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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NAME

Bio::EnsEMBL::MiscFeature - A miscelaneous feature with arbitrary features and associations.

SYNOPSIS

  use Bio::EnsEMBL::MiscFeature;
  use Bio::EnsEMBL::MiscSet;
  use Bio::EnsEMBL::Attribute;

  my $mfeat = Bio::EnsEMBL::MiscFeature->new(
    -START  => 1200,
    -END    => 100_000,
    -STRAND => 1,
    -SLICE  => $slice
  );

  # Can add attributes to the misc feature and associate with various
  # sets
  my $clone_set = Bio::EnsEMBL::MiscSet->new(
    -CODE        => 'clone',
    -NAME        => '1MB clone set',
    -DESCRIPTION => '1MB CloneSet'
  );

  my $tiling_path_set = Bio::EnsEMBL::MiscSet->new(
    -CODE => 'tilingpath',
    -NAME => 'tiling path set'
  );

  my $attrib1 = Bio::EnsEMBL::Attribute->new(
    -VALUE => 'RLX12451',
    -CODE  => 'name',
    -NAME  => 'name'
  );

  my $attrib2 = Bio::EnsEMBL::Attribute->new(
    -VALUE => '4',
    -CODE  => 'version',
    -NAME  => 'version'
  );

  my $attrib3 = Bio::EnsEMBL::Attribute->new(
    -VALUE => 'AL42131.4',
    -CODE  => 'synonym',
    -NAME  => 'synonym'
  );

  # can associate a misc feature with any number of sets

  $mfeat->add_MiscSet($clone_set);
  $mfeat->add_MiscSet($tiling_path_set);

  # can add arbitrary attributes to a misc feature

  $mfeat->add_Attribute($attrib1);
  $mfeat->add_Attribute($attrib2);
  $mfeat->add_Attribute($attrib3);

  my ($name_attrib) = @{ $mfeat->get_all_Attributes('name') };
  my @all_attribs = @{ $mfeat->get_all_Attributes() };

  my @all_sets = @{ $mfeat->get_all_MiscSets() };
  my ($clone_set) = @{ $mfeat->get_all_CloneSets('clone') };


  # Can do normal feature operations as well
  $mfeat = $mfeat->transform('supercontig');
  print $mfeat->slice->seq_region_name, ' ', $mfeat->start, '-',
    $mfeat->end;

DESCRIPTION

MiscFeatures are extremely general features with a location, and an arbitrary group of attributes. They are grouped with other features of the same 'type' through the use of MiscSets (see Bio::EnsEMBL::MiscSet). Attributes are attached in the fom of Bio::EnsEMBL::Attribute objects. See Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor for ways to fetch or store MiscFeatures.

new

  Arg [-SLICE]: Bio::EnsEMBL::SLice - Represents the sequence that this
                feature is on. The coordinates of the created feature are
                relative to the start of the slice.
  Arg [-START]: The start coordinate of this feature relative to the start
                of the slice it is sitting on.  Coordinates start at 1 and
                are inclusive.
  Arg [-END]  : The end coordinate of this feature relative to the start of
                the slice it is sitting on.  Coordinates start at 1 and are
                inclusive.
  Arg [-STRAND]: The orientation of this feature.  Valid values are 1,-1,0.
  Arg [-SEQNAME] : A seqname to be used instead of the default name of the
                of the slice.  Useful for features that do not have an
                attached slice such as protein features.
  Arg [-dbID]   : (optional) internal database id
  Arg [-ADAPTOR]: (optional) Bio::EnsEMBL::DBSQL::BaseAdaptor
  Example    : $feature = Bio::EnsEMBL::MiscFeature->new(-start    => 1,
                                                     -end      => 100,
                                                     -strand   => 1,
                                                     -slice    => $slice,
                                                     -analysis => $analysis);
  Description: Constructs a new Bio::EnsEMBL::Feature.  Generally subclasses
               of this method are instantiated, rather than this class itself.
  Returntype : Bio::EnsEMBL::MiscFeature
  Exceptions : Thrown on invalid -SLICE, -ANALYSIS, -STRAND ,-ADAPTOR arguments
  Caller     : general, subclass constructors
  Status     : Stable

add_Attribute

  Arg [1]    : Bio::EnsEMBL::Attribute $attribute
  Example    : $misc_feature->add_attribute($attribute);
  Description: Adds an attribute to this misc. feature
  Returntype : none
  Exceptions : throw on wrong argument type
  Caller     : general
  Status     : Stable

add_MiscSet

  Arg [1]    : Bio::EnsEMBL::MiscSet $set
               The set to add
  Example    : $misc_feature->add_MiscSet(Bio::EnsEMBL::MiscSet->new(...));
  Description: Associates this MiscFeature with a given Set.
  Returntype : none
  Exceptions : throw if the set arg is not provided,
               throw if the set to be added does not have a code
  Caller     : general
  Status     : Stable

get_all_MiscSets

  Arg [1]    : optional string $code
               The code of the set to retrieve
  Example    : $set = $misc_feature->get_all_MiscSets($code);
  Description: Retrieves a set that this feature is associated with via its
               code. Can return empty lists. Usually returns about one elements lists.
  Returntype : listref of Bio::EnsEMBL::MiscSet
  Exceptions : throw if the code arg is not provided
  Caller     : general
  Status     : Stable

get_all_Attributes

  Arg [1]    : optional string $code
               The code of the Attribute objects to retrieve
  Example    : @attributes = @{ $misc_feature->get_all_Attributes('name') };
  Description: Retrieves a list of Attribute objects for given code or all
               of the associated Attributes.
  Returntype : listref of Bio::EnsEMBL::Attribute
  Exceptions : 
  Caller     : general
  Status     : Stable

get_all_attribute_values

  Arg [1]    : string $code
               The code of the Attribute object values to retrieve
  Example    : @attributes_vals = @{$misc_feature->get_all_attribute_values('name')};
  Description: Retrieves a list of Attribute object values for given code or all
               of the associated Attributes.
  Returntype : listref of values
  Exceptions : 
  Caller     : general
  Status     : Stable

get_scalar_attribute

  Arg [1]    : string $code
               The code of the Attribute object values to retrieve
  Example    : $vals = $misc_feature->get_scalar_attribute('name');
  Description: Retrieves a value for given code or all
               of the associated Attributes.
  Returntype : scalar value
  Exceptions : 
  Caller     : general
  Status     : Stable

display_id

  Arg [1]    : none
  Example    : print $kb->display_id();
  Description: This method returns a string that is considered to be
               the 'display' identifier.  For misc_features this is the first
               name or synonym attribute or '' if neither are defined.
  Returntype : string
  Exceptions : none
  Caller     : web drawing code
  Status     : Stable

summary_as_hash

  Example    : my $hash = $misc_feature->summary_as_hash();
  Description: Generates a HashRef compatible with GFFSerializer. Adds
               all attribute key value pairs plus MiscSet codes and names
  Returntype : Hash
  Exceptions : none
  Caller     : general
  Status     : Stable

cpanm Bio::EnsEMBL

perl -MCPAN -e shell
install Bio::EnsEMBL