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Summary

Bio::EnsEMBL::ExternalData::DAS::Feature

Package variables

Included modules

Inherit

Bio::EnsEMBL::Feature

Synopsis

  my $f = Bio::EnsEMBL::ExternalData::DAS::Feature->new( {
  
    # Core Ensembl attributes:
    'start'  => 100,
    'end'    => 200,
    'strand' => -1,     # or can use "orientation"
    'slice'  => $slice, # optional, for genomic features
    'seqname'=> 'foo',  # optional, for non-genomic features
    
    # DAS-specific attributes:
    'orientation'   => '+', # + or - or .
    'feature_id'    => 'feature1',
    'feature_label' => 'Feature 1',
    'type'          => 'exon',
    'type_id'       => 'SO:0000147',
    'type_category' => 'inferred from electronic annotation (ECO:00000067)',
    'score'         => 85,
    'note'          => [ 'Something useful to know' ],
    'link'          => [
                        { 'href' => 'http://...',
                          'txt'  => 'Feature Link' }
                       ],
    'group'         => [
                        #  hashref, see Bio::EnsEMBL::ExternalData::DAS::FeatureGroup
                       ],
    'target'        => [
                        { 'target_id'    => 'Seq 1',
                          'target_start' => '500',
                          'target_stop'  => '600'  }
                       ]
    
  } );
  
  printf "ID:           %s\n"     , $f->display_id();
  printf "Label:        %s\n"     , $f->display_label();
  printf "Start:        %d (%d)\n", $f->start(), $f->seq_region_start;
  printf "End:          %d (%d)\n", $f->end()  , $f->seq_region_end;
  printf "Type Label:   %s\n"     , $f->type_label();
  printf "Type ID:      %s\n"     , $f->type_id();
  printf "Category:     %s\n"     , $f->type_category();
  printf "Score:        %s\n"     , $f->score();
  
  for my $l ( @{ $f->links() } ) {
    printf "Link:         %s -> %s\n", $l->{'href'}, $l->{'txt'};
  }
  
  for my $n ( @{ $f->notes() } ) {
    printf "Note:         %s\n", $n;
  }
  
  for my $t ( @{ $f->targets() } ) {
    printf "Target:       %s:%s,%s\n", $t->{'target_id'},
                                       $t->{'target_start'},
                                       $t->{'target_stop'};
  }
  
  for my $g ( @{ $f->groups() } ) {
    printf "Group ID:     %s\n", $g->display_id();
    printf "Group Label:  %s\n", $g->display_label();
    printf "Group Type:   %s\n", $g->type_label();
    
    for my $l ( @{ $g->links() } ) {
      printf "Group Link:   %s -> %s\n", $l->{'href'}, $l->{'txt'};
    }
    
    for my $n ( @{ $g->notes() } ) {
      printf "Group Note:   %s\n", $n;
    }
    
    for my $t ( @{ $g->targets() } ) {
      printf "Group Target: %s:%s,%s\n", $t->{'target_id'},
                                         $t->{'target_start'},
                                         $t->{'target_stop'};
    }
  }

Description

An object representation of a DAS feature using Bio::EnsEMBL::Feature as a base.
The constructor is designed to work with the output of the DAS features command,
as obtained from the Bio::Das::Lite module.
See http://www.biodas.org/documents/spec.html for more information about DAS
and its data types.

Methods

Methods description

  Arg [1]    : none
  Example    : print $f->display_id();
  Description: This method returns the DAS feature identifier.
  Returntype : string
  Exceptions : none
  Caller     : web drawing code
  Status     : Stable

  Arg [1]    : none
  Example    : print $f->display_label();
  Description: This method returns the DAS feature label.
  Returntype : string
  Exceptions : none
  Caller     : web drawing code
  Status     : Stable

  Arg [1]    : none
  Example    : @groups = @{ $f->groups() };
  Description: This method returns the DAS feature groups.
  Returntype : arrayref of Bio::EnsEMBL::ExternalData::DAS::FeatureGroup ojects
  Exceptions : none
  Caller     : web drawing code
  Status     : Stable

  Arg [1]    : none
  Example    : @links = @{ $f->links() };
  Description: This method returns the DAS feature external links.
  Returntype : arrayref of { href=>$, txt=>$ } hashes
  Exceptions : none
  Caller     : web drawing code
  Status     : Stable

  Arg [1]    : Hash reference (see SYNOPSIS for details and example)
  Description: Constructs a new Bio::EnsEMBL::ExternalData::DAS::Feature.
  Returntype : Bio::EnsEMBL::ExternalData::DAS::Feature
  Exceptions : none
  Caller     : Bio::EnsEMBL::ExternalData::DAS::Coordinator
  Status     : Stable

  Arg [1]    : none
  Example    : @notes = @{ $f->notes() };
  Description: This method returns the DAS feature notes.
  Returntype : arrayref of strings
  Exceptions : none
  Caller     : web drawing code
  Status     : Stable

  Arg [1]    : none
  Example    : print $f->score();
  Description: This method returns the DAS feature score.
  Returntype : string
  Exceptions : none
  Caller     : web drawing code
  Status     : Stable

  Arg [1]    : none
  Example    : @targets = @{ $f->targets() };
  Description: This method returns the DAS feature targets.
  Returntype : arrayref of { target_id=>$, target_start=>$, target_stop=>$ } hashes
  Exceptions : none
  Caller     : web drawing code
  Status     : Stable

  Arg [1]    : none
  Example    : print $f->type_category();
  Description: This method returns the DAS feature type category.
  Returntype : string
  Exceptions : none
  Caller     : web drawing code
  Status     : Stable

  Arg [1]    : none
  Example    : print $f->type_id();
  Description: This method returns the DAS feature type identifier.
  Returntype : string
  Exceptions : none
  Caller     : web drawing code
  Status     : Stable

  Arg [1]    : none
  Example    : print $f->type_label();
  Description: This method returns the DAS feature type label.
  Returntype : string
  Exceptions : none
  Caller     : web drawing code
  Status     : Stable

Methods code

sub display_id {

  my $self = shift;
  return $self->{'feature_id'};

}

sub display_label {

  my $self = shift;
  return $self->{'feature_label'} || $self->display_id;

}

sub groups {

  my $self = shift;
  return $self->{'group'} || [];

}

sub links {

  my $self = shift;
  return $self->{'link'} || [];

}

sub new {

  my $proto = shift;
  my $class = ref $proto || $proto;
  my $raw   = shift;
  
  # DAS-style "orientation" is fine:
  if (!defined $raw->{'strand'} && defined $raw->{'orientation'}) {
    $raw->{'strand'} = $raw->{'orientation'} eq '+'   ?  1
                     : $raw->{'orientation'} eq '-'   ? -1
                     : 0;
  }
  $raw->{'strand'} ||= 0;
  $raw->{'start'}  ||= 0;
  $raw->{'end'}    ||= 0;
  
  my $self = {};
  for my $key qw( start end strand slice seqname
                  feature_id feature_label
                  type type_id type_category
                  score
                  note link target ) {
    $self->{$key} = $raw->{$key} if exists $raw->{$key};
  }
  
  if ( $raw->{'group'} && ref $raw->{'group'} eq 'ARRAY' ) {
    $self->{'group'} = [
      map {
        Bio::EnsEMBL::ExternalData::DAS::FeatureGroup->new($_)
      } @{ $raw->{'group'} }
    ];
  }
  
  bless $self, $class;
  return $self;

}

sub notes {

  my $self = shift;
  return $self->{'note'} || [];

}

sub score {

  my $self = shift;
  return $self->{'score'};
}

# The following are zero-to-many, thus return arrayrefs:

}

sub targets {

  my $self = shift;
  return $self->{'target'} || [];
}

1;

}

sub type_category {

  my $self = shift;
  return $self->{'type_category'};

}

sub type_id {

  my $self = shift;
  return $self->{'type_id'};

}

sub type_label {

  my $self = shift;
  return $self->{'type'} || $self->type_id;

}

General documentation

Andy Jenkinson

Post questions to the EnsEMBL development list ensembl-dev@ebi.ac.uk