LICENSE

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

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

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

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CONTACT

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NAME

Bio::EnsEMBL::RepeatFeature - A feature representing a repeat on a piece of sequence.

SYNOPSIS

  my $rf = new Bio::EnsEMBL::Feature(
    -start            => 100,
    -end              => 220,
    -strand           => -1,
    -slice            => $slice,
    -analysis         => $analysis,
    -repeat_consensus => $rc,
    -hstart           => 10,
    -hend             => 100,
    -hstrand          => 1,
    -score            => 83.2
  );

  my $hstart = $feat->hstart;
  my $hend   = $feat->hend;

  # move the feature to the chromosomal coordinate system
  $feature = $feature->transform('chromosome');

  # move the feature to a different slice
  # (possibly on another coord system)
  $feature = $feature->transfer($new_slice);

  # project the feature onto another coordinate system possibly across
  # boundaries:
  @projection = @{ $feature->project('contig') };

  # change the start, end, and strand of the feature in place
  $feature->move( $new_start, $new_end, $new_strand );

DESCRIPTION

This a feature representing a repeat region on a sequence

METHODS

new

  Arg [REPEAT_CONSENSUS] : Bio::EnsEMBL::RepeatConsensus (optional)
                           The repeat consensus for this repeat feature
  Arg [HSTART] : int (optional)
                 The hit start on the consensus sequence
  Arg [HEND]   : int (optional)
                 The hit end on the consensus sequence
  Arg [SCORE]  : float (optional)
                 The score
  Arg [...]    : Named arguments to superclass constructor
                 (see Bio::EnsEMBL::Feaure)
  Example    : $rf = Bio::EnsEMBL::RepeatFeature->new(-REPEAT_CONSENSUS => $rc,
                                                      -HSTART => 10,
                                                      -HEND   => 100,
                                                      -SCORE  => 58.0,
                                                      -START  => 1_000_100,
                                                      -END    => 1_000_190,
                                                      -STRAND => 1,
                                                      -ANALYSIS => $an,
                                                      -SLICE  => $chr_slice);
  Description: Creates a new Bio::EnsEMBL::RepeatFeature object
  Returntype : Bio::EnsEMBL::RepeatFeature
  Exceptions : none
  Caller     : RepeatFeatureAdaptors
  Status     : Stable

repeat_consensus

  Arg [1]    : (optional) Bio::EnsEMBL::RepeatConsensus
  Example    : $repeat_consensus = $repeat->repeat_consensus;
  Description: Getter/Setter for the repeat consensus of this repeat
  Returntype : Bio::EnsEMBL::RepeatConsensus
  Exceptions : none
  Caller     : general
  Status     : Stable

hstart

  Arg [1]    : (optional) int $hstart
  Example    : $hit_start = $repeat->hstart;
  Description: Getter/Setter for the start bp of this repeat match on the 
               consensus sequence.
  Returntype : int
  Exceptions : none 
  Caller     : general
  Status     : Stable

score

  Arg [1]    : (optional) float $score
  Example    : $score = $repeat->score();
  Description: Getter/Setter for the score of this repeat feature
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

hend

  Arg [1]    : (optional) int $hend
  Example    : $hit_end = $repeat->hend;
  Description: Getter/Setter for the end bp of this repeat match on the 
               consensus sequence.
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

hstrand

  Arg [1]    : none
  Example    : none
  Description: always returns 1. method exists for consistancy with other 
               features.
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

display_id

  Arg [1]    : none
  Example    : print $rf->display_id();
  Description: This method returns a string that is considered to be
               the 'display' identifier.  For repeat_features this is the 
               name of the repeat consensus if it is available otherwise it is
               an empty string.
  Returntype : string
  Exceptions : none
  Caller     : web drawing code
  Status     : Stable

summary_as_hash

  Example       : $repeat_feature_summary = $protein_feature->summary_as_hash();
  Description   : Retrieves a textual summary of this Repeat feature.
                  Not inherited from Feature.
  Returns       : hashref of arrays of descriptive strings
  Status        : Intended for internal use

NAME - Bio::EnsEMBL::RepeatFeature

cpanm Bio::EnsEMBL

perl -MCPAN -e shell
install Bio::EnsEMBL