ensembl-hive
2.6
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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.
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
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 :
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
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 :
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
public Reference Bio::EnsEMBL::RepeatMaskedSlice::repeat_mask_logic_names | ( | ) |
Arg [1] : reference to list of strings $logic_names (optional) Example :
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
public String Bio::EnsEMBL::RepeatMaskedSlice::seq | ( | ) |
Arg [1] : none Example :
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
public Boolean Bio::EnsEMBL::RepeatMaskedSlice::soft_mask | ( | ) |
Arg [1] : boolean $soft_mask (optional) Example :
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
public String Bio::EnsEMBL::RepeatMaskedSlice::subseq | ( | ) |
Arg [1] : none Example :
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