = 1;
 
  # 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 );
 
    # perform the mapping between this slice and the requested system
    my @coords;
 
    if ( defined $asm_mapper ) {
      @coords = $asm_mapper->map( $normal_slice->seq_region_name(),
                                  $normal_slice->start(),
                                  $normal_slice->end(),
                                  $normal_slice->strand(),
                                  $slice_cs,
                                  undef,
                                  $to_slice );
    } else {
      $coords[0] =
        Bio::EnsEMBL::Mapper::Gap->new( $normal_slice->start(),
                                        $normal_slice->end() );
    }
 
    #construct a projection from the mapping results and return it
    foreach my $coord (@coords) {
      my $coord_start = $coord->start();
      my $coord_end   = $coord->end();
      my $length      = $coord_end - $coord_start + 1;
 
      #skip gaps
      if ( $coord->isa('Bio::EnsEMBL::Mapper::Coordinate') ) {
        my $coord_cs = $coord->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( $coord->id(),
                           $coord_start, $coord_end, $coord->strand() );
 
        my $current_end = $current_start + $length - 1;
 
        push @projection,
          bless( [ $current_start, $current_end, $slice ],
                 "Bio::EnsEMBL::ProjectionSegment" );
      }
 
      $current_start += $length;
    } ## end foreach my $coord (@coords)
  } ## end foreach my $segment (@$normal_slice_proj)
 
# 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;
} ## end sub project_to_slice

◆ seq()

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

  Arg [1]    : none
  Example    :

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

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

Code:

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◆ subseq()

public Txt Bio::EnsEMBL::CircularSlice::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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The documentation for this class was generated from the following file:

ensembl/modules/Bio/EnsEMBL/CircularSlice.pm

Public Member Functions

Detailed Description

Synopsis

Description

Member Function Documentation

◆ _split()

◆ accession_number()

◆ alphabet()

◆ centrepoint()

◆ desc()

◆ display_id()

◆ expand()

◆ get_all_DASFeatures()

◆ get_all_genotyped_VariationFeatures()

◆ get_all_VariationFeatures()

◆ id()

◆ is_circular()

◆ length()

◆ moltype()

◆ new()

◆ primary_id()

◆ project_to_slice()

◆ seq()

◆ subseq()