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Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

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     http://www.apache.org/licenses/LICENSE-2.0

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NAME

Bio::EnsEMBL::RepeatMaskedSlice - Arbitary Slice of a genome

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.

METHODS

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 B<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

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

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

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

seq

  Arg [1]    : none
  Example    : print $rmslice->seq(), "\n";
  Description: Retrieves the entire repeat masked sequence for this slice.
               See also the B<Bio::EnsEMBL::Slice> implementation of this 
               method.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

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 B<Bio::EnsEMBL::Slice> 
               implementation of this method.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

_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