Bio::EnsEMBL::RepeatMaskedSlice Class Reference

Inheritance diagram for Bio::EnsEMBL::RepeatMaskedSlice:

Public Member Functions
public Bio::EnsEMBL::RepeatMaskedSlice	new ()
public Reference	repeat_mask_logic_names ()
public Boolean	soft_mask ()
public Hash	not_default_masking_cases ()
public String	seq ()
public String	subseq ()
protected ArrayRef	_get_repeat_features ()
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 );
 
$repeat_masked_slice = $slice->get_repeatmasked_seq();
 
# get repeat masked sequence:
my $dna = $repeat_masked_slice->seq();
$dna = $repeat_masked_slice->subseq( 1, 1000 );

Description

This is a specialised Bio::EnsEMBL::Slice class that is used to retrieve
repeat masked genomic sequence rather than normal genomic sequence.

Definition at line 28 of file RepeatMaskedSlice.pm.

Member Function Documentation

_get_repeat_features()

protected ArrayRef Bio::EnsEMBL::RepeatMaskedSlice::_get_repeat_features

(

)

  Args [1]      : Bio::EnsEMBL::Slice to fetch features for 
  Description   : Gets repeat features for the given slice
  Returntype    : ArrayRef[Bio::EnsEMBL::RepeatFeature] array of repeats

Code:

new()

public Bio::EnsEMBL::RepeatMaskedSlice Bio::EnsEMBL::RepeatMaskedSlice::new

(

)

  Arg [-REPEAT_MASK] : The logic name of the repeats to be used for masking.
                      If not provided, all repeats in the database are used.
  Arg [...]  : Named superclass arguments. See Bio::EnsEMBL::Slice.
  Example    :

my $slice = Bio::EnsEMBL::RepeatMaskedSlice->new
                 (-START  => $start,
                  -END    => $end,
                  -STRAND => $strand,
                  -SEQ_REGION_NAME => $seq_region,
                  -SEQ_REGION_LENGTH => $seq_region_length,
                  -COORD_SYSTEM  => $cs,
                  -ADAPTOR => $adaptor,
                  -REPEAT_MASK => ['repeat_masker'],
                  -SOFT_MASK => 1,
                  -NOT_DEFAULT_MASKING_CASES => {"repeat_class_SINE/MIR" => 1,
                                                 "repeat_name_AluSp" => 0});

  Description: Creates a Slice which behaves exactly as a normal slice but
               that returns repeat masked sequence from the seq method.
  Returntype : Bio::EnsEMBL::RepeatMaskedSlice
  Exceptions : none
  Caller     : RawComputes (PredictionTranscript creation code).
  Status     : Stable

Code:

not_default_masking_cases()

public Hash Bio::EnsEMBL::RepeatMaskedSlice::not_default_masking_cases

(

)

  Arg [1]    : 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)
  Example    :

$rm_slice->not_default_masking_cases({"repeat_class_SINE/MIR" => 1,
                                                    "repeat_name_AluSp" => 0});

  Description: Getter/Setter which is used to escape some repeat class or name from the default 
               masking in place. 
  Returntype : hash reference
  Exceptions : none
  Caller     : seq() and subseq() methods
  Status     : Stable

Code:

repeat_mask_logic_names()

public Reference Bio::EnsEMBL::RepeatMaskedSlice::repeat_mask_logic_names

(

)

  Arg [1]    : reference to list of strings $logic_names (optional)
  Example    :

$rm_slice->repeat_mask_logic_name(['repeat_masker']);

  Description: Getter/Setter for the logic_names of the repeats that are used
               to mask this slices sequence.
  Returntype : reference to list of strings
  Exceptions : none
  Caller     : seq() method
  Status     : Stable

Code:

seq()

public String Bio::EnsEMBL::RepeatMaskedSlice::seq

(

)

  Arg [1]    : none
  Example    :

print $rmslice->seq(), "\n";

  Description: Retrieves the entire repeat masked sequence for this slice.
               See also the Bio::EnsEMBL::Slice implementation of this 
               method.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

soft_mask()

public Boolean Bio::EnsEMBL::RepeatMaskedSlice::soft_mask

(

)

  Arg [1]    : boolean $soft_mask (optional)
  Example    :

$rm_slice->soft_mask(0);

  Description: Getter/Setter which is used to turn on/off softmasking of the
               sequence returned by seq.
  Returntype : boolean
  Exceptions : none
  Caller     : seq() method
  Status     : Stable

Code:

subseq()

public String Bio::EnsEMBL::RepeatMaskedSlice::subseq

(

)

  Arg [1]    : none
  Example    :

print $rmslice->subseq(1, 1000);

  Description: Retrieves a repeat masked sequence from a specified subregion
               of this slice.  See also the Bio::EnsEMBL::Slice 
               implementation of this method.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

---

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

• ensembl/modules/Bio/EnsEMBL/RepeatMaskedSlice.pm